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de Vries PS, Reventun P, Brown MR, Heath AS, Huffman JE, Le NQ, Bebo A, Brody JA, Temprano-Sagrera G, Raffield LM, Ozel AB, Thibord F, Jain D, Lewis JP, Rodriguez BAT, Pankratz N, Taylor KD, Polasek O, Chen MH, Yanek LR, Carrasquilla GD, Marioni RE, Kleber ME, Trégouët DA, Yao J, Li-Gao R, Joshi PK, Trompet S, Martinez-Perez A, Ghanbari M, Howard TE, Reiner AP, Arvanitis M, Ryan KA, Bartz TM, Rudan I, Faraday N, Linneberg A, Ekunwe L, Davies G, Delgado GE, Suchon P, Guo X, Rosendaal FR, Klaric L, Noordam R, van Rooij F, Curran JE, Wheeler MM, Osburn WO, O'Connell JR, Boerwinkle E, Beswick A, Psaty BM, Kolcic I, Souto JC, Becker LC, Hansen T, Doyle MF, Harris SE, Moissl AP, Deleuze JF, Rich SS, van Hylckama Vlieg A, Campbell H, Stott DJ, Soria JM, de Maat MPM, Almasy L, Brody LC, Auer PL, Mitchell BD, Ben-Shlomo Y, Fornage M, Hayward C, Mathias RA, Kilpeläinen TO, Lange LA, Cox SR, März W, Morange PE, Rotter JI, Mook-Kanamori DO, Wilson JF, van der Harst P, Jukema JW, Ikram MA, Blangero J, Kooperberg C, Desch KC, Johnson AD, Sabater-Lleal M, Lowenstein CJ, Smith NL, Morrison AC. A genetic association study of circulating coagulation factor VIII and von Willebrand factor levels. Blood 2024; 143:1845-1855. [PMID: 38320121 DOI: 10.1182/blood.2023021452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
ABSTRACT Coagulation factor VIII (FVIII) and its carrier protein von Willebrand factor (VWF) are critical to coagulation and platelet aggregation. We leveraged whole-genome sequence data from the Trans-Omics for Precision Medicine (TOPMed) program along with TOPMed-based imputation of genotypes in additional samples to identify genetic associations with circulating FVIII and VWF levels in a single-variant meta-analysis, including up to 45 289 participants. Gene-based aggregate tests were implemented in TOPMed. We identified 3 candidate causal genes and tested their functional effect on FVIII release from human liver endothelial cells (HLECs) and VWF release from human umbilical vein endothelial cells. Mendelian randomization was also performed to provide evidence for causal associations of FVIII and VWF with thrombotic outcomes. We identified associations (P < 5 × 10-9) at 7 new loci for FVIII (ST3GAL4, CLEC4M, B3GNT2, ASGR1, F12, KNG1, and TREM1/NCR2) and 1 for VWF (B3GNT2). VWF, ABO, and STAB2 were associated with FVIII and VWF in gene-based analyses. Multiphenotype analysis of FVIII and VWF identified another 3 new loci, including PDIA3. Silencing of B3GNT2 and the previously reported CD36 gene decreased release of FVIII by HLECs, whereas silencing of B3GNT2, CD36, and PDIA3 decreased release of VWF by HVECs. Mendelian randomization supports causal association of higher FVIII and VWF with increased risk of thrombotic outcomes. Seven new loci were identified for FVIII and 1 for VWF, with evidence supporting causal associations of FVIII and VWF with thrombotic outcomes. B3GNT2, CD36, and PDIA3 modulate the release of FVIII and/or VWF in vitro.
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Affiliation(s)
- Paul S de Vries
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Paula Reventun
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michael R Brown
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Adam S Heath
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Jennifer E Huffman
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA
| | - Ngoc-Quynh Le
- Unit of Genomics of Complex Disease, Institut de Recerca Sant Pau, Barcelona, Spain
| | - Allison Bebo
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | | | - Laura M Raffield
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Florian Thibord
- Division of Intramural Research, Population Sciences Branch, National Heart, Lung, and Blood Institute, Framingham Heart Study, Framingham, MA
| | - Deepti Jain
- Department of Biostatistics, Genetic Analysis Center, School of Public Health, University of Washington, Seattle, WA
| | - Joshua P Lewis
- Department of Medicine, University of Maryland, Baltimore, MD
| | - Benjamin A T Rodriguez
- Division of Intramural Research, Population Sciences Branch, National Heart, Lung, and Blood Institute, Framingham Heart Study, Framingham, MA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Kent D Taylor
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Ming-Huei Chen
- Division of Intramural Research, Population Sciences Branch, National Heart, Lung, and Blood Institute, Framingham Heart Study, Framingham, MA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - German D Carrasquilla
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | - Marcus E Kleber
- SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
- Fifth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Jie Yao
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Angel Martinez-Perez
- Unit of Genomics of Complex Disease, Institut de Recerca Sant Pau, Barcelona, Spain
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Tom E Howard
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Alex P Reiner
- Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Marios Arvanitis
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kathleen A Ryan
- Department of Medicine, University of Maryland, Baltimore, MD
| | - Traci M Bartz
- Departments of Biostatistics and Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lynette Ekunwe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Gail Davies
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Scotland
| | - Graciela E Delgado
- Fifth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Pierre Suchon
- C2VN, INSERM, INRAE, Aix Marseille University, Marseille, France
- Laboratory of Haematology, La Timone Hospital, Marseille, France
| | - Xiuqing Guo
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Frank van Rooij
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Marsha M Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - William O Osburn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Andrew Beswick
- Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Departments of Epidemiology and Health Systems and Population Health, Seattle, WA
| | - Ivana Kolcic
- Faculty of Medicine, University of Split, Split, Croatia
| | - Juan Carlos Souto
- Unit of Genomics of Complex Disease, Institut de Recerca Sant Pau, Barcelona, Spain
- Unit of Thrombosis and Hemostasis, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Lewis C Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Margaret F Doyle
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Colchester, VT
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Scotland
| | - Angela P Moissl
- Institute of Nutritional Sciences, Friedrich-Schiller-University Jena, Jena, Germany
- Competence Cluster for Nutrition and Cardiovascular Health Halle-Jena-Leipzig, Jena, Germany
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, CEA, Evry, France
- Centre d'Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | | | - Harry Campbell
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - David J Stott
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland
| | - Jose Manuel Soria
- Unit of Genomics of Complex Disease, Institut de Recerca Sant Pau, Barcelona, Spain
| | - Moniek P M de Maat
- Department of Hematology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Laura Almasy
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Lawrence C Brody
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Paul L Auer
- Department of Biostatistics, Medical College of Wisconsin, Milwaukee, WI
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland, Baltimore, MD
- Geriatric Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD
| | - Yoav Ben-Shlomo
- Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Myriam Fornage
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Simon R Cox
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Scotland
| | - Winfried März
- Fifth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, Germany
| | - Pierre-Emmanuel Morange
- C2VN, INSERM, INRAE, Aix Marseille University, Marseille, France
- Laboratory of Haematology, La Timone Hospital, Marseille, France
| | - Jerome I Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Pim van der Harst
- Division of Heart and Lungs, Department of Cardiology, Utrecht University, University Medical Center Utrecht, Utrecht, The Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | | | - Karl C Desch
- Department of Pediatrics, University of Michigan, C.S. Mott Children's Hospital, Ann Arbor, MI
| | - Andrew D Johnson
- Division of Intramural Research, Population Sciences Branch, National Heart, Lung, and Blood Institute, Framingham Heart Study, Framingham, MA
| | - Maria Sabater-Lleal
- Unit of Genomics of Complex Disease, Institut de Recerca Sant Pau, Barcelona, Spain
- Department of Medicine, Cardiovascular Medicine Unit, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
| | - Charles J Lowenstein
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA
- Department of Veterans Affairs Office of Research and Development, Seattle Epidemiologic and Information Center, Seattle, WA
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
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Kachuri L, Mak ACY, Hu D, Eng C, Huntsman S, Elhawary JR, Gupta N, Gabriel S, Xiao S, Keys KL, Oni-Orisan A, Rodríguez-Santana JR, LeNoir MA, Borrell LN, Zaitlen NA, Williams LK, Gignoux CR, Burchard EG, Ziv E. Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture. Nat Genet 2023; 55:952-963. [PMID: 37231098 PMCID: PMC10260401 DOI: 10.1038/s41588-023-01377-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 03/21/2023] [Indexed: 05/27/2023]
Abstract
We explored ancestry-related differences in the genetic architecture of whole-blood gene expression using whole-genome and RNA sequencing data from 2,733 African Americans, Puerto Ricans and Mexican Americans. We found that heritability of gene expression significantly increased with greater proportions of African genetic ancestry and decreased with higher proportions of Indigenous American ancestry, reflecting the relationship between heterozygosity and genetic variance. Among heritable protein-coding genes, the prevalence of ancestry-specific expression quantitative trait loci (anc-eQTLs) was 30% in African ancestry and 8% for Indigenous American ancestry segments. Most anc-eQTLs (89%) were driven by population differences in allele frequency. Transcriptome-wide association analyses of multi-ancestry summary statistics for 28 traits identified 79% more gene-trait associations using transcriptome prediction models trained in our admixed population than models trained using data from the Genotype-Tissue Expression project. Our study highlights the importance of measuring gene expression across large and ancestrally diverse populations for enabling new discoveries and reducing disparities.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Angel C Y Mak
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer R Elhawary
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Shujie Xiao
- Center for Individualized and Genomic Medicine Research, Henry Ford Health System, Detroit, MI, USA
| | - Kevin L Keys
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Berkeley Institute for Data Science, University of California, Berkeley, Berkeley, CA, USA
| | - Akinyemi Oni-Orisan
- Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Luisa N Borrell
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA
| | - Noah A Zaitlen
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research, Henry Ford Health System, Detroit, MI, USA
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Esteban González Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
| | - Elad Ziv
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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Bartoszewicz M, Rać M. Prognostic Value of the Selected Polymorphisms in the CD36 Gene in the Domain-Encoding Lipid-Binding Region at a 10-Year Follow-Up for Early-Onset CAD Patients. Biomedicines 2023; 11:biomedicines11051332. [PMID: 37239003 DOI: 10.3390/biomedicines11051332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
The polymorphism of the CD36 gene may have a decisive impact on the formation and progression of atherosclerotic changes. The aim of the study was to confirm the prognostic values of the previously studied polymorphisms in the CD36 gene within a 10-year follow-up period. This is the first published report confirming the long-term observation of patients with CAD. The study group covered 100 early-onset CAD patients. It included 26 women not older than 55 years and 74 men not older than 50 years, tested in a ten-year study as a long-term follow-up after the first cardiovascular episode. There are no notable differences between the CD36 variants and the number of fatalities during observation, fatalities due to cardiological reasons, cases of myocardial infarction within a ten-year observation period, hospitalizations for cardiovascular issues, all cardiovascular occurrences, and the number of months lived. We have shown that the CD36 variants analyzed in this study do not appear to be related to the risk of early CAD occurrence in the Caucasian population in long-term observation.
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Affiliation(s)
- Michał Bartoszewicz
- Psychosocial and Medical Rehabilitation Centre, West Pomeranian Centre Oncology, 71-730 Szczecin, Poland
| | - Monika Rać
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, 70-204 Szczecin, Poland
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Genetic modulation of anemia severity, hemolysis level, and hospitalization rate in Angolan children with Sickle Cell Anemia. Mol Biol Rep 2022; 49:10347-10356. [PMID: 36097125 DOI: 10.1007/s11033-022-07831-1] [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: 05/13/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Sickle Cell Anemia (SCA) is a genetic disease caused by the c.20 A > T mutation in HBB gene, generally characterized by sickle erythrocytes, chronic hemolytic anemia, and vaso-occlusive events. This study aimed to investigate genetic modulators of anemia severity, chronic hemolytic rate, and clinical manifestations in pediatric SCA patients from Angola, where the disease is a severe public health problem. METHODS AND RESULTS The study was conducted on 200 SCA children living in Luanda or Caxito province. Their clinical phenotype was collected from patients' hospital records. Hematological and biochemical phenotypes were characterized in steady state condition. Twelve polymorphic regions in VCAM1, CD36 and NOS3 genes were genotyped using PCR, RFLP, and Sanger sequencing. CD36 gene promoter variants showed a significant impact on anemia severity. Particularly, the rs1413661_C allele was associated with lower hemoglobin levels, and increased number of hospitalizations and transfusions. This is the first report associating this SNP with SCA phenotypic heterogeneity. Moreover, the rs1041163_C allele in VCAM1 was associated with lower LDH levels; inversely the rs2070744_C allele in NOS3 was related with higher LDH levels and number of hospitalizations, being a risk factor for increased hemolytic rate. CONCLUSION This study highlights, for the first time in the Angolan population, the importance of the genetic modifiers of vascular cell adhesion and nitric oxide metabolism in SCA pediatric phenotypic variability.
