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Gupta N, Waas B, Austin D, De Mazière AM, Kujala P, Stockwell AD, Li T, Yaspan BL, Klumperman J, Scales SJ. Apolipoprotein L1 (APOL1) renal risk variant-mediated podocyte cytotoxicity depends on African haplotype and surface expression. Sci Rep 2024; 14:3765. [PMID: 38355600 PMCID: PMC10866943 DOI: 10.1038/s41598-024-53298-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
Homozygous Apolipoprotein L1 (APOL1) variants G1 and G2 cause APOL1-mediated kidney disease, purportedly acting as surface cation channels in podocytes. APOL1-G0 exhibits various single nucleotide polymorphisms, most commonly haplotype E150K, M228I and R255K ("KIK"; the Reference Sequence is "EMR"), whereas variants G1 and G2 are mostly found in a single "African" haplotype background ("EIK"). Several labs reported cytotoxicity with risk variants G1 and G2 in KIK or EIK background haplotypes, but used HEK-293 cells and did not verify equal surface expression. To see if haplotype matters in a more relevant cell type, we induced APOL1-G0, G1 and G2 EIK, KIK and EMR at comparable surface levels in immortalized podocytes. G1 and G2 risk variants (but not G0) caused dose-dependent podocyte death within 48h only in their native African EIK haplotype and correlated with K+ conductance (thallium FLIPR). We ruled out differences in localization and trafficking, except for possibly greater surface clustering of cytotoxic haplotypes. APOL1 surface expression was required, since Brefeldin A rescued cytotoxicity; and cytoplasmic isoforms vB3 and vC were not cytotoxic. Thus, APOL1-EIK risk variants kill podocytes in a dose and haplotype-dependent manner (as in HEK-293 cells), whereas unlike in HEK-293 cells the KIK risk variants did not.
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Affiliation(s)
- Nidhi Gupta
- Department of Discovery Immunology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Bridget Waas
- Department of Discovery Immunology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Daniel Austin
- Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ann M De Mazière
- Section of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pekka Kujala
- Section of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Amy D Stockwell
- Department of Human Genetics, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Tianbo Li
- Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Brian L Yaspan
- Department of Human Genetics, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Judith Klumperman
- Section of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Suzie J Scales
- Department of Discovery Immunology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
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Schwantes-An TH, Robinson-Cohen C, Liu S, Zheng N, Stedman M, Wetherill L, Edenberg HJ, Vatta M, Foroud TM, Chertow GM, Moe SM. APOL1 G3 Variant Is Associated with Cardiovascular Mortality and Sudden Cardiac Death in Patients Receiving Maintenance Hemodialysis of European Ancestry. Cardiorenal Med 2022; 12:229-235. [PMID: 36310009 PMCID: PMC10445292 DOI: 10.1159/000525448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 05/27/2022] [Indexed: 01/31/2023] Open
Abstract
INTRODUCTION The G1 and G2 variants in the APOL1 gene convey high risk for the progression of chronic kidney disease in African Americans. The G3 variant in APOL1 is more common in patients of European ancestry (EA); outcomes associated with this variant have not been explored previously in EA patients receiving dialysis. METHODS DNA was collected from approximately half of the patients enrolled in the Evaluation of Cinacalcet HCl Therapy to Lower Cardiovascular Events (EVOLVE) trial and genotyped for the G3 variants. We utilized an additive genetic model to test associations of G3 with the EVOLVE adjudicated endpoints of all-cause mortality, cardiovascular mortality, sudden cardiac death (SCD), and heart failure. EA and African ancestry samples were analyzed separately. Validation was done in the Vanderbilt BioVU using ICD codes for cardiovascular events that parallel the adjudicated endpoints in EVOLVE. RESULTS In EVOLVE, G3 in EA patients was associated with the adjudicated endpoints of cardiovascular mortality and SCD. In a validation cohort from the Vanderbilt BioVU, cardiovascular events and cardiovascular mortality defined by ICD codes showed similar associations in EA participants who had been on dialysis for 2 to <5 years. DISCUSSION/CONCLUSIONS G3 in APOL1 variant was associated with cardiovascular events and cardiovascular mortality in the EA patients receiving dialysis. This suggests that variations in the APOL1 gene that differ in populations of different ancestry may contribute to cardiovascular disease.
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Affiliation(s)
- Tae-Hwi Schwantes-An
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Cassianne Robinson-Cohen
- Division of Nephrology, Department of Medicine, Vanderbilt University School of Medicine, Memphis, TN
| | - Sai Liu
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Neil Zheng
- Division of Nephrology, Department of Medicine, Vanderbilt University School of Medicine, Memphis, TN
| | - Margaret Stedman
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Howard J. Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Matteo Vatta
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Tatiana M. Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Glenn M. Chertow
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Sharon M. Moe
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States of America
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Alladagbin DJ, da Silva CGR, Silva LK, Dos-Santos WL, de Sá Oliveira GG. APOL1 genotyping via buccal mucosa cell samples to establish risk of kidney disease. BMC Nephrol 2022; 23:329. [PMID: 36217118 PMCID: PMC9549854 DOI: 10.1186/s12882-022-02954-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/18/2022] [Accepted: 09/19/2022] [Indexed: 11/26/2022] Open
Abstract
Two alleles (G1 and G2) of the apolipoprotein 1 gene (APOL1) predispose people of African descent to developing or accelerating the course of certain types of kidney disease. Population studies to determine the frequency of the G1 and G2 alleles are important to inform resource allocation by public health authorities. Traditionally, APOL1 genotyping is carried out in blood samples. However, sample collection, transport, and storage is cumbersome. Here we compared APOL1 genotyping in blood and buccal mucosa cell samples obtained from 23 individuals. Alleles G0 (wild), G1, and G2, as well as genotypes G0/G0, G0/G1, G1/G1, G0/G2, G1/G2, and G2/G2 were detected using both blood and buccal mucosa cells with 100% coincidence. Our data indicate that buccal mucosa cell samples may represent a suitable alternative to blood samples for APOL1 genotyping in the field.
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Affiliation(s)
- Dona Jeanne Alladagbin
- Fundação Oswaldo Cruz, Laboratory of Molecular and Strutural Pathology (LAPEM), Gonçalo Moniz Institute, FIOCRUZ-BA, Rua Waldemar Falcão, no. 121, CEP 40.296-710, Salvador, Brazil
| | - Carlos Gustavo Regis da Silva
- Fundação Oswaldo Cruz, Laboratory of Molecular and Strutural Pathology (LAPEM), Gonçalo Moniz Institute, FIOCRUZ-BA, Rua Waldemar Falcão, no. 121, CEP 40.296-710, Salvador, Brazil
| | - Luciano Kalabric Silva
- Fundação Oswaldo Cruz, Laboratory of Molecular and Strutural Pathology (LAPEM), Gonçalo Moniz Institute, FIOCRUZ-BA, Rua Waldemar Falcão, no. 121, CEP 40.296-710, Salvador, Brazil
| | - Washington Lc Dos-Santos
- Fundação Oswaldo Cruz, Laboratory of Molecular and Strutural Pathology (LAPEM), Gonçalo Moniz Institute, FIOCRUZ-BA, Rua Waldemar Falcão, no. 121, CEP 40.296-710, Salvador, Brazil
| | - Geraldo Gileno de Sá Oliveira
- Fundação Oswaldo Cruz, Laboratory of Molecular and Strutural Pathology (LAPEM), Gonçalo Moniz Institute, FIOCRUZ-BA, Rua Waldemar Falcão, no. 121, CEP 40.296-710, Salvador, Brazil.