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Pankratz N, Wei P, Brody JA, Chen MH, de Vries PS, Huffman JE, Stimson MR, Auer PL, Boerwinkle E, Cushman M, de Maat MPM, Folsom AR, Franco OH, Gibbs RA, Haagenson KK, Hofman A, Johnsen JM, Kovar CL, Kraaij R, McKnight B, Metcalf GA, Muzny D, Psaty BM, Tang W, Uitterlinden AG, van Rooij JGJ, Dehghan A, O'Donnell CJ, Reiner AP, Morrison AC, Smith NL. Whole-exome sequencing of 14 389 individuals from the ESP and CHARGE consortia identifies novel rare variation associated with hemostatic factors. Hum Mol Genet 2022; 31:3120-3132. [PMID: 35552711 PMCID: PMC9476613 DOI: 10.1093/hmg/ddac100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/07/2022] [Accepted: 04/27/2022] [Indexed: 11/12/2022] Open
Abstract
Plasma levels of fibrinogen, coagulation factors VII and VIII and von Willebrand factor (vWF) are four intermediate phenotypes that are heritable and have been associated with the risk of clinical thrombotic events. To identify rare and low-frequency variants associated with these hemostatic factors, we conducted whole-exome sequencing in 10 860 individuals of European ancestry (EA) and 3529 African Americans (AAs) from the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium and the National Heart, Lung and Blood Institute's Exome Sequencing Project. Gene-based tests demonstrated significant associations with rare variation (minor allele frequency < 5%) in fibrinogen gamma chain (FGG) (with fibrinogen, P = 9.1 × 10-13), coagulation factor VII (F7) (with factor VII, P = 1.3 × 10-72; seven novel variants) and VWF (with factor VIII and vWF; P = 3.2 × 10-14; one novel variant). These eight novel rare variant associations were independent of the known common variants at these loci and tended to have much larger effect sizes. In addition, one of the rare novel variants in F7 was significantly associated with an increased risk of venous thromboembolism in AAs (Ile200Ser; rs141219108; P = 4.2 × 10-5). After restricting gene-based analyses to only loss-of-function variants, a novel significant association was detected and replicated between factor VIII levels and a stop-gain mutation exclusive to AAs (rs3211938) in CD36 molecule (CD36). This variant has previously been linked to dyslipidemia but not with the levels of a hemostatic factor. These efforts represent the largest integration of whole-exome sequence data from two national projects to identify genetic variation associated with plasma hemostatic factors.
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Affiliation(s)
- Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Peng Wei
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ming-Huei Chen
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung and Blood Institute, Framingham, MA, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jennifer E Huffman
- Framingham Heart Study, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Center for Population Genomics, MAVERIC, VA Boston Healthcare System, Boston, MA, USA
| | - Mary Rachel Stimson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Mary Cushman
- Departments of Medicine and Pathology, University of Vermont, Colchester, VT, USA
| | - Moniek P M de Maat
- Department of Hematology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Aaron R Folsom
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Oscar H Franco
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Kelly K Haagenson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jill M Johnsen
- Research Institute Bloodworks, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | | | - Abbas Dehghan
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Biostatistics and Epidemiology, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Christopher J O'Donnell
- Framingham Heart Study, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Cardiology Section, Department of Medicine, Boston Veterans Administration Healthcare, Harvard Medical School, Boston, MA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle WA, USA
- Seattle Epidemiologic Research and Information Center, Veterans Administration Office of Research and Development, Seattle, WA, USA
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6
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Chen Y, Zhang J, Cui W, Silverstein RL. CD36, a signaling receptor and fatty acid transporter that regulates immune cell metabolism and fate. J Exp Med 2022; 219:213166. [PMID: 35438721 PMCID: PMC9022290 DOI: 10.1084/jem.20211314] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 12/13/2022] Open
Abstract
CD36 is a type 2 cell surface scavenger receptor widely expressed in many immune and non-immune cells. It functions as both a signaling receptor responding to DAMPs and PAMPs, as well as a long chain free fatty acid transporter. Recent studies have indicated that CD36 can integrate cell signaling and metabolic pathways through its dual functions and thereby influence immune cell differentiation and activation, and ultimately help determine cell fate. Its expression along with its dual functions in both innate and adaptive immune cells contribute to pathogenesis of common diseases, including atherosclerosis and tumor progression, which makes CD36 and its downstream effectors potential therapeutic targets. This review comprehensively examines the dual functions of CD36 in a variety of immune cells, especially macrophages and T cells. We also briefly discuss CD36 function in non-immune cells, such as adipocytes and platelets, which impact the immune system via intercellular communication. Finally, outstanding questions in this field are provided for potential directions of future studies.
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Affiliation(s)
- Yiliang Chen
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI.,Versiti, Blood Research Institute, Milwaukee, WI
| | - Jue Zhang
- Versiti, Blood Research Institute, Milwaukee, WI
| | - Weiguo Cui
- Versiti, Blood Research Institute, Milwaukee, WI.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
| | - Roy L Silverstein
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI.,Versiti, Blood Research Institute, Milwaukee, WI
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7
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Potapova NA. Nonsense Mutations in Eukaryotes. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:400-412. [PMID: 35790376 DOI: 10.1134/s0006297922050029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/14/2022] [Accepted: 03/22/2022] [Indexed: 06/15/2023]
Abstract
Nonsense mutations are a type of mutations which results in a premature termination codon occurrence. In general, these mutations have been considered to be among the most harmful ones which lead to premature protein translation termination and result in shortened nonfunctional polypeptide. However, there is evidence that not all nonsense mutations are harmful as well as some molecular mechanisms exist which allow to avoid pathogenic effects of these mutations. This review addresses relevant information on nonsense mutations in eukaryotic genomes, characteristics of these mutations, and different molecular mechanisms preventing or mitigating harmful effects thereof.
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Affiliation(s)
- Nadezhda A Potapova
- Kharkevich Institute for Information Transmission Problems (IITP), Russian Academy of Sciences, Moscow, 127051, Russia.
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8
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Wooding SP, Ramirez VA. Worldwide diversity, association potential, and natural selection in the superimposed taste genes, CD36 and GNAT3. Chem Senses 2022; 47:6491270. [PMID: 34972209 DOI: 10.1093/chemse/bjab052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
CD36 and GNAT3 mediate taste responses, with CD36 acting as a lipid detector and GNAT3 acting as the α subunit of gustducin, a G protein governing sweet, savory, and bitter transduction. Strikingly, the genes encoding CD36 and GNAT3 are genomically superimposed, with CD36 completely encompassing GNAT3. To characterize genetic variation across the CD36-GNAT3 region, its implications for phenotypic diversity, and its recent evolution, we analyzed from ~2,500 worldwide subjects sequenced by the 1000 Genomes Project (1000GP). CD36-GNAT3 harbored extensive diversity including 8,688 single-nucleotide polymorphisms (SNPs), 414 indels, and other complex variants. Sliding window analyses revealed that nucleotide diversity and population differentiation across CD36-GNAT3 were consistent with genome-wide trends in the 1000GP (π = 0.10%, P = 0.64; FST = 9.0%, P = 0.57). In addition, functional predictions using SIFT and PolyPhen-2 identified 60 variants likely to alter protein function, and they were in weak linkage disequilibrium (r2 < 0.17), suggesting their effects are largely independent. However, the frequencies of predicted functional variants were low (P¯ = 0.0013), indicating their contributions to phenotypic variance on population scales are limited. Tests using Tajima's D statistic revealed that pressures from natural selection have been relaxed across most of CD36-GNAT3 during its recent history (0.39 < P < 0.67). However, CD36 exons showed signs of local adaptation consistent with prior reports (P < 0.035). Thus, CD36 and GNAT3 harbor numerous variants predicted to affect taste sensitivity, but most are rare and phenotypic variance on a population level is likely mediated by a small number of sites.
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Affiliation(s)
- Stephen P Wooding
- Department of Anthropology, University of California, Merced, Merced, CA, USA
| | - Vicente A Ramirez
- Department of Public Health, University of California, Merced, Merced, CA, USA
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9
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Contribution of Evolutionary Selected Immune Gene Polymorphism to Immune-Related Disorders: The Case of Lymphocyte Scavenger Receptors CD5 and CD6. Int J Mol Sci 2021; 22:ijms22105315. [PMID: 34070159 PMCID: PMC8158487 DOI: 10.3390/ijms22105315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 01/23/2023] Open
Abstract
Pathogens are one of the main selective pressures that ancestral humans had to adapt to. Components of the immune response system have been preferential targets of natural selection in response to such pathogen-driven pressure. In turn, there is compelling evidence showing that positively selected immune gene variants conferring increased resistance to past or present infectious agents are today associated with increased risk for autoimmune or inflammatory disorders but decreased risk of cancer, the other side of the same coin. CD5 and CD6 are lymphocytic scavenger receptors at the interphase of the innate and adaptive immune responses since they are involved in both: (i) microbial-associated pattern recognition; and (ii) modulation of intracellular signals mediated by the clonotypic antigen-specific receptor present in T and B cells (TCR and BCR, respectively). Here, we review available information on CD5 and CD6 as targets of natural selection as well as on the role of CD5 and CD6 variation in autoimmunity and cancer.
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10
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The population genomics of adaptive loss of function. Heredity (Edinb) 2021; 126:383-395. [PMID: 33574599 PMCID: PMC7878030 DOI: 10.1038/s41437-021-00403-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 12/23/2022] Open
Abstract
Discoveries of adaptive gene knockouts and widespread losses of complete genes have in recent years led to a major rethink of the early view that loss-of-function alleles are almost always deleterious. Today, surveys of population genomic diversity are revealing extensive loss-of-function and gene content variation, yet the adaptive significance of much of this variation remains unknown. Here we examine the evolutionary dynamics of adaptive loss of function through the lens of population genomics and consider the challenges and opportunities of studying adaptive loss-of-function alleles using population genetics models. We discuss how the theoretically expected existence of allelic heterogeneity, defined as multiple functionally analogous mutations at the same locus, has proven consistent with empirical evidence and why this impedes both the detection of selection and causal relationships with phenotypes. We then review technical progress towards new functionally explicit population genomic tools and genotype-phenotype methods to overcome these limitations. More broadly, we discuss how the challenges of studying adaptive loss of function highlight the value of classifying genomic variation in a way consistent with the functional concept of an allele from classical population genetics.
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11
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Liu J, Shao Y, Ding H, Deng J, Xu X, Wang J, Xia W, Santoso S, Ye X, Fu Y. Distribution of CD36 deficiency in different Chinese ethnic groups. Hum Immunol 2020; 81:366-371. [PMID: 32487483 DOI: 10.1016/j.humimm.2020.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/29/2020] [Accepted: 05/12/2020] [Indexed: 01/27/2023]
Abstract
BACKGROUND CD36 is a multifunctional receptor in cells that plays a role in important cellular processes including immune regulation. Evidence indicates that mutations in the CD36 gene are associated with malaria. Moreover, studies on the frequency of CD36 deficiency have been conducted in specific provinces of China. However, the frequency of CD36 deficiency may differ among various ethnic populations. In this study, we analyzed the frequency of CD36 deficiency among seven different provinces and minorities in China. METHODS AND MATERIALS In this study, 5313 samples were randomly collected from seven provinces in China. CD36 deficiency on platelets and monocytes was determined via flow cytometry using a monoclonal antibody (mAb) against CD36. DNA sequencing analysis was performed to identify mutations associated with CD36 deficiency. RESULTS The frequency of CD36 deficiency among individuals from different provinces (n = 7) was 1.60%, comprising 0.38% of type-I deficiency and 1.22% of type-II deficiency. The distribution among provinces ranged from 0.81% to 1.99%. The largest ethnic group, Han, showed a lower frequency of deficiency than ethnic minorities (1.30% versus 2.37%). The most common mutations found in our overall cohort were 329-330delAC and 1228-1239delATTGTGCCTATT. Significant high frequencies of CD36 deficiency were detected in two ethnic minorities, Zhuang (3.69%) and BuYi (3.05%), living in southern China. CONCLUSIONS Through an analysis of a large cohort, we determined the frequencies of CD36 deficiency among different Chinese ethnic groups. A high frequency of type-I deficiency was found in certain minorities living in southern China, which is known to be vulnerable to malaria epidemics. These findings may help us understand the phenotypic consequences of CD36-deficient alleles associated with malaria.