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4
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Blazer A, Qian Y, Schlegel MP, Algasas H, Buyon JP, Cadwell K, Cammer M, Heffron SP, Liang FX, Mehta-Lee S, Niewold T, Rasmussen SE, Clancy RM. APOL1 variant-expressing endothelial cells exhibit autophagic dysfunction and mitochondrial stress. Front Genet 2022; 13:769936. [PMID: 36238153 PMCID: PMC9551299 DOI: 10.3389/fgene.2022.769936] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 08/16/2022] [Indexed: 12/09/2022] Open
Abstract
Polymorphisms in the Apolipoprotein L1 (APOL1) gene are common in ancestrally African populations, and associate with kidney injury and cardiovascular disease. These risk variants (RV) provide an advantage in resisting Trypanosoma brucei, the causal agent of African trypanosomiasis, and are largely absent from non-African genomes. Clinical associations between the APOL1 high risk genotype (HRG) and disease are stronger in those with comorbid infectious or immune disease. To understand the interaction between cytokine exposure and APOL1 cytotoxicity, we established human umbilical vein endothelial cell (HUVEC) cultures representing each APOL1 genotype. Untreated HUVECs were compared to IFNɣ-exposed; and APOL1 expression, mitochondrial function, lysosome integrity, and autophagic flux were measured. IFNɣ increased median APOL1 expression across all genotypes 22.1 (8.3 to 29.8) fold (p=0.02). Compared to zero risk variant-carrying HUVECs (0RV), HUVECs carrying 2 risk variant copies (2RV) showed both depressed baseline and maximum mitochondrial oxygen consumption (p<0.01), and impaired mitochondrial networking on MitoTracker assays. These cells also demonstrated a contracted lysosomal compartment, and an accumulation of autophagosomes suggesting a defect in autophagic flux. Upon blocking autophagy with non-selective lysosome inhibitor, hydroxychloroquine, autophagosome accumulation between 0RV HUVECs and untreated 2RV HUVECs was similar, implicating lysosomal dysfunction in the HRG-associated autophagy defect. Compared to 0RV and 2RV HUVECs, HUVECs carrying 1 risk variant copy (1RV) demonstrated intermediate mitochondrial respiration and autophagic flux phenotypes, which were exacerbated with IFNɣ exposure. Taken together, our data reveal that IFNɣ induces APOL1 expression, and that each additional RV associates with mitochondrial dysfunction and autophagy inhibition. IFNɣ amplifies this phenotype even in 1RV HUVECs, representing the first description of APOL1 pathobiology in variant heterozygous cell cultures.
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Affiliation(s)
- Ashira Blazer
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, United States
| | - Yingzhi Qian
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY, United States
| | - Martin Paul Schlegel
- Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Huda Algasas
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, United States
| | - Jill P. Buyon
- Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States
| | - Ken Cadwell
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Michael Cammer
- DART Microscopy Laboratory, New York University Grossman School of Medicine, New York University School of Medicine, New York, NY, United States
| | - Sean P. Heffron
- Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Feng-Xia Liang
- DART Microscopy Laboratory, New York University Grossman School of Medicine, New York University School of Medicine, New York, NY, United States
| | - Shilpi Mehta-Lee
- Department of Obstetrics and Gynecology, New York University Grossman School of Medicine, New York, NY, United States
| | - Timothy Niewold
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, United States
| | - Sara E. Rasmussen
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, United States
| | - Robert M. Clancy
- Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States
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5
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Khan A, Turchin MC, Patki A, Srinivasasainagendra V, Shang N, Nadukuru R, Jones AC, Malolepsza E, Dikilitas O, Kullo IJ, Schaid DJ, Karlson E, Ge T, Meigs JB, Smoller JW, Lange C, Crosslin DR, Jarvik GP, Bhatraju PK, Hellwege JN, Chandler P, Torvik LR, Fedotov A, Liu C, Kachulis C, Lennon N, Abul-Husn NS, Cho JH, Ionita-Laza I, Gharavi AG, Chung WK, Hripcsak G, Weng C, Nadkarni G, Irvin MR, Tiwari HK, Kenny EE, Limdi NA, Kiryluk K. Genome-wide polygenic score to predict chronic kidney disease across ancestries. Nat Med 2022; 28:1412-1420. [PMID: 35710995 PMCID: PMC9329233 DOI: 10.1038/s41591-022-01869-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/11/2022] [Indexed: 01/03/2023]
Abstract
Chronic kidney disease (CKD) is a common complex condition associated with high morbidity and mortality. Polygenic prediction could enhance CKD screening and prevention; however, this approach has not been optimized for ancestrally diverse populations. By combining APOL1 risk genotypes with genome-wide association studies (GWAS) of kidney function, we designed, optimized and validated a genome-wide polygenic score (GPS) for CKD. The new GPS was tested in 15 independent cohorts, including 3 cohorts of European ancestry (n = 97,050), 6 cohorts of African ancestry (n = 14,544), 4 cohorts of Asian ancestry (n = 8,625) and 2 admixed Latinx cohorts (n = 3,625). We demonstrated score transferability with reproducible performance across all tested cohorts. The top 2% of the GPS was associated with nearly threefold increased risk of CKD across ancestries. In African ancestry cohorts, the APOL1 risk genotype and polygenic component of the GPS had additive effects on the risk of CKD.
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Affiliation(s)
- Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Michael C Turchin
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amit Patki
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vinodh Srinivasasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Rajiv Nadukuru
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alana C Jones
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Ozan Dikilitas
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Daniel J Schaid
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth Karlson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Tian Ge
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - James B Meigs
- Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Jordan W Smoller
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Pavan K Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jacklyn N Hellwege
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paulette Chandler
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Laura Rasmussen Torvik
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alex Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - Cong Liu
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | | | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nita A Limdi
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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Cuadros-Espinoza S, Laval G, Quintana-Murci L, Patin E. The genomic signatures of natural selection in admixed human populations. Am J Hum Genet 2022; 109:710-726. [PMID: 35259336 DOI: 10.1016/j.ajhg.2022.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
Admixture has been a pervasive phenomenon in human history, extensively shaping the patterns of population genetic diversity. There is increasing evidence to suggest that admixture can also facilitate genetic adaptation to local environments, i.e., admixed populations acquire beneficial mutations from source populations, a process that we refer to as "adaptive admixture." However, the role of adaptive admixture in human evolution and the power to detect it remain poorly characterized. Here, we use extensive computer simulations to evaluate the power of several neutrality statistics to detect natural selection in the admixed population, assuming multiple admixture scenarios. We show that statistics based on admixture proportions, Fadm and LAD, show high power to detect mutations that are beneficial in the admixed population, whereas other statistics, including iHS and FST, falsely detect neutral mutations that have been selected in the source populations only. By combining Fadm and LAD into a single, powerful statistic, we scanned the genomes of 15 worldwide, admixed populations for signatures of adaptive admixture. We confirm that lactase persistence and resistance to malaria have been under adaptive admixture in West Africans and in Malagasy, North Africans, and South Asians, respectively. Our approach also uncovers other cases of adaptive admixture, including APOL1 in Fulani nomads and PKN2 in East Indonesians, involved in resistance to infection and metabolism, respectively. Collectively, our study provides evidence that adaptive admixture has occurred in human populations whose genetic history is characterized by periods of isolation and spatial expansions resulting in increased gene flow.