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Affiliation(s)
- Jing Liu
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Yuan Shao
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Haoqiang Ding
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Jing Deng
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Xiuzhang Xu
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Jiali Wang
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Wenjie Xia
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Sentot Santoso
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China; Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig University, Giessen, Germany
| | - Xin Ye
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Yongshui Fu
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China; School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China.
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12
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Rosetting revisited: a critical look at the evidence for host erythrocyte receptors in Plasmodium falciparum rosetting. Parasitology 2019; 147:1-11. [PMID: 31455446 PMCID: PMC7050047 DOI: 10.1017/s0031182019001288] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Malaria remains a major cause of mortality in African children, with no adjunctive treatments currently available to ameliorate the severe clinical forms of the disease. Rosetting, the adhesion of infected erythrocytes (IEs) to uninfected erythrocytes, is a parasite phenotype strongly associated with severe malaria, and hence is a potential therapeutic target. However, the molecular mechanisms of rosetting are complex and involve multiple distinct receptor–ligand interactions, with some similarities to the diverse pathways involved in P. falciparum erythrocyte invasion. This review summarizes the current understanding of the molecular interactions that lead to rosette formation, with a particular focus on host uninfected erythrocyte receptors including the A and B blood group trisaccharides, complement receptor one, heparan sulphate, glycophorin A and glycophorin C. There is strong evidence supporting blood group A trisaccharides as rosetting receptors, but evidence for other molecules is incomplete and requires further study. It is likely that additional host erythrocyte rosetting receptors remain to be discovered. A rosette-disrupting low anti-coagulant heparin derivative is being investigated as an adjunctive therapy for severe malaria, and further research into the receptor–ligand interactions underlying rosetting may reveal additional therapeutic approaches to reduce the unacceptably high mortality rate of severe malaria.
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13
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Human Immunology through the Lens of Evolutionary Genetics. Cell 2019; 177:184-199. [DOI: 10.1016/j.cell.2019.02.033] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 01/04/2023]
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14
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The demographic and adaptive history of central African hunter-gatherers and farmers. Curr Opin Genet Dev 2018; 53:90-97. [PMID: 30103089 DOI: 10.1016/j.gde.2018.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/18/2018] [Indexed: 01/06/2023]
Abstract
Central Africa, a forested region that supports an exceptionally high biodiversity, hosts the world's largest group of hunter-gatherers, who live in close proximity with groups that have adopted agriculture over the past 5000 years. Our understanding of the prehistory of these populations has been dramatically hampered by the almost total absence of fossil remains in this region, a limitation that has recently been circumvented by population genomics approaches. Different studies have estimated that ancestors of rainforest hunter-gatherers and Bantu-speaking farmers separated more than 60 000 years ago, supporting the occurrence of ancient population structure in Africa since the Late Pleistocene. Conversely, the Holocene in central Africa was characterized by large-scale population migrations associated with the emergence of agriculture, and increased genetic interactions between autochthonous rainforest hunter-gatherers and expanding Bantu-speaking farmers. Genomic scans have detected numerous candidate loci for positive selection in these populations, including convergent adaptation for short stature in groups of rainforest hunter-gatherers and local adaptation to endemic malaria in western and central Africans. Furthermore, there is recent increasing evidence that adaptive variation has been acquired by various African populations through admixture, suggesting a previously unappreciated role of intraspecies gene flow in local adaptation. Ancient and modern DNA studies will greatly broaden, and probably challenge, our view on the past history of central Africa, where introgression from yet uncharacterized archaic hominins and long-term adaptation to distinct ecological niches are suspected.
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15
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Thorne L, Nalwoga A, Mentzer AJ, de Rougemont A, Hosmillo M, Webb E, Nampiija M, Muhwezi A, Carstensen T, Gurdasani D, Hill AV, Sandhu MS, Elliott A, Goodfellow I. The First Norovirus Longitudinal Seroepidemiological Study From Sub-Saharan Africa Reveals High Seroprevalence of Diverse Genotypes Associated With Host Susceptibility Factors. J Infect Dis 2018; 218:716-725. [PMID: 29912471 PMCID: PMC6057498 DOI: 10.1093/infdis/jiy219] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/17/2018] [Indexed: 11/14/2022] Open
Abstract
Background Human noroviruses (HuNoVs) are a prominent cause of gastroenteritis, yet fundamental questions remain regarding epidemiology, diversity, and immunity in sub-Saharan African children. We investigated HuNoV seroprevalence and genetic and sociodemographic risk factors in Ugandan children. Methods We randomly screened 797 participants of a longitudinal birth cohort (Entebbe, EMaBS) and 378 from a cross-sectional survey (rural Lake Victoria, LaVIISWA), for antibodies against HuNoV genotypes by ELISA. We used linear regression modeling to test for associations between HuNoV antibody levels and sociodemographic factors, and with the human susceptibility rs601338 FUT2 secretor SNP and histo-blood group antigens (A/B/O). Results Of EMaBS participants, 76.6% were seropositive by age 1, rising to 94.5% by age 2 years. Seroprevalence in 1 year olds of the rural LaVIISWA survey was even higher (95%). In the birth cohort, 99% of seropositive 2 year olds had responses to multiple HuNoV genotypes. We identified associations between secretor status and genogroup GII antibody levels (GII.4 P = 3.1 × 10-52), as well as ABO and GI (GI.2 P = 2.1 × 10-12). Conclusions HuNoVs are highly prevalent in Ugandan children, indicating a substantial burden of diarrhea-associated morbidity with recurrent infections. Public health interventions, including vaccination, and increased surveillance are urgently needed.
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Affiliation(s)
- Lucy Thorne
- Division of Virology, Department of Pathology, University of Cambridge, UK
- Division of Infection and Immunity, University College London, Medical Research Council Centre for Medical Molecular Virology, UK
| | - Angela Nalwoga
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit, Entebbe, Uganda
| | | | - Alexis de Rougemont
- Centre National de Référence des Virus Entériques, Laboratoire de Virologie-Sérologie, Centre Hospitalier Universitaire de Dijon, France
- L'Unité Mixte de Recherche Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté/AgroSup Dijon, France
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, UK
| | - Emily Webb
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, UK
| | - Margaret Nampiija
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit, Entebbe, Uganda
| | - Allan Muhwezi
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit, Entebbe, Uganda
| | | | | | - Adrian V Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, UK
- The Jenner Institute, University of Oxford, UK
| | - Manj S Sandhu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Alison Elliott
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit, Entebbe, Uganda
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, UK
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, UK
- School of Public Health, University of Makeni, Sierra Leone
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16
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Casanova JL, Abel L. Human genetics of infectious diseases: Unique insights into immunological redundancy. Semin Immunol 2018; 36:1-12. [PMID: 29254755 PMCID: PMC5910248 DOI: 10.1016/j.smim.2017.12.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/13/2017] [Indexed: 01/18/2023]
Abstract
For almost any given human-tropic virus, bacterium, fungus, or parasite, the clinical outcome of primary infection is enormously variable, ranging from asymptomatic to lethal infection. This variability has long been thought to be largely determined by the germline genetics of the human host, and this is increasingly being demonstrated to be the case. The number and diversity of known inborn errors of immunity is continually increasing, and we focus here on autosomal and X-linked recessive traits underlying complete deficiencies of the encoded protein. Schematically, four types of infectious phenotype have been observed in individuals with such deficiencies, each providing information about the redundancy of the corresponding human gene, in terms of host defense in natural conditions. The lack of a protein can confer vulnerability to a broad range of microbes in most, if not all patients, through the disruption of a key immunological component. In such cases, the gene concerned is of low redundancy. However, the lack of a protein may also confer vulnerability to a narrow range of microbes, sometimes a single pathogen, and not necessarily in all patients. In such cases, the gene concerned is highly redundant. Conversely, the deficiency may be apparently neutral, conferring no detectable predisposition to infection in any individual. In such cases, the gene concerned is completely redundant. Finally, the lack of a protein may, paradoxically, be advantageous to the host, conferring resistance to one or more infections. In such cases, the gene is considered to display beneficial redundancy. These findings reflect the current state of evolution of humans and microbes, and should not be considered predictive of redundancy, or of a lack of redundancy, in the distant future. Nevertheless, these observations are of potential interest to present-day biologists testing immunological hypotheses experimentally and physicians managing patients with immunological or infectious conditions.
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Affiliation(s)
- Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, New York, NY, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, Paris, France, EU; Paris Descartes University, Imagine Institute, Paris, France, EU; Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, Paris, France, EU.
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, Paris, France, EU; Paris Descartes University, Imagine Institute, Paris, France, EU.
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17
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Szpak M, Mezzavilla M, Ayub Q, Chen Y, Xue Y, Tyler-Smith C. FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations. Genome Biol 2018; 19:5. [PMID: 29343290 PMCID: PMC5771147 DOI: 10.1186/s13059-017-1380-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/12/2017] [Indexed: 12/30/2022] Open
Abstract
We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold standard" positively selected variants and simulations. FineMAV has good sensitivity and a low false discovery rate. Applying FineMAV to the 1000 Genomes Project Phase 3 SNP dataset, we report many novel selected variants, including ones in TGM3 and PRSS53 associated with hair phenotypes that we validate using available independent data. FineMAV is widely applicable to sequence data from both human and other species.
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Affiliation(s)
- Michał Szpak
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Massimo Mezzavilla
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Qasim Ayub
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Genomics Facility, School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Darul Ehsan Malaysia
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
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18
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Saitou M, Lizardo DY, Taskent RO, Millner A, Gokcumen O, Atilla-Gokcumen GE. An evolutionary transcriptomics approach links CD36 to membrane remodeling in replicative senescence. Mol Omics 2018; 14:237-246. [DOI: 10.1039/c8mo00099a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CD36 was identified as a core replicative senescence gene and a potential mediator of this process through membrane remodeling.
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Affiliation(s)
- Marie Saitou
- Department of Biological Sciences
- University at Buffalo
- The State University of New York
- Buffalo
- USA
| | - Darleny Y. Lizardo
- Department of Chemistry
- University at Buffalo
- The State University of New York
- Buffalo
- USA
| | - Recep Ozgur Taskent
- Department of Biological Sciences
- University at Buffalo
- The State University of New York
- Buffalo
- USA
| | - Alec Millner
- Department of Chemistry
- University at Buffalo
- The State University of New York
- Buffalo
- USA
| | - Omer Gokcumen
- Department of Biological Sciences
- University at Buffalo
- The State University of New York
- Buffalo
- USA
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19
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Walakira A, Tukwasibwe S, Kiggundu M, Verra F, Kakeeto P, Ruhamyankaka E, Drakeley C, Dorsey G, Kamya MR, Nsobya SL, Rosenthal PJ. Marked variation in prevalence of malaria-protective human genetic polymorphisms across Uganda. INFECTION GENETICS AND EVOLUTION 2017; 55:281-287. [PMID: 28939159 DOI: 10.1016/j.meegid.2017.09.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/16/2017] [Accepted: 09/18/2017] [Indexed: 11/28/2022]
Abstract
A number of human genetic polymorphisms are prevalent in tropical populations and appear to offer protection against symptomatic and/or severe malaria. We compared the prevalence of four polymorphisms, the sickle hemoglobin mutation (β globin E6V), the α-thalassemia 3.7kb deletion, glucose-6-phosphate dehydrogenase deficiency caused by the common African variant (G6PD A-), and the CD36 T188G mutation in 1344 individuals residing in districts in eastern (Tororo), south-central (Jinja), and southwestern (Kanungu) Uganda. Genes of interest were amplified, amplicons subjected to mutation-specific restriction endonuclease digestion (for sickle hemoglobin, G6PD A-, and CD36 T188G), reaction products resolved by electrophoresis, and genotypes determined based on the sizes of reaction products. Mutant genotypes were common, with many more heterozygous than homozygous alleles identified. The prevalences (heterozygotes plus homozygotes) of sickle hemoglobin (28% Tororo, 25% Jinja, 7% Kanungu), α-thalassemia (53% Tororo, 45% Jinja, 18% Kanungu) and G6PD A- (29% Tororo, 18% Jinja, 8% Kanungu) were significantly greater in Tororo and Jinja compared to Kanungu (p<0.0001 for all three alleles); prevalences were also significantly greater in Tororo compared to Jinja for α-thalassemia (p=0.03) and G6PD A- (p<0.0001). For the CD36 T188G mutation, the prevalence was significantly greater in Tororo compared to Jinja or Kanungu (27% Tororo, 17% Jinja, 18% Kanungu; p=0.0004 and 0.0017, respectively). Considering ethnicity of study subjects, based on primary language spoken, the prevalence of mutant genotypes was lower in Bantu compared to non-Bantu language speakers, but in the Jinja cohort, the only study population with a marked diversity of language groups, prevalence did not differ between Bantu and non-Bantu speakers. These results indicate marked differences in human genetic features between populations in different regions of Uganda. These differences might be explained by both ethnic variation and by varied malaria risk in different regions of Uganda.