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DeGiorgio M, Szpiech ZA. A spatially aware likelihood test to detect sweeps from haplotype distributions. PLoS Genet 2022; 18:e1010134. [PMID: 35404934 PMCID: PMC9022890 DOI: 10.1371/journal.pgen.1010134] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 04/21/2022] [Accepted: 03/04/2022] [Indexed: 01/13/2023] Open
Abstract
The inference of positive selection in genomes is a problem of great interest in evolutionary genomics. By identifying putative regions of the genome that contain adaptive mutations, we are able to learn about the biology of organisms and their evolutionary history. Here we introduce a composite likelihood method that identifies recently completed or ongoing positive selection by searching for extreme distortions in the spatial distribution of the haplotype frequency spectrum along the genome relative to the genome-wide expectation taken as neutrality. Furthermore, the method simultaneously infers two parameters of the sweep: the number of sweeping haplotypes and the "width" of the sweep, which is related to the strength and timing of selection. We demonstrate that this method outperforms the leading haplotype-based selection statistics, though strong signals in low-recombination regions merit extra scrutiny. As a positive control, we apply it to two well-studied human populations from the 1000 Genomes Project and examine haplotype frequency spectrum patterns at the LCT and MHC loci. We also apply it to a data set of brown rats sampled in NYC and identify genes related to olfactory perception. To facilitate use of this method, we have implemented it in user-friendly open source software.
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Affiliation(s)
- Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Zachary A. Szpiech
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
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8
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Hung RK, Binns-Roemer E, Booth JW, Hilton R, Harber M, Santana-Suarez B, Campbell L, Fox J, Ustianowski A, Cosgrove C, Burns JE, Clarke A, Price DA, Chadwick D, Onyango D, Hamzah L, Bramham K, Sabin CA, Winkler CA, Post FA. Genetic Variants of APOL1 Are Major Determinants of Kidney Failure in People of African Ancestry With HIV. Kidney Int Rep 2022; 7:786-796. [PMID: 35497797 PMCID: PMC9039486 DOI: 10.1016/j.ekir.2022.01.1054] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 12/11/2022] Open
Abstract
Introduction Variants of the APOL1 gene are associated with chronic kidney disease (CKD) in people of African ancestry, although evidence for their impact in people with HIV are sparse. Methods We conducted a cross-sectional study investigating the association between APOL1 renal risk alleles and kidney disease in people of African ancestry with HIV in the UK. The primary outcome was end-stage kidney disease (ESKD; estimated glomerular filtration rate [eGFR] of <15 ml/min per 1.73 m2, chronic dialysis, or having received a kidney transplant). The secondary outcomes included renal impairment (eGFR <60 ml/min per 1.73 m2), albuminuria (albumin-to-creatinine ratio [ACR] >30 mg/mmol), and biopsy-proven HIV-associated nephropathy (HIVAN). Multivariable logistic regression was used to estimate the associations between APOL1 high-risk genotypes (G1/G1, G1/G2, G2/G2) and kidney disease outcomes. Results A total of 2864 participants (mean age 48.1 [SD 10.3], 57.3% female) were genotyped, of whom, 354 (12.4%) had APOL1 high-risk genotypes, and 99 (3.5%) had ESKD. After adjusting for demographic, HIV, and renal risk factors, individuals with APOL1 high-risk genotypes were at increased odds of ESKD (odds ratio [OR] 10.58, 95% CI 6.22-17.99), renal impairment (OR 5.50, 95% CI 3.81-7.95), albuminuria (OR 3.34, 95% CI 2.00-5.56), and HIVAN (OR 30.16, 95% CI 12.48-72.88). An estimated 49% of ESKD was attributable to APOL1 high-risk genotypes. Conclusion APOL1 high-risk genotypes were strongly associated with kidney disease in people of African ancestry with HIV and accounted for approximately half of ESKD cases in this cohort.
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Affiliation(s)
| | - Elizabeth Binns-Roemer
- Basic Research Laboratory, Frederick National Laboratory for Cancer Research and the National Cancer Institute, Frederick, Maryland, USA
| | | | - Rachel Hilton
- Guy’s and St Thomas’ NHS Foundation Trust, London, UK
| | - Mark Harber
- Royal Free London Hospital NHS Foundation Trust, London, UK
| | | | | | - Julie Fox
- King’s College London, London, UK
- Guy’s and St Thomas’ NHS Foundation Trust, London, UK
| | | | | | - James E. Burns
- University College London, London, UK
- Central and North West London NHS Foundation Trust, London, UK
| | - Amanda Clarke
- Brighton and Sussex University Hospital NHS Trust, Brighton, UK
- Brighton and Sussex Medical School Department of Infectious Disease, Brighton, UK
| | | | - David Chadwick
- South Tees Hospitals NHS Foundation Trust, Middlesbrough, UK
| | | | - Lisa Hamzah
- St George’s Hospital NHS Foundation Trust, London, UK
| | - Kate Bramham
- King’s College London, London, UK
- King’s College Hospital NHS Foundation Trust, London, UK
| | | | - Cheryl A. Winkler
- Basic Research Laboratory, Frederick National Laboratory for Cancer Research and the National Cancer Institute, Frederick, Maryland, USA
| | - Frank A. Post
- King’s College London, London, UK
- King’s College Hospital NHS Foundation Trust, London, UK
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9
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Ma J, Zheng Q, Zhang H, Wen Y, Ye W, Ye W, Zheng K, Gao R, Chen L, Li T, Li X, Yu Y, Lyu W. The spectrum of kidney biopsy findings in Chinese HIV-infected patients. HIV Med 2022; 23 Suppl 1:23-31. [PMID: 35293105 DOI: 10.1111/hiv.13246] [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: 11/27/2022]
Abstract
OBJECTIVES HIV-associated kidney disease is common but data on the pathology spectrum of kidney biopsy in China is lacking. This study aimed to illustrate the clinical presentation, laboratory findings and pathological spectrum of different subtypes of HIV-associated kidney disease in China. METHODS Eighteen HIV patients with renal biopsy indications at the Peking Union Medical College Hospital from January 2002 to October 2021 were retrospectively enrolled. All had CD4 counts and HIV viral load measurements. Renal biopsies were examined with light microscopy, immunofluorescence, and electron microscopy. Shapiro-Wilk test was used to test whether the data was normally distributed. The data is presented as medians (interquartile range), number (%), or means (±SD) according to their distribution. RESULTS Seventeen patients had glomerular disease, and one patient had interstitial nephritis. Membranous nephropathy was present in eight patients (47.1%), and IgA nephropathy in four patients (23.5%). The difference in urine protein and serum albumin before and after treatment was statistically significant and no deaths or dialysis were observed to the end of follow-up. CONCLUSION This study found that classic HIV-associated nephropathy (HIVAN) was uncommon in Chinese HIV patients. HIV immune complex kidney (HIVICK) disease, such as membranous or IgA nephropathy, was more common, and associated with better prognosis. Antiretroviral therapy, ACE inhibitors, and angiotensin II receptor blockers were effective in decreasing proteinuria and preserving renal function. The use of corticosteroids and immunosuppressive agents seems safe. However, the nephrotoxic effect of antiretroviral agents and other medications should be carefully monitored.
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Affiliation(s)
- Jie Ma
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qingyue Zheng
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Eight-year MD Program, Peking Union Medical College, Beijing, China
| | - Hanlin Zhang
- Eight-year MD Program, Peking Union Medical College, Beijing, China.,Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yubing Wen
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenling Ye
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Ye
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ke Zheng
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruitong Gao
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Limeng Chen
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Taisheng Li
- Department of Infectious Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xuemei Li
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Yu
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Lyu
- Department of Infectious Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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10
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Saitou M, Masuda N, Gokcumen O. Similarity-Based Analysis of Allele Frequency Distribution among Multiple Populations Identifies Adaptive Genomic Structural Variants. Mol Biol Evol 2022; 39:msab313. [PMID: 34718708 PMCID: PMC8896759 DOI: 10.1093/molbev/msab313] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Structural variants have a considerable impact on human genomic diversity. However, their evolutionary history remains mostly unexplored. Here, we developed a new method to identify potentially adaptive structural variants based on a similarity-based analysis that incorporates genotype frequency data from 26 populations simultaneously. Using this method, we analyzed 57,629 structural variants and identified 576 structural variants that show unusual population differentiation. Of these putatively adaptive structural variants, we further showed that 24 variants are multiallelic and overlap with coding sequences, and 20 variants are significantly associated with GWAS traits. Closer inspection of the haplotypic variation associated with these putatively adaptive and functional structural variants reveals deviations from neutral expectations due to: 1) population differentiation of rapidly evolving multiallelic variants, 2) incomplete sweeps, and 3) recent population-specific negative selection. Overall, our study provides new methodological insights, documents hundreds of putatively adaptive variants, and introduces evolutionary models that may better explain the complex evolution of structural variants.
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Affiliation(s)
- Marie Saitou
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Naoki Masuda
- Department of Mathematics, University at Buffalo, State University of New York, Buffalo, NY, USA
- Computational and Data-Enabled Science and Engineering Program, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
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11
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Daneshpajouhnejad P, Kopp JB, Winkler CA, Rosenberg AZ. The evolving story of apolipoprotein L1 nephropathy: the end of the beginning. Nat Rev Nephrol 2022; 18:307-320. [PMID: 35217848 PMCID: PMC8877744 DOI: 10.1038/s41581-022-00538-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2022] [Indexed: 01/13/2023]
Abstract
Genetic coding variants in APOL1, which encodes apolipoprotein L1 (APOL1), were identified in 2010 and are relatively common among individuals of sub-Saharan African ancestry. Approximately 13% of African Americans carry two APOL1 risk alleles. These variants, termed G1 and G2, are a frequent cause of kidney disease — termed APOL1 nephropathy — that typically manifests as focal segmental glomerulosclerosis and the clinical syndrome of hypertension and arterionephrosclerosis. Cell culture studies suggest that APOL1 variants cause cell dysfunction through several processes, including alterations in cation channel activity, inflammasome activation, increased endoplasmic reticulum stress, activation of protein kinase R, mitochondrial dysfunction and disruption of APOL1 ubiquitinylation. Risk of APOL1 nephropathy is mostly confined to individuals with two APOL1 risk variants. However, only a minority of individuals with two APOL1 risk alleles develop kidney disease, suggesting the need for a ‘second hit’. The best recognized factor responsible for this ‘second hit’ is a chronic viral infection, particularly HIV-1, resulting in interferon-mediated activation of the APOL1 promoter, although most individuals with APOL1 nephropathy do not have an obvious cofactor. Current therapies for APOL1 nephropathies are not adequate to halt progression of chronic kidney disease, and new targeted molecular therapies are in clinical trials. This Review summarizes current understanding of the role of APOL1 variants in kidney disease. The authors discuss the genetics, protein structure and biological functions of APOL1 variants and provide an overview of promising therapeutic strategies. In contrast to other APOL family members, which are primarily intracellular, APOL1 contains a unique secretory signal peptide, resulting in its secretion into plasma. APOL1 renal risk alleles provide protection from African human trypanosomiasis but are a risk factor for progressive kidney disease in those carrying two risk alleles. APOL1 risk allele frequency is ~35% in the African American population in the United States, with ~13% of individuals having two risk alleles; the highest allele frequencies are found in West African populations and their descendants. Cell and mouse models implicate endolysosomal and mitochondrial dysfunction, altered ion channel activity, altered autophagy, and activation of protein kinase R in the pathogenesis of APOL1-associated kidney disease; however, the relevance of these injury pathways to human disease has not been resolved. APOL1 kidney disease tends to be progressive, and current standard therapies are generally ineffective; targeted therapeutic strategies hold the most promise.
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Affiliation(s)
- Parnaz Daneshpajouhnejad
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pathology, University of Pennsylvania Hospital, Philadelphia, PA, USA
| | | | - Cheryl A Winkler
- Basic Research Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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12
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Zhang C, Hansen MEB, Tishkoff SA. Advances in integrative African genomics. Trends Genet 2022; 38:152-168. [PMID: 34740451 PMCID: PMC8752515 DOI: 10.1016/j.tig.2021.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022]
Abstract
There has been a rapid increase in human genome sequencing in the past two decades, resulting in the identification of millions of previously unknown genetic variants. However, African populations are under-represented in sequencing efforts. Additional sequencing from diverse African populations and the construction of African-specific reference genomes is needed to better characterize the full spectrum of variation in humans. However, sequencing alone is insufficient to address the molecular and cellular mechanisms underlying variable phenotypes and disease risks. Determining functional consequences of genetic variation using multi-omics approaches is a fundamental post-genomic challenge. We discuss approaches to close the knowledge gaps about African genomic diversity and review advances in African integrative genomic studies and their implications for precision medicine.