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Affiliation(s)
| | | | - Moses Kiggundu
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Federica Verra
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Grant Dorsey
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Moses R Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda; Department of Medicine, Makerere University, Kampala, Uganda
| | - Samuel L Nsobya
- Infectious Diseases Research Collaboration, Kampala, Uganda; Department of Pathology, Makerere University, Kampala, Uganda
| | - Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, CA, USA.
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20
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Ankyrin-1 Gene Exhibits Allelic Heterogeneity in Conferring Protection Against Malaria. G3-GENES GENOMES GENETICS 2017; 7:3133-3144. [PMID: 28751503 PMCID: PMC5592938 DOI: 10.1534/g3.117.300079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Allelic heterogeneity is a common phenomenon where a gene exhibits a different phenotype depending on the nature of its genetic mutations. In the context of genes affecting malaria susceptibility, it allowed us to explore and understand the intricate host–parasite interactions during malaria infections. In this study, we described a gene encoding erythrocytic ankyrin-1 (Ank-1) which exhibits allelic-dependent heterogeneous phenotypes during malaria infections. We conducted an ENU mutagenesis screen on mice and identified two Ank-1 mutations, one resulting in an amino acid substitution (MRI95845), and the other a truncated Ank-1 protein (MRI96570). Both mutations caused hereditary spherocytosis-like phenotypes and confer differing protection against Plasmodium chabaudi infections. Upon further examination, the Ank-1(MRI96570) mutation was found to inhibit intraerythrocytic parasite maturation, whereas Ank-1(MRI95845) caused increased bystander erythrocyte clearance during infection. This is the first description of allelic heterogeneity in ankyrin-1 from the direct comparison between two Ank-1 mutations. Despite the lack of direct evidence from population studies, this data further supported the protective roles of ankyrin-1 mutations in conferring malaria protection. This study also emphasized the importance of such phenomena in achieving a better understanding of host–parasite interactions, which could be the basis of future studies.
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21
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Sepúlveda N, Manjurano A, Campino SG, Lemnge M, Lusingu J, Olomi R, Rockett KA, Hubbart C, Jeffreys A, Rowlands K, Clark TG, Riley EM, Drakeley CJ. Malaria Host Candidate Genes Validated by Association With Current, Recent, and Historical Measures of Transmission Intensity. J Infect Dis 2017; 216:45-54. [PMID: 28541483 PMCID: PMC5853769 DOI: 10.1093/infdis/jix250] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 05/24/2017] [Indexed: 01/19/2023] Open
Abstract
Background Human malaria susceptibility is determined by multiple genetic factors. It is unclear, however, which genetic variants remain important over time. Methods Genetic associations of 175 high-quality polymorphisms within several malaria candidate genes were examined in a sample of 8096 individuals from northeast Tanzania using altitude, seroconversion rates, and parasite rates as proxies of historical, recent, and current malaria transmission intensity. A principal component analysis was used to derive 2 alternative measures of overall malaria propensity of a location across different time scales. Results Common red blood cell polymorphisms (ie, hemoglobin S, glucose-6-phosphate dehydrogenase, and α-thalassemia) were the only ones to be associated with all 3 measures of transmission intensity and the first principal component. Moderate associations were found between some immune response genes (ie, IL3 and IL13) and parasite rates, but these could not be reproduced using the alternative measures of malaria propensity. Conclusions We have demonstrated the potential of using altitude and seroconversion rate as measures of malaria transmission capturing medium- to long-term time scales to detect genetic associations that are likely to persist over time. These measures also have the advantage of minimizing the deleterious effects of random factors affecting parasite rates on the respective association signals.
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Affiliation(s)
- Nuno Sepúlveda
- London School of Hygiene and Tropical Medicine
- Centre of Statistics and Applications, University of Lisbon, Portugal
| | - Alphaxard Manjurano
- London School of Hygiene and Tropical Medicine
- Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Moshi
| | - Susana G Campino
- London School of Hygiene and Tropical Medicine
- Wellcome Trust Sanger Institute, Hinxton
| | - Martha Lemnge
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - John Lusingu
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Raimos Olomi
- Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Moshi
| | - Kirk A Rockett
- Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
| | - Christina Hubbart
- Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
| | - Anna Jeffreys
- Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
| | - Kate Rowlands
- Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
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22
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Quach H, Quintana-Murci L. Living in an adaptive world: Genomic dissection of the genus Homo and its immune response. J Exp Med 2017; 214:877-894. [PMID: 28351985 PMCID: PMC5379985 DOI: 10.1084/jem.20161942] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 02/14/2017] [Accepted: 03/06/2017] [Indexed: 12/14/2022] Open
Abstract
More than a decade after the sequencing of the human genome, a deluge of genome-wide population data are generating a portrait of human genetic diversity at an unprecedented level of resolution. Genomic studies have provided new insight into the demographic and adaptive history of our species, Homo sapiens, including its interbreeding with other hominins, such as Neanderthals, and the ways in which natural selection, in its various guises, has shaped genome diversity. These studies, combined with functional genomic approaches, such as the mapping of expression quantitative trait loci, have helped to identify genes, functions, and mechanisms of prime importance for host survival and involved in phenotypic variation and differences in disease risk. This review summarizes new findings in this rapidly developing field, focusing on the human immune response. We discuss the importance of defining the genetic and evolutionary determinants driving immune response variation, and highlight the added value of population genomic approaches in settings relevant to immunity and infection.
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Affiliation(s)
- Hélène Quach
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique, URA3012, 75015 Paris, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France .,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique, URA3012, 75015 Paris, France
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23
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Deschamps M, Laval G, Fagny M, Itan Y, Abel L, Casanova JL, Patin E, Quintana-Murci L. Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes. Am J Hum Genet 2016; 98:5-21. [PMID: 26748513 DOI: 10.1016/j.ajhg.2015.11.014] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/06/2015] [Indexed: 01/25/2023] Open
Abstract
Human genes governing innate immunity provide a valuable tool for the study of the selective pressure imposed by microorganisms on host genomes. A comprehensive, genome-wide study of how selective constraints and adaptations have driven the evolution of innate immunity genes is missing. Using full-genome sequence variation from the 1000 Genomes Project, we first show that innate immunity genes have globally evolved under stronger purifying selection than the remainder of protein-coding genes. We identify a gene set under the strongest selective constraints, mutations in which are likely to predispose individuals to life-threatening disease, as illustrated by STAT1 and TRAF3. We then evaluate the occurrence of local adaptation and detect 57 high-scoring signals of positive selection at innate immunity genes, variation in which has been associated with susceptibility to common infectious or autoimmune diseases. Furthermore, we show that most adaptations targeting coding variation have occurred in the last 6,000-13,000 years, the period at which populations shifted from hunting and gathering to farming. Finally, we show that innate immunity genes present higher Neandertal introgression than the remainder of the coding genome. Notably, among the genes presenting the highest Neandertal ancestry, we find the TLR6-TLR1-TLR10 cluster, which also contains functional adaptive variation in Europeans. This study identifies highly constrained genes that fulfill essential, non-redundant functions in host survival and reveals others that are more permissive to change-containing variation acquired from archaic hominins or adaptive variants in specific populations-improving our understanding of the relative biological importance of innate immunity pathways in natural conditions.
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Affiliation(s)
- Matthieu Deschamps
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France; CNRS URA3012, 75015 Paris, France; Université Pierre et Marie Curie, Cellule Pasteur UPMC, 75015 Paris, France
| | - Guillaume Laval
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France; CNRS URA3012, 75015 Paris, France
| | - Maud Fagny
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France; CNRS URA3012, 75015 Paris, France; Université Pierre et Marie Curie, Cellule Pasteur UPMC, 75015 Paris, France
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U.1163, 75015 Paris, France; Imagine Institute, Paris Descartes University, 75015 Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U.1163, 75015 Paris, France; Imagine Institute, Paris Descartes University, 75015 Paris, France; Howard Hughes Medical Institute, New York, NY 10065, USA; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, 75015 Paris, France
| | - Etienne Patin
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France; CNRS URA3012, 75015 Paris, France
| | - Lluis Quintana-Murci
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France; CNRS URA3012, 75015 Paris, France.
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24
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Lo SC, Lin KH, Hsieh HH, Lin DT, Hu CY. Genetic variations of CD36 and low platelet CD36 expression - a risk factor for lipemic plasma donation in Taiwanese apheresis donors. Vox Sang 2015; 110:236-43. [PMID: 26528880 DOI: 10.1111/vox.12356] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 09/03/2015] [Accepted: 09/16/2015] [Indexed: 12/01/2022]
Abstract
BACKGROUND New CD36 mutations are constantly being identified, although no study has specifically targeted a Taiwanese population. CD36 deficiency can result in dyslipid state and slow clearance of chylomicron. This could be linked to more frequent lipemic donations. STUDY DESIGN AND METHODS We used flow cytometric methods to study the CD36 deficiency in 640 regular volunteer platelet apheresis donors from Taipei blood centre. The coding exons of CD36 gene were sequenced in CD36-deficient individuals, and the allele frequencies of CD36 variants were determined in the larger population by mutation-specific PCR and oligonucleotide hybridization. Visual inspection of lipemic plasma was routinely performed on samples taken before commencement of apheresis. Individuals found to have lipemic plasma are deferred until next donation. We investigated the link between positive lipemic deferral record and low platelet CD36 expression status. RESULTS We found four donors (0·6%) with type I CD36 deficiency (both platelets and monocytes CD36(null) ) and six (1·0%) with type II CD36 deficiency (PLT: CD36(null) , monocyte: CD36(low) ). Six CD36 genetic variants were identified, two of them were novel, all but one are found exclusively in CD36(null) and CD36(low) expressors. Subjects with CD36 genetic variants also displayed deficient or reduced CD36 on monocytes. Donors with null or low PLT CD36 expression were more likely to have a lipemic deferral record than control subjects with normal PLT CD36 expression (X(2) = 27·36, odds ratio = 2·6, 95% conference interval: 1·8-3·8, P < 0·0001). CONCLUSION Through this study, we established a donor registry to supply CD36-negative platelets for patients in need.
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Affiliation(s)
- S-C Lo
- Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - K-H Lin
- Taiwan Blood Services Foundation, Taipei, Taiwan.,Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - H-H Hsieh
- Taiwan Blood Services Foundation, Taipei, Taiwan
| | - D-T Lin
- Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - C-Y Hu
- Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
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25
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Abstract
Parasites still impose a high death and disability burden on human populations, and are therefore likely to act as selective factors for genetic adaptations. Genetic epidemiological investigation of parasitic diseases is aimed at disentangling the mechanisms underlying immunity and pathogenesis by looking for associations or linkages between loci and susceptibility phenotypes. Until recently, most studies used a candidate gene approach and were relatively underpowered, with few attempts at replicating findings in different populations. However, in the last 5 years, genome-wide and/or multicentre studies have been conducted for severe malaria, visceral leishmaniasis, and cardiac Chagas disease, providing some novel important insights. Furthermore, studies of helminth infections have repeatedly shown the involvement of common loci in regulating susceptibility to distinct diseases such as schistosomiasis, ascariasis, trichuriasis, and onchocherciasis. As more studies are conducted, evidence is increasing that at least some of the identified susceptibility loci are shared not only among parasitic diseases but also with immunological disorders such as allergy or autoimmune disease, suggesting that parasites may have played a role in driving the evolution of the immune system.
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Affiliation(s)
- V D Mangano
- Department of Public Health and Infectious Diseases, University of Rome 'La Sapienza', Rome, Italy; Istituto Pasteur, Fondazione Cenci Bolognetti, University of Rome 'La Sapienza', Rome, Italy
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26
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Human knockout research: new horizons and opportunities. Trends Genet 2014; 31:108-15. [PMID: 25497971 DOI: 10.1016/j.tig.2014.11.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/15/2014] [Accepted: 11/17/2014] [Indexed: 12/12/2022]
Abstract
Although numerous approaches have been pursued to understand the function of human genes, Mendelian genetics has by far provided the most compelling and medically actionable dataset. Biallelic loss-of-function (LOF) mutations are observed in the majority of autosomal recessive Mendelian disorders, representing natural human knockouts and offering a unique opportunity to study the physiological and developmental context of these genes. The restriction of such context to 'disease' states is artificial, however, and the recent ability to survey entire human genomes for biallelic LOF mutations has revealed a surprising landscape of knockout events in 'healthy' individuals, sparking interest in their role in phenotypic diversity beyond disease causation. As I discuss in this review, the potentially wide implications of human knockout research warrant increased investment and multidisciplinary collaborations to overcome existing challenges and reap its benefits.