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Affiliation(s)
- Chao Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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13
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Shahian DM, Badhwar V, O'Brien SM, Habib RH, Han J, McDonald DE, Antman MS, Higgins RSD, Preventza O, Estrera AL, Calhoon JH, Grondin SC, Cooke DT. Social Risk Factors in Society of Thoracic Surgeons Risk Models Part 1: Concepts, Indicator Variables, and Controversies. Ann Thorac Surg 2022; 113:1703-1717. [PMID: 34998732 DOI: 10.1016/j.athoracsur.2021.11.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/01/2022]
Affiliation(s)
- David M Shahian
- Division of Cardiac Surgery, Department of Surgery, and Center for Quality and Safety, Massachusetts General Hospital and Harvard Medical School, Boston, MA.
| | - Vinay Badhwar
- Department of Cardiovascular and Thoracic Surgery, West Virginia University, Morgantown WV
| | | | | | - Jane Han
- Society of Thoracic Surgeons, Chicago, IL
| | | | | | - Robert S D Higgins
- Johns Hopkins University School of Medicine and Johns Hopkins Hospital, Baltimore, MD
| | - Ourania Preventza
- Baylor College of Medicine, Texas Heart Institute, Baylor St. Luke's Medical Center, Houston, TX
| | - Anthony L Estrera
- McGovern Medical School at UTHealth; Memorial Hermann Heart and Vascular Institute; Houston, TX
| | - John H Calhoon
- Department of Cardiothoracic Surgery, University of Texas Health Science Center at San Antonio
| | - Sean C Grondin
- Cumming School of Medicine, University of Calgary, and Foothills Medical Centre, Calgary, Alberta, Canada
| | - David T Cooke
- Division of General Thoracic Surgery, UC Davis Health, Sacramento, CA
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14
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Kun Á. Is there still evolution in the human population? Biol Futur 2022; 73:359-374. [PMID: 36592324 PMCID: PMC9806833 DOI: 10.1007/s42977-022-00146-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/08/2022] [Indexed: 01/03/2023]
Abstract
It is often claimed that humanity has stopped evolving because modern medicine erased all selection on survival. Even if that would be true, and it is not, there would be other mechanisms of evolution which could still led to changes in allelic frequencies. Here I show, by applying basic evolutionary genetics knowledge, that we expect humanity to evolve. The results from genome sequencing projects have repeatedly affirmed that there are still recent signs of selection in our genomes. I give some examples of such adaptation. Then I briefly discuss what our evolutionary future has in store for us.
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Affiliation(s)
- Ádám Kun
- grid.5591.80000 0001 2294 6276Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös University, Budapest, Hungary ,Parmenides Center for the Conceptual Foundations of Science, Pöcking, Germany ,grid.481817.3Institute of Evolution, Centre for Ecological Research, Budapest, Hungary ,grid.5018.c0000 0001 2149 4407MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Budapest, Hungary ,grid.5018.c0000 0001 2149 4407MTA-ELTE-MTM Ecology Research Group, Budapest, Hungary
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15
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Lo YH, Cheng HC, Hsiung CN, Yang SL, Wang HY, Peng CW, Chen CY, Lin KP, Kang ML, Chen CH, Chu HW, Lin CF, Lee MH, Liu Q, Satta Y, Lin CJ, Lin M, Chaw SM, Loo JH, Shen CY, Ko WY. Detecting Genetic Ancestry and Adaptation in the Taiwanese Han People. Mol Biol Evol 2021; 38:4149-4165. [PMID: 33170928 PMCID: PMC8476137 DOI: 10.1093/molbev/msaa276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Taiwanese people are composed of diverse indigenous populations and the Taiwanese Han. About 95% of the Taiwanese identify themselves as Taiwanese Han, but this may not be a homogeneous population because they migrated to the island from various regions of continental East Asia over a period of 400 years. Little is known about the underlying patterns of genetic ancestry, population admixture, and evolutionary adaptation in the Taiwanese Han people. Here, we analyzed the whole-genome single-nucleotide polymorphism genotyping data from 14,401 individuals of Taiwanese Han collected by the Taiwan Biobank and the whole-genome sequencing data for a subset of 772 people. We detected four major genetic ancestries with distinct geographic distributions (i.e., Northern, Southeastern, Japonic, and Island Southeast Asian ancestries) and signatures of population mixture contributing to the genomes of Taiwanese Han. We further scanned for signatures of positive natural selection that caused unusually long-range haplotypes and elevations of hitchhiked variants. As a result, we identified 16 candidate loci in which selection signals can be unambiguously localized at five single genes: CTNNA2, LRP1B, CSNK1G3, ASTN2, and NEO1. Statistical associations were examined in 16 metabolic-related traits to further elucidate the functional effects of each candidate gene. All five genes appear to have pleiotropic connections to various types of disease susceptibility and significant associations with at least one metabolic-related trait. Together, our results provide critical insights for understanding the evolutionary history and adaption of the Taiwanese Han population.
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Affiliation(s)
- Yun-Hua Lo
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Hsueh-Chien Cheng
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Ni Hsiung
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Show-Ling Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Han-Yu Wang
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Wei Peng
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chun-Yu Chen
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Kung-Ping Lin
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Mei-Ling Kang
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | | | - Mei-Hsuan Lee
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Quintin Liu
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Cheng-Jui Lin
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Marie Lin
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Jun-Hun Loo
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Wen-Ya Ko
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
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16
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Olabisi OA, Freedman BI. APOL1-associated kidney disease in northern Nigerians with treated HIV infection. Kidney Int 2021; 100:19-21. [PMID: 34154709 PMCID: PMC9827565 DOI: 10.1016/j.kint.2021.04.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/05/2021] [Accepted: 04/14/2021] [Indexed: 01/11/2023]
Abstract
Apolipoprotein L1 (APOL1) high-risk genotypes strongly associate with HIV-associated nephropathy, and antiretroviral therapy reduces the incidence of HIV-associated nephropathy and progression to end-stage kidney disease. Wudil et al. report cross-sectional APOL1 associations with proteinuria and estimated glomerular filtration rate in a northern Nigerian sample with HIV infection on antiretroviral therapy. Multiple ethnic groups with different APOL1 risk variant frequencies were included. Overall, APOL1 was associated with proteinuric chronic kidney disease; however, relationships with underlying causes of nephropathy and progression rates require further study.
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Affiliation(s)
- Opeyemi A Olabisi
- Department of Medicine, Division of Nephrology and Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.
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17
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African genetic diversity and adaptation inform a precision medicine agenda. Nat Rev Genet 2021; 22:284-306. [PMID: 33432191 DOI: 10.1038/s41576-020-00306-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2020] [Indexed: 01/29/2023]
Abstract
The deep evolutionary history of African populations, since the emergence of modern humans more than 300,000 years ago, has resulted in high genetic diversity and considerable population structure. Selected genetic variants have increased in frequency due to environmental adaptation, but recent exposures to novel pathogens and changes in lifestyle render some of them with properties leading to present health liabilities. The unique discoverability potential from African genomic studies promises invaluable contributions to understanding the genomic and molecular basis of health and disease. Globally, African populations are understudied, and precision medicine approaches are largely based on data from European and Asian-ancestry populations, which limits the transferability of findings to the continent of Africa. Africa needs innovative precision medicine solutions based on African data that use knowledge and implementation strategies aligned to its climatic, cultural, economic and genomic diversity.
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18
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Freedman BI, Kopp JB, Sampson MG, Susztak K. APOL1 at 10 years: progress and next steps. Kidney Int 2021; 99:1296-1302. [PMID: 33794228 DOI: 10.1016/j.kint.2021.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/17/2021] [Accepted: 02/25/2021] [Indexed: 12/29/2022]
Abstract
APOL1 kidney risk variants (RVs) were identified in 2010 as major drivers of glomerular, tubulointerstitial, and renal microvascular disease in individuals with sub-Saharan African ancestry. In December 2020, the "APOL1 at Ten" conference summarized the first decade of progress and discussed controversies and uncertainties that remain to be addressed. Topics included trypanosome infection and its role in the evolution of APOL1 kidney RVs, clinical phenotypes in APOL1-associated nephropathy, relationships between APOL1 RVs and background haplotypes on cell injury and molecular mechanisms initiating disease, the role of clinical APOL1 genotyping, and development of novel therapies for kidney disease. Future goals were defined, including improved characterization of various APOL1 RV phenotypes in patients and experimental preclinical models; further dissection of APOL1-mediated pathways to cellular injury and dysfunction in kidney (and other) cells; clarification of gene-gene and gene-environment interactions; and evaluation of the role for existing and novel therapies.
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Affiliation(s)
- Barry I Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Matthew G Sampson
- Division of Pediatric Nephrology, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Broad Institute, Cambridge, Massachusetts, USA
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
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19
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An P, Sezgin E, Kirk GD, Duggal P, Binns-Roemer E, Nelson G, Limou S, Van Natta ML, Jabs DA, Estrella M, Kopp JB, Winkler CA. APOL1 variant alleles associate with reduced risk for opportunistic infections in HIV infection. Commun Biol 2021; 4:284. [PMID: 33674766 PMCID: PMC7977062 DOI: 10.1038/s42003-021-01812-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/08/2021] [Indexed: 11/10/2022] Open
Abstract
Apolipoprotein L1 (APOL1), an innate immune factor against African trypanosoma brucei, inhibits HIV-1 in vitro. The impact of APOL1 G1-G2 variants on HIV-1-associated opportunistic infections (OIs) is unknown. Here, we report findings from a metaanalysis of four HIV/AIDS prospective cohorts (ALIVE, LSOCA, MACS, and WIHS) including 2066 African American participants. Using a global test combining all four cohorts, carriage of two APOL1 variant alleles is associated with a 50% reduction in odds of OI (combined OR 0.50, 95% CI 0.33-0.76). Subgroup analysis of OI etiological categories (viral, parasitic, fungal and Mycobacterial) suggests the possibility of specific protection from fungal infections (OR 0.54. 95% CI 0.32-0.93; PBonferroni corrected = 0.08). We observe an association of APOL1 variant alleles with host protection against OI in HIV-positive individuals. The study suggests a broader role of APOL1 variant alleles in innate immunity in vivo.
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Affiliation(s)
- Ping An
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Efe Sezgin
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Department of Epidemiology, the Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Laboratory of Nutrigenomics and Epidemiology, Izmir Institute of Technology, Izmir, Turkey
| | - Gregory D Kirk
- Department of Epidemiology, the Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Priya Duggal
- Department of Epidemiology, the Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Elizabeth Binns-Roemer
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - George Nelson
- Center for Cancer Research Informatics Core, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sophie Limou
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- CRTI UMR1064, Inserm, Université de Nantes & ITUN, CHU Nantes, Nantes, France
- Ecole Centrale de Nantes, Nantes, France
| | - Mark L Van Natta
- Department of Epidemiology, the Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Douglas A Jabs
- Department of Epidemiology, the Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Ophthalmology, the Wilmer Eye Institute, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michelle Estrella
- Kidney Health Research Collaborative, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- San Francisco VA Health Care System, San Francisco, CA, USA
| | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - Cheryl A Winkler
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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20
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Blazer A, Dey ID, Nwaukoni J, Reynolds M, Ankrah F, Algasas H, Ahmed T, Divers J. Apolipoprotein L1 risk genotypes in Ghanaian patients with systemic lupus erythematosus: a prospective cohort study. Lupus Sci Med 2021; 8:8/1/e000460. [PMID: 33461980 PMCID: PMC7816898 DOI: 10.1136/lupus-2020-000460] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/13/2020] [Accepted: 12/23/2020] [Indexed: 01/13/2023]
Abstract
Objective Two apolipoprotein L1 (APOL1) risk variants (RV) are enriched in sub-Saharan African populations due to conferred resistance to Trypanosoma brucei. These variants associate with adverse renal outcomes by multiple causes including SLE. Despite emerging reports that SLE is common in Ghana, where APOL1 variant allelic frequencies are high, the regional contribution to SLE outcomes has not been described. Accordingly, this prospective longitudinal cohort study tested the associations between APOL1 high-risk genotypes and kidney outcomes, organ damage accrual and death in 100 Ghanaian patients with SLE. Methods This was a prospective cohort study of 100 SLE outpatients who sought care at Korle bu Teaching Hospital in Accra, Ghana. Adult patients who met 4 American College of Rheumatology criteria for SLE were genotyped for APOL1 and followed longitudinally for SLE activity as measured by the Safety of Estrogens in Lupus National Assessment-Systemic Lupus Erythematosus Disease Activity Index (SELENA-SLEDAI) hybrid and organ injury as measured by the Systemic Lupus International Collaborating Clinics Damage Index (SDI) at baseline and every 6 months for 1 year. Outcomes of interest were kidney function, SDI and case fatality. Results Assuming a recessive inheritance, the APOL1 high-risk genotype (2RV) associated with end-stage renal disease (ESRD) at an OR of 14 (p=0.008). These patients accrued more SDI points particularly in renal and neurological domains. The SDI was 81.3% higher in 2RV patients compared with 0RV or 1RV patients despite no difference in SLE activity (p=0.01). After a 12-month period of observation, 3/12 (25%) of the 2RV patients died compared with 2/88 (2.3%) of the 0RV or 1RV carriers (OR=13.6, p=0.01). Deaths were due to end-stage kidney disease and heart failure. Conclusion APOL1 RVs were heritable risk factors for morbidity and mortality in this Ghanaian SLE cohort. Despite no appreciable differences in SLE activity, APOL1 high-risk patients exhibited progressive renal disease, organ damage accrual and a 13-fold higher case fatality.