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27
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Ali IM, Evehe MSB, Netongo PM, Atogho-Tiedeu B, Akindeh-Nji M, Ngora H, Domkam IK, Diakite M, Baldip K, Ranford-Cartwright L, Mimche PN, Lamb T, Mbacham WF. Host candidate gene polymorphisms and associated clearance of P. falciparum amodiaquine and fansidar resistance mutants in children less than 5 years in Cameroon. Pathog Glob Health 2014; 108:323-33. [PMID: 25388906 PMCID: PMC4241784 DOI: 10.1179/2047773214y.0000000159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND In this post-hoc analysis, we determined the influence of single nucleotide polymorphisms in host candidate immune genes on the outcome of drug resistant malaria in Cameroon. METHODS Human DNA from 760 patients from a previous clinical trial was subjected to mass spectrometry-based single nucleotide polymorphism (SNP) genotyping. Allele frequencies of candidate immune genes were calculated for 62 SNPs on 17 human chromosomes for their possible involvement in clearance of drug-resistant parasites with the triple mutations of pfcrt76T, pfmdr86Y, and pfmdr1246Y (TY) and pfdhfr51I, pfdhfr59R, pfdhfr108N, and pfdhps437G (IRNG) which were determined by dotblot or PCR-restriction analysis. Differences in SNP frequencies and association analysis were carried out by comparing Chi-square odds ratios (ORs) and stratified by Mantel-Haenzel statistics. An adjusted P value (OR) <0·0008 was considered significant. RESULTS Post-treatment drug failure rates were amodiaquine (36·4%); sulpadoxine/pyrimethamine-amodiaquine combination (15·4%); and sulphadoxine/pyrimethamine (18·1%). SNPs in IL22, IL-4R1, and CD36 appeared to have been associated with clearance of resistant parasites [p = 0·017, OR (C allele):1·44, 95% CI (OR): 1·06-1·95]; [P = 0·014, OR = 1·31, 95% CI (OR): 1·07-1·83]; [P = 5·78×10(-5), OR = 0·27, 95%CI (OR): 0·13-0·54], respectively, with high fever (>39°C for 48 hours) [IL-22, P = 0·01, OR = 1·5, 95% CI (OR): 1·8-2·1] and also in high frequency among the Fulani participants [P = 0·006, OR = 1·83, 95% CI (OR): 1·11-3·08)]. The CD36-1264 null allele was completely absent in the northern population. CONCLUSION Independent association of SNPs in IL22 and IL-4 with clearance of amodiaquine- and sulphadoxine/pyrimethamine-resistant parasites did not reach statistical significance, but may suggest that not all drug-resistant mutants are adversely affected by the same immune-mediated mechanisms of clearance.
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28
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Cabrera A, Neculai D, Kain KC. CD36 and malaria: friends or foes? A decade of data provides some answers. Trends Parasitol 2014; 30:436-44. [PMID: 25113859 DOI: 10.1016/j.pt.2014.07.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 02/07/2023]
Abstract
The past 10 years have generated new insights into the complex interaction between CD36 (cluster of differentiation 36) and malaria. These range from the crystallization of the CD36 homolog, LIMPII (lysosomal integral membrane protein II), permitting modeling of CD36 and its binding to diverse ligands, to cell biology-based studies of CD36 and large population genetic studies assessing the association of CD36 polymorphisms and malarial disease severity. Collectively these lines of evidence indicate that a receptor other than CD36 is associated with severity. CD36 plays an important role in innate immunity and in the phagocytic uptake of multiple pathogens including malaria. CD36 polymorphisms lack association with severity, and isolates that cause severe disease primarily bind to endothelial protein C receptor (EPCR) rather than to CD36.
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Affiliation(s)
- Ana Cabrera
- Sandra Ann Rotman (SAR) Laboratories, SAR Centre, Toronto General Hospital, University Health Network, Tropical Disease Unit, Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Dante Neculai
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kevin C Kain
- Sandra Ann Rotman (SAR) Laboratories, SAR Centre, Toronto General Hospital, University Health Network, Tropical Disease Unit, Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
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29
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Ellis J, Lange EM, Li J, Dupuis J, Baumert J, Walston JD, Keating BJ, Durda P, Fox ER, Palmer CD, Meng YA, Young T, Farlow DN, Schnabel RB, Marzi CS, Larkin E, Martin LW, Bis JC, Auer P, Ramachandran VS, Gabriel SB, Willis MS, Pankow JS, Papanicolaou GJ, Rotter JI, Ballantyne CM, Gross MD, Lettre G, Wilson JG, Peters U, Koenig W, Tracy RP, Redline S, Reiner AP, Benjamin EJ, Lange LA. Large multiethnic Candidate Gene Study for C-reactive protein levels: identification of a novel association at CD36 in African Americans. Hum Genet 2014; 133:985-95. [PMID: 24643644 PMCID: PMC4104766 DOI: 10.1007/s00439-014-1439-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 03/06/2014] [Indexed: 10/25/2022]
Abstract
C-reactive protein (CRP) is a heritable biomarker of systemic inflammation and a predictor of cardiovascular disease (CVD). Large-scale genetic association studies for CRP have largely focused on individuals of European descent. We sought to uncover novel genetic variants for CRP in a multiethnic sample using the ITMAT Broad-CARe (IBC) array, a custom 50,000 SNP gene-centric array having dense coverage of over 2,000 candidate CVD genes. We performed analyses on 7,570 African Americans (AA) from the Candidate gene Association Resource (CARe) study and race-combined meta-analyses that included 29,939 additional individuals of European descent from CARe, the Women's Health Initiative (WHI) and KORA studies. We observed array-wide significance (p < 2.2 × 10(-6)) for four loci in AA, three of which have been reported previously in individuals of European descent (IL6R, p = 2.0 × 10(-6); CRP, p = 4.2 × 10(-71); APOE, p = 1.6 × 10(-6)). The fourth significant locus, CD36 (p = 1.6 × 10(-6)), was observed at a functional variant (rs3211938) that is extremely rare in individuals of European descent. We replicated the CD36 finding (p = 1.8 × 10(-5)) in an independent sample of 8,041 AA women from WHI; a meta-analysis combining the CARe and WHI AA results at rs3211938 reached genome-wide significance (p = 1.5 × 10(-10)). In the race-combined meta-analyses, 13 loci reached significance, including ten (CRP, TOMM40/APOE/APOC1, HNF1A, LEPR, GCKR, IL6R, IL1RN, NLRP3, HNF4A and BAZ1B/BCL7B) previously associated with CRP, and one (ARNTL) previously reported to be nominally associated with CRP. Two novel loci were also detected (RPS6KB1, p = 2.0 × 10(-6); CD36, p = 1.4 × 10(-6)). These results highlight both shared and unique genetic risk factors for CRP in AA compared to populations of European descent.
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Affiliation(s)
- Jaclyn Ellis
- Department of Genetics, University of North Carolina, 5112 Genetic Medicine Bldg., Chapel Hill, NC, 27599-7264, USA
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30
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Mangano VD, Modiano D. An evolutionary perspective of how infection drives human genome diversity: the case of malaria. Curr Opin Immunol 2014; 30:39-47. [PMID: 24996199 DOI: 10.1016/j.coi.2014.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/31/2014] [Accepted: 06/04/2014] [Indexed: 11/26/2022]
Abstract
Infection with malaria parasites has imposed a strong selective pressure on the human genome, promoting the convergent evolution of a diverse range of genetic adaptations, many of which are harboured by the red blood cell, which hosts the pathogenic stage of the Plasmodium life cycle. Recent genome-wide and multi-centre association studies of severe malaria have consistently identified ATP2B4, encoding the major Ca(2+) pump of erythrocytes, as a novel resistance locus. Evidence is also accumulating that interaction occurs among resistance loci, the most recent example being negative epistasis among alpha-thalassemia and haptoglobin type 2. Finally, studies on the effect of haemoglobin S and C on parasite transmission to mosquitoes have suggested that protective variants could increase in frequency enhancing parasite fitness.
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Affiliation(s)
- Valentina D Mangano
- Department of Public Health and Infectious Diseases, University of Rome 'La Sapienza', Rome, Italy; Istituto Pasteur, Fondazione Cenci Bolognetti, University of Rome 'La Sapienza', Rome, Italy.
| | - David Modiano
- Department of Public Health and Infectious Diseases, University of Rome 'La Sapienza', Rome, Italy; Istituto Pasteur, Fondazione Cenci Bolognetti, University of Rome 'La Sapienza', Rome, Italy.
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31
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Smith JD, Rowe JA, Higgins MK, Lavstsen T. Malaria's deadly grip: cytoadhesion of Plasmodium falciparum-infected erythrocytes. Cell Microbiol 2013; 15:1976-83. [PMID: 23957661 PMCID: PMC3836831 DOI: 10.1111/cmi.12183] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/07/2013] [Accepted: 08/12/2013] [Indexed: 12/17/2022]
Abstract
Cytoadhesion of Plasmodium falciparum-infected erythrocytes to host microvasculature is a key virulence determinant. Parasite binding is mediated by a large family of clonally variant adhesion proteins, termed P. falciparum erythrocyte membrane protein 1 (PfEMP1), encoded by var genes and expressed at the infected erythrocyte surface. Although PfEMP1 proteins have extensively diverged under opposing selection pressure to maintain ligand binding while avoiding antibody-mediated detection, recent work has revealed they can be classified into different groups based on chromosome location and domain composition. This grouping reflects functional specialization of PfEMP1 proteins for different human host and microvascular binding niches and appears to be maintained by gene recombination hierarchies. Inone extreme, a specific PfEMP1 variant is associated with placental binding and malaria during pregnancy, while other PfEMP1 subtypes appear to be specialized for infection of malaria naïve hosts. Here, we discuss recent findings on the origins and evolution of the var gene family, the structure-function of PfEMP1 proteins, and a distinct subset of PfEMP1 variants that have been associated with severe childhood malaria.
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Affiliation(s)
- Joseph D. Smith
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America, 98109
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - J. Alexandra Rowe
- Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| | - Matthew K. Higgins
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Thomas Lavstsen
- Centre for Medical Parasitology, Department of International Health, Immunology & Microbiology, University of Copenhagen and Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
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Pybus M, Dall'Olio GM, Luisi P, Uzkudun M, Carreño-Torres A, Pavlidis P, Laayouni H, Bertranpetit J, Engelken J. 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans. Nucleic Acids Res 2013; 42:D903-9. [PMID: 24275494 PMCID: PMC3965045 DOI: 10.1093/nar/gkt1188] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Searching for Darwinian selection in natural populations has been the focus of a multitude of studies over the last decades. Here we present the 1000 Genomes Selection Browser 1.0 (http://hsb.upf.edu) as a resource for signatures of recent natural selection in modern humans. We have implemented and applied a large number of neutrality tests as well as summary statistics informative for the action of selection such as Tajima’s D, CLR, Fay and Wu’s H, Fu and Li’s F* and D*, XPEHH, ΔiHH, iHS, FST, ΔDAF and XPCLR among others to low coverage sequencing data from the 1000 genomes project (Phase 1; release April 2012). We have implemented a publicly available genome-wide browser to communicate the results from three different populations of West African, Northern European and East Asian ancestry (YRI, CEU, CHB). Information is provided in UCSC-style format to facilitate the integration with the rich UCSC browser tracks and an access page is provided with instructions and for convenient visualization. We believe that this expandable resource will facilitate the interpretation of signals of selection on different temporal, geographical and genomic scales.