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Affiliation(s)
- Ashira Blazer
- Department of Medicine, Division of Rheumatology, NYU Langone Health, New York, New York, USA
| | - Ida Dzifa Dey
- Department of Medicine, Division of Rheumatology, University of Ghana, Legon, Greater Accra, Ghana
| | - Janet Nwaukoni
- Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania, USA
| | | | - Festus Ankrah
- Internal Medicine, University of Ghana, Legon, Greater Accra, Ghana
| | | | - Tasneem Ahmed
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Jasmin Divers
- Department of Biostatistics, Division of Health Sciences Research, NYU Winthrop Hospital, Mineola, New York, USA
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21
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Musa HH, Musa TH, Musa IH, Musa IH, Ranciaro A, Campbell MC. Addressing Africa's pandemic puzzle: Perspectives on COVID-19 transmission and mortality in sub-Saharan Africa. Int J Infect Dis 2021; 102:483-488. [PMID: 33010461 PMCID: PMC7526606 DOI: 10.1016/j.ijid.2020.09.1456] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 09/21/2020] [Indexed: 12/12/2022] Open
Abstract
To date, SARS-CoV-2 (the virus that causes COVID-19) has spread to almost every region of the world, infecting millions and resulting in the deaths of hundreds of thousands of people. Although it was predicted that Africa would suffer a massive loss of life due to this pandemic, the number of COVID-19 cases has been relatively low across the continent. Researchers have speculated that several factors may be responsible for this outcome in Africa, including the extensive experience that countries have with infectious diseases and the young median age of their populations. However, it is still important for African countries to adopt aggressive and bold approaches against COVID-19, in case the nature of the pandemic changes. This short review will summarize the status of the outbreak in Africa and propose possible reasons for current trends, as well as discuss interventions aimed at preventing a rapid increase in the number of COVID-19 cases in the future.
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Affiliation(s)
- Hassan H Musa
- Biomedical Research Institute, Darfur College, Nyala, Sudan; Faculty of Medical Laboratory Sciences, University of Khartoum, Sudan
| | - Taha H Musa
- Biomedical Research Institute, Darfur College, Nyala, Sudan; School of Medicine, Darfur College, Nyala, Sudan
| | | | - Ibrahim H Musa
- Biomedical Research Institute, Darfur College, Nyala, Sudan
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
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22
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23
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Abstract
Genetic variants in the APOL1 gene, found only in individuals of recent African ancestry, greatly increase risk of multiple types of kidney disease. These APOL1 kidney risk alleles are a rare example of genetic variants that are common but also have a powerful effect on disease susceptibility. These alleles rose to high frequency in sub-Saharan Africa because they conferred protection against pathogenic trypanosomes that cause African sleeping sickness. We consider the genetic evidence supporting the association between APOL1 and kidney disease across the range of clinical phenotypes in the APOL1 nephropathy spectrum. We then explore the origins of the APOL1 risk variants and evolutionary struggle between humans and trypanosomes at both the molecular and population genetic level. Finally, we survey the rapidly growing literature investigating APOL1 biology as elucidated from experiments in cell-based systems, cell-free systems, mouse and lower organism models of disease, and through illuminating natural experiments in humans.
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Affiliation(s)
- David J Friedman
- Division of Nephrology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA; ,
| | - Martin R Pollak
- Division of Nephrology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA; ,
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24
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Bien SA, Wojcik GL, Hodonsky CJ, Gignoux CR, Cheng I, Matise TC, Peters U, Kenny EE, North KE. The Future of Genomic Studies Must Be Globally Representative: Perspectives from PAGE. Annu Rev Genomics Hum Genet 2019; 20:181-200. [PMID: 30978304 DOI: 10.1146/annurev-genom-091416-035517] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The past decade has seen a technological revolution in human genetics that has empowered population-level investigations into genetic associations with phenotypes. Although these discoveries rely on genetic variation across individuals, association studies have overwhelmingly been performed in populations of European descent. In this review, we describe limitations faced by single-population studies and provide an overview of strategies to improve global representation in existing data sets and future human genomics research via diversity-focused, multiethnic studies. We highlight the successes of individual studies and meta-analysis consortia that have provided unique knowledge. Additionally, we outline the approach taken by the Population Architecture Using Genomics and Epidemiology (PAGE) study to develop best practices for performing genetic epidemiology in multiethnic contexts. Finally, we discuss how limiting investigations to single populations impairs findings in the clinical domain for both rare-variant identification and genetic risk prediction.
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Affiliation(s)
- Stephanie A Bien
- Department of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; ,
| | - Genevieve L Wojcik
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Chani J Hodonsky
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; ,
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado 80045, USA;
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94158, USA;
| | - Tara C Matise
- Department of Genetics, Rutgers University, New Brunswick, New Jersey 08554, USA;
| | - Ulrike Peters
- Department of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; ,
| | - Eimear E Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; ,
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25
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An P, Kirk GD, Limou S, Binns-Roemer E, Kopp JB, Winkler CA. Impact of APOL1 Genetic Variants on HIV-1 Infection and Disease Progression. Front Immunol 2019; 10:53. [PMID: 30733721 PMCID: PMC6353846 DOI: 10.3389/fimmu.2019.00053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/09/2019] [Indexed: 01/03/2023] Open
Abstract
Apolipoprotein L1 (APOL1) has broad innate immune functions and has been shown to restrict HIV replication in vitro by multiple mechanisms. Coding variants in APOL1 are strongly associated with HIV-associated nephropathy (HIVAN) in persons with untreated HIV infection; however, the mechanism by which APOL1 variant protein potentiates renal injury in the presence of high viral load is not resolved. Little is known about the association of APOL1 genotypes with HIV viral load, HIV acquisition, or progression to AIDS. We assessed the role of APOL1 coding variants on HIV-1 acquisition using the conditional logistic regression test, on viral load using the t-test or ANOVA, and on progression to AIDS using Cox proportional hazards models among African Americans enrolled in the ALIVE HIV natural history cohort (n = 775). APOL1 variants were not associated with susceptibility to HIV-1 acquisition by comparing genotype frequencies between HIV-1 positive and exposed or at-risk HIV-1 uninfected groups (recessive model, 12.8 vs. 12.5%, respectively; OR 1.02, 95% CI 0.62-1.70). Similar null results were observed for dominant and additive models. APOL1 variants were not associated with HIV-1 viral load or with risk of progression to AIDS [Relative hazards (RH) 1.33, 95% CI 0.30-5.89 and 0.96, 95% CI 0.49-1.88, for recessive and additive models, respectively]. In summary, we found no evidence that APOL1 variants are associated with host susceptibility to HIV-1 acquisition, set-point HIV-1 viral load or time to incident AIDS. These results suggest that APOL1 variants are unlikely to influence HIV infection or progression among individuals of African ancestry.