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Affiliation(s)
- Marc Pybus
- Program for Population Genetics, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain, Population Genomics Node, National Institute for Bioinformatics (INB), Universitat Pompeu Fabra, 08003 Barcelona, Spain, Institute of Molecular Biology and Biotechnology-FORTH, Heraklion, Crete GR 700 13, Greece and Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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Maiga B, Dolo A, Touré O, Dara V, Tapily A, Campino S, Sepulveda N, Risley P, Silva N, Corran P, Rockett KA, Kwiatkowski D, Clark TG, Troye-Blomberg M, Doumbo OK. Human candidate polymorphisms in sympatric ethnic groups differing in malaria susceptibility in Mali. PLoS One 2013; 8:e75675. [PMID: 24098393 PMCID: PMC3788813 DOI: 10.1371/journal.pone.0075675] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 08/16/2013] [Indexed: 11/30/2022] Open
Abstract
Malaria still remains a major public health problem in Mali, although disease susceptibility varies between ethnic groups, particularly between the Fulani and Dogon. These two sympatric groups share similar socio-cultural factors and malaria transmission rates, but Fulani individuals tend to show significantly higher spleen enlargement scores, lower parasite prevalence, and seem less affected by the disease than their Dogon neighbours. We have used genetic polymorphisms from malaria-associated genes to investigate associations with various malaria metrics between the Fulanai and Dogon groups. Two cross sectional surveys (transmission season 2006, dry season 2007) were performed. Healthy volunteers from the both ethnic groups (n=939) were recruited in a rural setting. In each survey, clinical (spleen enlargement, axillary temperature, weight) and parasitological data (malaria parasite densities and species) were collected, as well as blood samples. One hundred and sixty six SNPs were genotyped and 5 immunoassays (AMA1, CSP, MSP1, MSP2, total IgE) were performed on the DNA and serum samples respectively. The data confirm the reduced malaria susceptibility in the Fulani, with a higher level of the protective O-blood group, and increased circulating antibody levels to several malaria antigens (p<10(-15)). We identified SNP allele frequency differences between the 2 ethnic groups in CD36, IL4, RTN3 and ADCY9. Moreover, polymorphisms in FCER1A, RAD50, TNF, SLC22A4, and IL13 genes were correlated with antibody production (p-value<0.003). Further work is required to understand the mechanisms underpinning these genetic factors.
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Affiliation(s)
- Bakary Maiga
- Malaria Research and Training Center / Department of Epidemiology of Parasitic Diseases / Faculty of Medicine, Pharmacy and Odonto – Stomatology, BP 1805, Bamako, USTTB, Mali
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Amagana Dolo
- Malaria Research and Training Center / Department of Epidemiology of Parasitic Diseases / Faculty of Medicine, Pharmacy and Odonto – Stomatology, BP 1805, Bamako, USTTB, Mali
| | - Ousmane Touré
- Malaria Research and Training Center / Department of Epidemiology of Parasitic Diseases / Faculty of Medicine, Pharmacy and Odonto – Stomatology, BP 1805, Bamako, USTTB, Mali
| | - Victor Dara
- Malaria Research and Training Center / Department of Epidemiology of Parasitic Diseases / Faculty of Medicine, Pharmacy and Odonto – Stomatology, BP 1805, Bamako, USTTB, Mali
| | - Amadou Tapily
- Malaria Research and Training Center / Department of Epidemiology of Parasitic Diseases / Faculty of Medicine, Pharmacy and Odonto – Stomatology, BP 1805, Bamako, USTTB, Mali
| | - Susana Campino
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Nuno Sepulveda
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Center of Statistics and Applications of University of Lisbon, Lisbon, Portugal
| | - Paul Risley
- National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom
| | - Nipula Silva
- National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom
| | - Patrick Corran
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom
| | - Kirk A. Rockett
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Dominic Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Marita Troye-Blomberg
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ogobara K. Doumbo
- Malaria Research and Training Center / Department of Epidemiology of Parasitic Diseases / Faculty of Medicine, Pharmacy and Odonto – Stomatology, BP 1805, Bamako, USTTB, Mali
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Rać M, Safranow K, Kurzawski G, Krzystolik A, Chlubek D. Is CD36 gene polymorphism in region encoding lipid-binding domain associated with early onset CAD? Gene 2013; 530:134-7. [PMID: 23856131 DOI: 10.1016/j.gene.2013.06.061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/22/2013] [Accepted: 06/16/2013] [Indexed: 12/21/2022]
Abstract
CD36 is a fatty acid translocase in striated muscle cells and cardiomyocytes. Some study suggested that alterations in CD36 gene may be associated with coronary artery disease (CAD) risk. The aim of the current study was to compare the frequency of CD36 variants in region encoding lipid-binding domain in Caucasian patients with early-onset CAD, no-CAD adult controls and neonates. The study group comprised 100 patients with early onset CAD. The genetic control groups were 306 infants and 40 no-CAD adults aged over 70years. Exons 4, 5 and 6 including fragments of flanking introns were studied using the denaturing high-performance liquid chromatography technique and direct sequencing. Changes detected in analyzed fragment of CD36: IVS3-6 T/C (rs3173798), IVS4-10 G/A (rs3211892), C311T (Thr104Ile, not described so far) in exon 5, G550A (Asp184Asn, rs138897347), C572T (Pro191Leu, rs143150225), G573A (Pro191Pro, rs5956) and A591T (Thr197Thr, rs141680676) in exon 6. No significant differences in the CD36 genotype, allele and haplotype frequencies were found between the three groups. Only borderline differences (p=0.066) were found between early onset CAD patients and newborns in the frequencies of 591T allele (2.00% vs 0.50%) and CGCGCGT haplotype (2.00% vs 0.50%) with both IVS3-6C and 591T variant alleles. In conclusion, CD36 variants: rs3173798, rs3211892, rs138897347, rs5956, rs143150225 rs141680676 and C311T do not seem to be involved in the risk of early-onset CAD in Caucasian population.
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Affiliation(s)
- Monika Rać
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Szczecin, Poland.
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35
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Conant KL, Kaleeba JAR. Dangerous liaisons: molecular basis for a syndemic relationship between Kaposi's sarcoma and P. falciparum malaria. Front Microbiol 2013; 4:35. [PMID: 23487416 PMCID: PMC3594938 DOI: 10.3389/fmicb.2013.00035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 02/07/2013] [Indexed: 11/13/2022] Open
Abstract
The most severe manifestations of malaria (caused by Plasmodium falciparum) occur as a direct result of parasitemia following invasion of erythrocytes by post-liver blood-stage merozoites, and during subsequent cyto-adherence of infected erythrocytes to the vascular endothelium. However, the disproportionate epidemiologic clustering of severe malaria with aggressive forms of endemic diseases such as Kaposi's sarcoma (KS), a neoplasm that is etiologically linked to infection with KS-associated herpesvirus (KSHV), underscores the significance of previously unexplored co-pathogenetic interactions that have the potential to modify the overall disease burden in co-infected individuals. Based on recent studies of the mechanisms that P. falciparum and KSHV have evolved to interact with their mutual human host, several new perspectives are emerging that highlight a surprising convergence of biological themes potentially underlying their associated co-morbidities. Against this background, ongoing studies are rapidly constructing a fascinating new paradigm in which the major host receptors that control parasite invasion (Basigin/CD147) and cyto-adherence (CD36) are, surprisingly, also important targets for exploitation by KSHV. In this article, we consider the major pathobiological implications of the co-option of Basigin/CD147 and CD36 signaling pathways by both P. falciparum and KSHV, not only as essential host factors for parasite persistence but also as important mediators of the pro-angiogenic phenotype within the virus-infected endothelial microenvironment. Consequently, the triangulation of interactions between P. falciparum, KSHV, and their mutual human host articulates a syndemic relationship that points to a conceptual framework for prevalence of aggressive forms of KS in malaria-endemic areas, with implications for the possibility of dual-use therapies against these debilitating infections in resource-limited parts of the world.
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Affiliation(s)
| | - Johnan A. R. Kaleeba
- Department of Microbiology and Immunology, Uniformed Services University of the Health SciencesBethesda, MD, USA
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36
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Elbers CC, Guo Y, Tragante V, van Iperen EPA, Lanktree MB, Castillo BA, Chen F, Yanek LR, Wojczynski MK, Li YR, Ferwerda B, Ballantyne CM, Buxbaum SG, Chen YDI, Chen WM, Cupples LA, Cushman M, Duan Y, Duggan D, Evans MK, Fernandes JK, Fornage M, Garcia M, Garvey WT, Glazer N, Gomez F, Harris TB, Halder I, Howard VJ, Keller MF, Kamboh MI, Kooperberg C, Kritchevsky SB, LaCroix A, Liu K, Liu Y, Musunuru K, Newman AB, Onland-Moret NC, Ordovas J, Peter I, Post W, Redline S, Reis SE, Saxena R, Schreiner PJ, Volcik KA, Wang X, Yusuf S, Zonderland AB, Anand SS, Becker DM, Psaty B, Rader DJ, Reiner AP, Rich SS, Rotter JI, Sale MM, Tsai MY, Borecki IB, Hegele RA, Kathiresan S, Nalls MA, Taylor HA, Hakonarson H, Sivapalaratnam S, Asselbergs FW, Drenos F, Wilson JG, Keating BJ. Gene-centric meta-analysis of lipid traits in African, East Asian and Hispanic populations. PLoS One 2012; 7:e50198. [PMID: 23236364 PMCID: PMC3517599 DOI: 10.1371/journal.pone.0050198] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/22/2012] [Indexed: 11/18/2022] Open
Abstract
Meta-analyses of European populations has successfully identified genetic variants in over 100 loci associated with lipid levels, but our knowledge in other ethnicities remains limited. To address this, we performed dense genotyping of ∼2,000 candidate genes in 7,657 African Americans, 1,315 Hispanics and 841 East Asians, using the IBC array, a custom ∼50,000 SNP genotyping array. Meta-analyses confirmed 16 lipid loci previously established in European populations at genome-wide significance level, and found multiple independent association signals within these lipid loci. Initial discovery and in silico follow-up in 7,000 additional African American samples, confirmed two novel loci: rs5030359 within ICAM1 is associated with total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) (p = 8.8×10(-7) and p = 1.5×10(-6) respectively) and a nonsense mutation rs3211938 within CD36 is associated with high-density lipoprotein cholesterol (HDL-C) levels (p = 13.5×10(-12)). The rs3211938-G allele, which is nearly absent in European and Asian populations, has been previously found to be associated with CD36 deficiency and shows a signature of selection in Africans and African Americans. Finally, we have evaluated the effect of SNPs established in European populations on lipid levels in multi-ethnic populations and show that most known lipid association signals span across ethnicities. However, differences between populations, especially differences in allele frequency, can be leveraged to identify novel signals, as shown by the discovery of ICAM1 and CD36 in the current report.
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Affiliation(s)
- Clara C. Elbers
- Department of Genetics, University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Medical Genetics, Biomedical Genetics, University Medical Center, Utrecht, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Yiran Guo
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Vinicius Tragante
- Department of Medical Genetics, Biomedical Genetics, University Medical Center, Utrecht, The Netherlands
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Erik P. A. van Iperen
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Matthew B. Lanktree
- Departments of Medicine and Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Berta Almoguera Castillo
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Fang Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Lisa R. Yanek
- GeneSTAR Research Program, Division of General Internal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Mary K. Wojczynski
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Division of Statistical Genomics and Department of Genetics Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yun R. Li
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Bart Ferwerda
- Department of Genetics, University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, United States of America
| | | | - Sarah G. Buxbaum
- Jackson Heart Study, Jackson State University, Jackson, Mississippi, United States of America
- School of Health Sciences, Department of Epidemiology and Biostatistics, Jackson State University, Jackson, Mississippi, United States of America
| | - Yii-Der Ida Chen
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - L. Adrienne Cupples
- Boston University, Boston, Massachusetts, United States of America
- The National Heart, Lung, Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Mary Cushman
- Department of Medicine, Thrombosis and Hemostasis Program, University of Vermont, Burlington, Vermont, United States of America
| | - Yanan Duan
- Division of Statistical Genomics and Department of Genetics Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Michele K. Evans
- Health Disparities Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Jyotika K. Fernandes
- Division of Endocrinology, Diabetes and Medical Genetics, College of Medicine, Medical University of South Carolina, Charleston, SC United States of America
| | - Myriam Fornage
- The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Melissa Garcia
- Laboratory for Epidemiology, Demography, and Biometry, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - W. Timothy Garvey
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Nicole Glazer
- Boston University, Boston, Massachusetts, United States of America
| | - Felicia Gomez
- Department of Genetics, University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Tamara B. Harris
- Laboratory for Epidemiology, Demography, and Biometry, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Indrani Halder
- Heart and Vascular Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Virginia J. Howard
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Margaux F. Keller
- Laboratory of Neurogenetics, Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - M. Ilyas Kamboh
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Stephen B. Kritchevsky
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Sticht Center on Aging, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Andrea LaCroix
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Kiang Liu
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Kiran Musunuru
- Broad Institute, Cambridge, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Anne B. Newman
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - N. Charlotte Onland-Moret
- Department of Medical Genetics, Biomedical Genetics, University Medical Center, Utrecht, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jose Ordovas
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, Massachusetts, United States of America
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Wendy Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Susan Redline
- Brigham and Women's Hospital and Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Steven E. Reis
- School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Richa Saxena
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Pamela J. Schreiner
- School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Kelly A. Volcik
- Division of Epidemiology, Human Genetics and Environmental Sciences, Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Xingbin Wang
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Salim Yusuf
- Population Health Research Institute, Hamilton Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Alan B. Zonderland
- Laboratory of Personality and Cognition, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sonia S. Anand
- Population Health Research Institute, Hamilton Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Diane M. Becker
- GeneSTAR Research Program, Division of General Internal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, Washington, United States of America
- Group Health Research Institute, Group Health Cooperative, Seattle, Washington, United States of America
| | - Daniel J. Rader
- Cardiovascular Institute, the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alex P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Michèle M. Sale
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Michael Y. Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ingrid B. Borecki
- Division of Statistical Genomics and Department of Genetics Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Robert A. Hegele
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Sekar Kathiresan
- Broad Institute, Cambridge, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Michael A. Nalls
- Laboratory of Neurogenetics, Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Herman A. Taylor
- Jackson State University, Tougaloo College, and the University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | | | - Folkert W. Asselbergs
- Department of Medical Genetics, Biomedical Genetics, University Medical Center, Utrecht, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Fotios Drenos
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, United Kingdom
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Brendan J. Keating
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
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Auer P, Johnsen J, Johnson A, Logsdon B, Lange L, Nalls M, Zhang G, Franceschini N, Fox K, Lange E, Rich S, O’Donnell C, Jackson R, Wallace R, Chen Z, Graubert T, Wilson J, Tang H, Lettre G, Reiner A, Ganesh S, Li Y. Imputation of exome sequence variants into population- based samples and blood-cell-trait-associated loci in African Americans: NHLBI GO Exome Sequencing Project. Am J Hum Genet 2012; 91:794-808. [PMID: 23103231 DOI: 10.1016/j.ajhg.2012.08.031] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 06/12/2012] [Accepted: 08/27/2012] [Indexed: 01/07/2023] Open
Abstract
Researchers have successfully applied exome sequencing to discover causal variants in selected individuals with familial, highly penetrant disorders. We demonstrate the utility of exome sequencing followed by imputation for discovering low-frequency variants associated with complex quantitative traits. We performed exome sequencing in a reference panel of 761 African Americans and then imputed newly discovered variants into a larger sample of more than 13,000 African Americans for association testing with the blood cell traits hemoglobin, hematocrit, white blood count, and platelet count. First, we illustrate the feasibility of our approach by demonstrating genome-wide-significant associations for variants that are not covered by conventional genotyping arrays; for example, one such association is that between higher platelet count and an MPL c.117G>T (p.Lys39Asn) variant encoding a p.Lys39Asn amino acid substitution of the thrombopoietin receptor gene (p = 1.5 × 10(-11)). Second, we identified an association between missense variants of LCT and higher white blood count (p = 4 × 10(-13)). Third, we identified low-frequency coding variants that might account for allelic heterogeneity at several known blood cell-associated loci: MPL c.754T>C (p.Tyr252His) was associated with higher platelet count; CD36 c.975T>G (p.Tyr325(∗)) was associated with lower platelet count; and several missense variants at the α-globin gene locus were associated with lower hemoglobin. By identifying low-frequency missense variants associated with blood cell traits not previously reported by genome-wide association studies, we establish that exome sequencing followed by imputation is a powerful approach to dissecting complex, genetically heterogeneous traits in large population-based studies.
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Cserti-Gazdewich CM, Dhabangi A, Musoke C, Ssewanyana I, Ddungu H, Nakiboneka-Ssenabulya D, Nabukeera-Barungi N, Mpimbaza A, Dzik WH. Cytoadherence in paediatric malaria: ABO blood group, CD36, and ICAM1 expression and severe Plasmodium falciparum infection. Br J Haematol 2012; 159:223-36. [PMID: 22909232 PMCID: PMC3470923 DOI: 10.1111/bjh.12014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 07/12/2012] [Indexed: 11/28/2022]
Abstract
As a leading cause of childhood mortality worldwide, selection pressure by Plasmodium falciparum continues to shape the human genome. Severe disturbances within the microcirculation result from the adhesion of infected erythrocytes to host receptors on monocytes, platelets, and endothelium. In this prospective study, we compared expression of all major host cytoadhesion receptors among Ugandan children presenting with uncomplicated malaria (n = 1078) versus children with severe malaria (n = 855), including cerebral malaria (n = 174), severe anaemia (n = 522), and lactic acidosis (n = 154). We report a significant survival advantage attributed to blood group O and increased monocyte expression of CD36 and ICAM1 (CD54). The high case fatality rate syndromes of cerebral malaria and lactic acidosis were associated with high platelet CD36 expression and thrombocytopenia, and severe malaria anaemia was characterized by low ICAM1 expression. In a logistic regression model of disease severity, odds ratios for the mitigating effects of blood group O, CD36, and ICAM1 phenotypes were greater than that of sickle haemoglobin. Host genetic adaptations to Plasmodium falciparum suggest new potential malaria treatment strategies.
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Kajeguka D, Mwanziva C, Daou M, Ndaro A, Matondo S, Mbugi E, Dolmans W, Chilongola J. CD36 c.1264 T>G null mutation impairs acquisition of IgG antibodies to Plasmodium falciparum MSP1₁₉ antigen and is associated with higher malaria incidences in Tanzanian children. Scand J Immunol 2012; 75:355-60. [PMID: 22050542 DOI: 10.1111/j.1365-3083.2011.02661.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polymorphisms in genes that encode crucial signalling molecules have been proposed as factors that influence susceptibility to, and outcome of malaria. We studied the role of a mutation, c.1264 T>G, that causes CD36 deficiency on IgG responses to MSP-1₁₉ antigen and malaria incidence. Children were genotyped for the c.1264 T>G mutation at the beginning of the study using PCR-RFLP. IgG levels [optical density (OD) readings] and per cent seropositivity to MSP-1₁₉ were determined at baseline by ELISA. Children were followed for 12 months for acquisition of anti-MSP-1₁₉ IgG antibody and malaria incidence. We observed a significant increase in the production of anti-MSP-1₁₉ IgG antibody in normal and heterozygous children during the 12 months of follow-up, but not in homozygous mutants. Normal children had a significantly lower malaria incidence rate compared to other genotypes (χ² = 115.59; P < 0.01). We conclude that the presence of the c.1264 T>G mutation that leads to CD36 deficiency is closely associated with reduced IgG production and higher malaria incidence. It is most likely that deficiency of CD36 which is known to modulate dendritic cell function suppresses the production of protective IgG antibodies directed to Plasmodium falciparum MSP-1₁₉ antigen, which predisposes to the acquisition of clinical malaria in children.
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Affiliation(s)
- D Kajeguka
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Tumaini University, Moshi, Tanzania
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MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IHA, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C. A systematic survey of loss-of-function variants in human protein-coding genes. Science 2012; 335:823-8. [PMID: 22344438 PMCID: PMC3299548 DOI: 10.1126/science.1215040] [Citation(s) in RCA: 874] [Impact Index Per Article: 72.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Genome-sequencing studies indicate that all humans carry many genetic variants predicted to cause loss of function (LoF) of protein-coding genes, suggesting unexpected redundancy in the human genome. Here we apply stringent filters to 2951 putative LoF variants obtained from 185 human genomes to determine their true prevalence and properties. We estimate that human genomes typically contain ~100 genuine LoF variants with ~20 genes completely inactivated. We identify rare and likely deleterious LoF alleles, including 26 known and 21 predicted severe disease-causing variants, as well as common LoF variants in nonessential genes. We describe functional and evolutionary differences between LoF-tolerant and recessive disease genes and a method for using these differences to prioritize candidate genes found in clinical sequencing studies.
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Jin W, Xu S, Wang H, Yu Y, Shen Y, Wu B, Jin L. Genome-wide detection of natural selection in African Americans pre- and post-admixture. Genome Res 2011; 22:519-27. [PMID: 22128132 DOI: 10.1101/gr.124784.111] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
It is particularly meaningful to investigate natural selection in African Americans (AfA) due to the high mortality their African ancestry has experienced in history. In this study, we examined 491,526 autosomal single nucleotide polymorphisms (SNPs) genotyped in 5210 individuals and conducted a genome-wide search for selection signals in 1890 AfA. Several genomic regions showing an excess of African or European ancestry, which were considered the footprints of selection since population admixture, were detected based on a commonly used approach. However, we also developed a new strategy to detect natural selection both pre- and post-admixture by reconstructing an ancestral African population (AAF) from inferred African components of ancestry in AfA and comparing it with indigenous African populations (IAF). Interestingly, many selection-candidate genes identified by the new approach were associated with AfA-specific high-risk diseases such as prostate cancer and hypertension, suggesting an important role these disease-related genes might have played in adapting to a new environment. CD36 and HBB, whose mutations confer a degree of protection against malaria, were also located in the highly differentiated regions between AAF and IAF. Further analysis showed that the frequencies of alleles protecting against malaria in AAF were lower than those in IAF, which is consistent with the relaxed selection pressure of malaria in the New World. There is no overlap between the top candidate genes detected by the two approaches, indicating the different environmental pressures AfA experienced pre- and post-population admixture. We suggest that the new approach is reasonably powerful and can also be applied to other admixed populations such as Latinos and Uyghurs.
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Affiliation(s)
- Wenfei Jin
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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42
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Polymorphism of the CD36 Gene and Cardiovascular Risk Factors in Patients with Coronary Artery Disease Manifested at a Young Age. Biochem Genet 2011; 50:103-11. [PMID: 22113854 PMCID: PMC3258388 DOI: 10.1007/s10528-011-9475-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 08/09/2011] [Indexed: 12/24/2022]
Abstract
This study investigates potential associations between CD36 gene variants and the presence of risk factors in Caucasians with coronary artery disease (CAD) manifested at a young age. The study group consisted of 90 patients; the men were ≤ 50 years old and the women were ≤ 55 years old. Amplicons of exons 4 and 5 including fragments of introns were analyzed by DHPLC. Two polymorphisms were found: IVS3-6 T/C (rs3173798) and IVS4-10 G/A (rs3211892). The C allele of the IVS3-6 T/C polymorphism was associated with higher prevalence of obesity and diabetes, higher hsCRP, lower Lp(a) serum concentrations, and younger age at myocardial infarction. The A allele of the IVS4-10 G/A polymorphism was associated with older age of myocardial infarction and higher white blood cell count. The functional role of CD36 polymorphisms in CAD development needs further research.
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Abstract
A linkage between presence of Sickle Haemoglobin (HbS) and protection from malaria infection and clinical manifestations in certain areas was suspected from early observations and progressively elucidated by more recent studies. Research has confirmed the abovementioned connection, but also clarified how such protection may be abolished by coexistence of sickle cell trait (HbS trait) and alpha thalassemia, which may explain the relatively low incidence of HbS trait in the Mediterranean. The mechanisms of such protective effect are now being investigated: factors of genetic, molecular and immunological nature are prominent. As for genetic factors attention is given to the role of the red blood cell (RBC) membrane complement regulatory proteins as polymorphisms of these components seem to be associated with resistance to severe malaria; genetic ligands like the Duffy group blood antigen, necessary for erythrocytic invasion, and human protein CD36, a major receptor for P. falciparum-infected RBC's, are also under scrutiny: attention is focused also on plasmodium erythrocyte-binding antigens, which bind to RBC surface components. Genome-wide linkage and association studies are now carried out too, in order to identify genes associated with malaria resistance. Only a minor role is attributed to intravascular sickling, phagocytosis and haemolysis, while specific molecular mechanisms are the object of intensive research: among these a decisive role is played by a biochemical sequence, involving activation of haeme oxygenase (HMO-1), whose effect appears mediated by carbon monoxide (CO). A central role in protection from malaria is also played by immunological factors, which may stimulate antibody production to plasmodium antigens in the early years of life; the role of agents like pathogenic CD8 T-cells has been suggested while the effects of molecular actions on the immunity mechanism are presently investigated. It thus appears that protection from malaria can be explained by interaction of different factors: the elucidation of such mechanisms may prove valuable for the prevention and treatment strategy of a disease which still affects large parts of the world.
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Affiliation(s)
- Sandro Eridani
- Department of Biomedical Science and Technology, University of Milan, Milan, Italy
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Bhatia G, Patterson N, Pasaniuc B, Zaitlen N, Genovese G, Pollack S, Mallick S, Myers S, Tandon A, Spencer C, Palmer CD, Adeyemo AA, Akylbekova EL, Cupples LA, Divers J, Fornage M, Kao WHL, Lange L, Li M, Musani S, Mychaleckyj JC, Ogunniyi A, Papanicolaou G, Rotimi CN, Rotter JI, Ruczinski I, Salako B, Siscovick DS, Tayo BO, Yang Q, McCarroll S, Sabeti P, Lettre G, De Jager P, Hirschhorn J, Zhu X, Cooper R, Reich D, Wilson JG, Price AL. Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection. Am J Hum Genet 2011; 89:368-81. [PMID: 21907010 DOI: 10.1016/j.ajhg.2011.07.025] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 07/18/2011] [Accepted: 07/29/2011] [Indexed: 12/11/2022] Open
Abstract
The study of recent natural selection in human populations has important applications to human history and medicine. Positive natural selection drives the increase in beneficial alleles and plays a role in explaining diversity across human populations. By discovering traits subject to positive selection, we can better understand the population level response to environmental pressures including infectious disease. Our study examines unusual population differentiation between three large data sets to detect natural selection. The populations examined, African Americans, Nigerians, and Gambians, are genetically close to one another (F(ST) < 0.01 for all pairs), allowing us to detect selection even with moderate changes in allele frequency. We also develop a tree-based method to pinpoint the population in which selection occurred, incorporating information across populations. Our genome-wide significant results corroborate loci previously reported to be under selection in Africans including HBB and CD36. At the HLA locus on chromosome 6, results suggest the existence of multiple, independent targets of population-specific selective pressure. In addition, we report a genome-wide significant (p = 1.36 × 10(-11)) signal of selection in the prostate stem cell antigen (PSCA) gene. The most significantly differentiated marker in our analysis, rs2920283, is highly differentiated in both Africa and East Asia and has prior genome-wide significant associations to bladder and gastric cancers.
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Affiliation(s)
- Gaurav Bhatia
- Harvard- Massachusetts Institute of Technology (MIT) Division of Health, Science and Technology, Cambridge, USA.
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Cserti-Gazdewich CM, Mayr WR, Dzik WH. Plasmodium falciparum malaria and the immunogenetics of ABO, HLA, and CD36 (platelet glycoprotein IV). Vox Sang 2011; 100:99-111. [PMID: 21175660 DOI: 10.1111/j.1423-0410.2010.01429.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plasmodium falciparum malaria has long been a killer of the young, and has selected for polymorphisms affecting not only erythrocytes, but the immunogenetics of three histocompatibility systems: ABO, human leukocyte antigen (HLA), and CD36. The ABO system is important because the original allele, encoding glycosylation with the A sugar, acts as an adhesion ligand with infected red blood cells (iRBC), thereby promoting vasoocclusion. The prevalence of blood group O, which reduces this cytoadhesion, has increased in endemic areas. Other adaptations which could mitigate A-mediated rosetting include weaker A expression and increased soluble A secretion. The role of the HLA system in malaria has been harder to verify. Although HLA-B53 and DRB1*04 may be associated with clinical outcome, HLA studies are challenged by numerous comparisons in this most polymorphic of systems, and confounded by increasingly heterogeneous populations. Certain HLA markers may also reflect linkage artefact with other malaria-relevant polymorphisms. HLA may be less important because the parasite predominantly invades a compartment which does not express HLA. Adhesion of iRBCs is also mediated by CD36, expressed on platelets, monocytes, and microvascular endothelium. CD36 on monocytes is involved in clearing iRBC, while CD36 on platelets and the endothelium may play a role in tissue sequestration. The genetics of CD36 expression are complex, and recent research is fraught with inconsistent results. The solution may lie in examining genotype-phenotype correlations, zygosity effects on differential tissue expression, or other mechanisms altering CD36 tissue expression. Carefully designed prospective studies should bridge the gap between in-vitro observations and clinical outcomes.
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Affiliation(s)
- C M Cserti-Gazdewich
- Department of Medicine (Hematology), University Health Network/Toronto General Hospital, Toronto, ON,
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Abstract
The high mortality and widespread impact of malaria have resulted in this disease being the strongest evolutionary selective force in recent human history, and genes that confer resistance to malaria provide some of the best-known case studies of strong positive selection in modern humans. I begin by reviewing JBS Haldane's initial contribution to the potential of malaria genetic resistance in humans. Further, I discuss the population genetics aspects of many of the variants, including globin, G6PD deficiency, Duffy, ovalocytosis, ABO and human leukocyte antigen variants. Many of the variants conferring resistance to malaria are 'loss-of-function' mutants and appear to be recent polymorphisms from the last 5000-10 000 years or less. I discuss estimation of selection coefficients from case-control data and make predictions about the change for S, C and G6PD-deficiency variants. In addition, I consider the predicted joint changes when the two β-globin alleles S and C are both variable in the same population and when there is a variation for α-thalassemia and S, two unlinked, but epistatic variants. As more becomes known about genes conferring genetic resistance to malaria in humans, population genetics approaches can contribute both to investigating past selection and predicting the consequences in future generations for these variants.
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Dzik WH, Cserti-Gazdewich CM, Ssewanyana I, Delelys M, Preffer FI. When monocytes and platelets compete: The effect of platelet count on the flow cytometric measurement of monocyte CD36. CYTOMETRY PART B-CLINICAL CYTOMETRY 2010; 78:81-7. [PMID: 19902557 DOI: 10.1002/cyto.b.20504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Flow cytometric measurement of monocyte surface CD36 is relevant to several conditions including diabetes, cardiovascular disease, lipid disorders, platelet isoimmunization, and susceptibility to P falciparum malaria. CD36 is also strongly expressed on platelets where it is also known as platelet glycoprotein IV. METHODS Whole blood samples, containing identical monocyte concentrations, were adjusted to contain platelets ranging from 20,000/uL to 600,000/uL, were stained with fluorescent-labeled anti-CD36, and analyzed by flow cytometry. RESULTS CD36 median fluorescent intensity (MFI) observed on monocytes decreased as the platelet concentration in the sample increased with more than a 50% decline in monocyte MFI over the normal range of platelet values. The effect was not abolished by using larger volumes of monoclonal antibody and was observed with different clones of reagent anti-CD36. The findings were most consistent with competition by platelets for the CD36 reagent. Similar findings were observed with antibody to class I HLA. Under defined assay conditions, monocyte CD36 MFI declined with rising platelet concentration in a predictable fashion following an inverse linear relationship. CONCLUSIONS Measurement of CD36 expression on monocytes by flow cytometry in whole blood samples is affected by the sample platelet count. When comparing the monocyte CD36 expression among different individuals, our approach can be used to adjust measured monocyte CD36 expression for the effect of the platelet concentration in the sample. Competition by platelets for monoclonal reagents may occur in other settings when whole blood assays are used and when the target antigen is strongly expressed on both platelets and leukocytes.
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Affiliation(s)
- W H Dzik
- Harvard Medical School, Massachusetts General Hospital, Department of Pathology, Boston, MA 02114, USA.
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Hawkes M, Li X, Crockett M, Diassiti A, Finney C, Min-Oo G, Liles WC, Liu J, Kain KC. CD36 deficiency attenuates experimental mycobacterial infection. BMC Infect Dis 2010; 10:299. [PMID: 20950462 PMCID: PMC2965149 DOI: 10.1186/1471-2334-10-299] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 10/15/2010] [Indexed: 01/27/2023] Open
Abstract
Background Members of the CD36 scavenger receptor family have been implicated as sensors of microbial products that mediate phagocytosis and inflammation in response to a broad range of pathogens. We investigated the role of CD36 in host response to mycobacterial infection. Methods Experimental Mycobacterium bovis Bacillus Calmette-Guérin (BCG) infection in Cd36+/+ and Cd36-/- mice, and in vitro co-cultivation of M. tuberculosis, BCG and M. marinum with Cd36+/+ and Cd36-/-murine macrophages. Results Using an in vivo model of BCG infection in Cd36+/+ and Cd36-/- mice, we found that mycobacterial burden in liver and spleen is reduced (83% lower peak splenic colony forming units, p < 0.001), as well as the density of granulomas, and circulating tumor necrosis factor (TNF) levels in Cd36-/- animals. Intracellular growth of all three mycobacterial species was reduced in Cd36-/- relative to wild type Cd36+/+ macrophages in vitro. This difference was not attributable to alterations in mycobacterial uptake, macrophage viability, rate of macrophage apoptosis, production of reactive oxygen and/or nitrogen species, TNF or interleukin-10. Using an in vitro model designed to recapitulate cellular events implicated in mycobacterial infection and dissemination in vivo (i.e., phagocytosis of apoptotic macrophages containing mycobacteria), we demonstrated reduced recovery of viable mycobacteria within Cd36-/- macrophages. Conclusions Together, these data indicate that CD36 deficiency confers resistance to mycobacterial infection. This observation is best explained by reduced intracellular survival of mycobacteria in the Cd36-/- macrophage and a role for CD36 in the cellular events involved in granuloma formation that promote early bacterial expansion and dissemination.
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Affiliation(s)
- Michael Hawkes
- Institute of Medical Sciences, University of Toronto, Toronto, Canada
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Love-Gregory L, Sherva R, Schappe T, Qi JS, McCrea J, Klein S, Connelly MA, Abumrad NA. Common CD36 SNPs reduce protein expression and may contribute to a protective atherogenic profile. Hum Mol Genet 2010; 20:193-201. [PMID: 20935172 DOI: 10.1093/hmg/ddq449] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Membrane CD36 functions in the uptake of fatty acids (FAs), oxidized lipoproteins and in signal transduction after binding these ligands. In rodents, CD36 is implicated in abnormal lipid metabolism, inflammation and atherosclerosis. In humans, CD36 variants have been identified to influence free FA and high-density lipoprotein (HDL) levels and to associate with the risk of the metabolic syndrome, coronary artery disease and stroke. In this study, 15 common lipid-associated CD36 single nucleotide polymorphisms (SNPs) were evaluated for the impact on monocyte CD36 expression (protein and transcript) in 104 African Americans. In a subset of subjects, the SNPs were tested for association with monocyte surface CD36 (n=65) and platelet total CD36 (n=57). The relationship between CD36 expression and serum HDL and very low-density lipoproteins (VLDLs) levels was also examined. After a permutation-based correction for multiple tests, four SNPs (rs1761667, rs3211909, rs3211913, rs3211938) influenced monocyte CD36 protein and two (rs3211909, rs3211938) platelet CD36. The effect of the HDL-associated SNPs on CD36 expression inversely related to the impact on serum HDL and potential causality was supported by Mendelian randomization analysis. Consistent with this, monocyte CD36 protein negatively correlated with total HDL and HDL subfractions. In contrast, positive correlations were documented between monocyte CD36 and VLDL lipid, particle number and apolipoprotein B. In conclusion, CD36 variants that reduce protein expression appear to promote a protective metabolic profile. The SNPs in this study may have predictive potential on CD36 expression and disease susceptibility in African Americans. Further studies are warranted to validate and determine whether these findings are population specific.
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Affiliation(s)
- Latisha Love-Gregory
- Department of Internal Medicine, Washington University School of Medicine, St Louis, MO 63110, USA.
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50
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Rać ME, Suchy J, Kurzawski G, Safranow K, Jakubowska K, Olszewska M, Garanty-Bogacka B, Rać M, Poncyljusz W, Chlubek D. Analysis of HumanCD36Gene Sequence Alterations in the Oxidized Low-Density Lipoprotein-Binding Region Using Denaturing High-Performance Liquid Chromatography. Genet Test Mol Biomarkers 2010; 14:551-7. [DOI: 10.1089/gtmb.2010.0031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Monika Ewa Rać
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Szczecin, Poland
| | - Janina Suchy
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Grzegorz Kurzawski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Krzysztof Safranow
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Jakubowska
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Szczecin, Poland
| | - Maria Olszewska
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Szczecin, Poland
| | - Barbara Garanty-Bogacka
- Independent Laboratory of Propedeutics in Pediatrics, Pomeranian Medical University, Szczecin, Poland
| | - Michał Rać
- Department of Diagnostic Imaging and Interventional Radiology, Pomeranian Medical University, Szczecin, Poland
| | - Wojciech Poncyljusz
- Department of Interventional Radiology, Pomeranian Medical University, Szczecin, Poland
| | - Dariusz Chlubek
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Szczecin, Poland
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