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Affiliation(s)
- Ping An
- Molecular Genetic Epidemiology Section, Basic Science Program, Basic Research Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Gregory D Kirk
- Departments of Epidemiology and Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Sophie Limou
- Molecular Genetic Epidemiology Section, Basic Science Program, Basic Research Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States.,CRTI UMR1064, Inserm, Université de Nantes & ITUN, CHU Nantes, Nantes, France.,Ecole Centrale de Nantes, Nantes, France
| | - Elizabeth Binns-Roemer
- Molecular Genetic Epidemiology Section, Basic Science Program, Basic Research Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, United States
| | - Cheryl A Winkler
- Molecular Genetic Epidemiology Section, Basic Science Program, Basic Research Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
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26
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Alladagbin DJ, Fernandes PN, Tavares MB, Brito JT, Oliveira GGS, Silva LK, Khouri NA, Oliveira MB, Amorim T, Matos CM, Ribeiro GS, Lopes AA, Gonçalves MS, dos-Santos WLC. The sickle cell trait and end stage renal disease in Salvador, Brazil. PLoS One 2018; 13:e0209036. [PMID: 30557319 PMCID: PMC6296547 DOI: 10.1371/journal.pone.0209036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/27/2018] [Indexed: 12/12/2022] Open
Abstract
Background Carriers of the sickle cell trait (HbAS) usually remain asymptomatic. However, under conditions of low tissue oxygenation, red blood cell sickling and vascular obstruction may develop. Chronic kidney disease (CKD) can arise from conditions promoting low-oxygen in kidney tissue, which may be aggravated by the presence of the sickle cell trait. In addition, CKD can arise from other genetic traits. Aim To compare the frequency of HbAS among hemodialysis patients and the general newborn population of Salvador (Bahia-Brazil), as well as to investigate the frequencies of apolipoprotein L1 risk variants in patients undergoing hemodialysis. Methods A cross-sectional study included 306 patients with ESRD (End Stage Renal Disease) on hemodialysis for no more than three years. Hemoglobin profiles were characterized by high-performance liquid chromatography. To estimate the sickle cell trait frequency in the general population of Salvador, we analyzed data collected by a local neonatal screening program between 2011 and 2016. To exclude the potential contributing effect of the apolipoprotein L1 (APOL1) gene variants, we performed genotyping by PCR and DNA sequencing of 45 patients. Results The frequency of HbAS was significantly higher in hemodialysis patients (9.8%) than in the general population (4.6%): Odds Ratio = 2.32 (95% CI = 1.59–3.38). No differences in demographic, clinical or laboratory data were found among patients with or without the sickle cell trait. The frequency of patients with none, one or two APOL1 risk haplotypes (G1 and G2) for CKD were 80%, 18% and 2%, respectively. Conclusions The frequency of the sickle cell trait is higher in patients with ESRD on hemodialysis compared to the general population. APOL1 haplotypes do not seem to be the determinant of ESRD in these patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Tatiana Amorim
- Serviço de Referência em Triagem Neonatal—SRTN, Salvador, Brazil
| | | | - Guilherme S. Ribeiro
- Instituto Gonçalo Moniz-FIOCRUZ-Bahia, Salvador, Brazil
- Universidade da Bahia, Salvador, Brazil
| | | | - Marilda S. Gonçalves
- Instituto Gonçalo Moniz-FIOCRUZ-Bahia, Salvador, Brazil
- Universidade da Bahia, Salvador, Brazil
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27
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Krause A, Seymour H, Ramsay M. Common and Founder Mutations for Monogenic Traits in Sub-Saharan African Populations. Annu Rev Genomics Hum Genet 2018; 19:149-175. [DOI: 10.1146/annurev-genom-083117-021256] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review highlights molecular genetic studies of monogenic traits where common pathogenic mutations occur in black families from sub-Saharan Africa. Examples of founder mutations have been identified for oculocutaneous albinism, cystic fibrosis, Fanconi anemia, and Gaucher disease. Although there are few studies from Africa, some of the mutations traverse populations across the continent, and they are almost all different from the common mutations observed in non-African populations. Myotonic dystrophy is curiously absent among Africans, and nonsyndromic deafness does not arise from mutations in GJB2 and GJB7. Locus heterogeneity is present for Huntington disease, with two common triplet expansion loci in Africa, HTT and JPH3. These findings have important clinical consequences for diagnosis, treatment, and genetic counseling in affected families. We currently have just a glimpse of the molecular etiology of monogenic diseases in sub-Saharan Africa, a proverbial “ears of the hippo” situation.
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Affiliation(s)
- Amanda Krause
- Division of Human Genetics, National Health Laboratory Service, and Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Heather Seymour
- Division of Human Genetics, National Health Laboratory Service, and Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Division of Human Genetics, National Health Laboratory Service, and Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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28
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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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29
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Choudhury A, Aron S, Sengupta D, Hazelhurst S, Ramsay M. African genetic diversity provides novel insights into evolutionary history and local adaptations. Hum Mol Genet 2018; 27:R209-R218. [PMID: 29741686 PMCID: PMC6061870 DOI: 10.1093/hmg/ddy161] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 12/22/2022] Open
Abstract
Genetic variation and susceptibility to disease are shaped by human demographic history and adaptation. We can now study the genomes of extant Africans and uncover traces of population migration, admixture, assimilation and selection by applying sophisticated computational algorithms. There are four major ethnolinguistic divisions among present day Africans: Hunter-gatherer populations in southern and central Africa; Nilo-Saharan speakers from north and northeast Africa; Afro-Asiatic speakers from north and east Africa; and Niger-Congo speakers who are the predominant ethnolinguistic group spread across most of sub-Saharan Africa. The enormous ethnolinguistic diversity in sub-Saharan African populations is largely paralleled by extensive genetic diversity and until a decade ago, little was known about detailed origins and divergence of these groups. Results from large-scale population genetic studies, and more recently whole genome sequence data, are unravelling the critical role of events like migration and admixture and environmental factors including diet, infectious diseases and climatic conditions in shaping current population diversity. It is now possible to start providing quantitative estimates of divergence times, population size and dynamic processes that have affected populations and their genetic risk for disease. Finally, the availability of ancient genomes from Africa provides historical insights of unprecedented depth. In this review, we highlight some key interpretations that have emerged from recent African genome studies.
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Affiliation(s)
- Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shaun Aron
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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30
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Sanz J, Randolph HE, Barreiro LB. Genetic and evolutionary determinants of human population variation in immune responses. Curr Opin Genet Dev 2018; 53:28-35. [PMID: 29960896 DOI: 10.1016/j.gde.2018.06.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/01/2018] [Accepted: 06/08/2018] [Indexed: 12/18/2022]
Abstract
Humans display remarkable immune response variation when exposed to identical immune challenges. However, our understanding of the genetic, evolutionary, and environmental factors that impact this inter-individual and inter-population immune response heterogeneity is still in its early days. In this review, we discuss three fundamental questions concerning the recent evolution of the human immune system: the degree to which individuals from different populations vary in their innate immune responses, the genetic variants accounting for such differences, and the evolutionary mechanisms that led to the establishment of these variants in modern human populations. We also discuss how past selective events might have contributed to the uneven distribution of immune-related disorders across populations.
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Affiliation(s)
- Joaquin Sanz
- Department of Biochemistry, Faculty of Medicine, Université de Montréal, QC H3T 1J4, Canada; Department of Genetics, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Haley E Randolph
- Department of Biochemistry, Faculty of Medicine, Université de Montréal, QC H3T 1J4, Canada; Department of Genetics, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1C5, Canada.
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31
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Palau L, Menez S, Rodriguez-Sanchez J, Novick T, Delsante M, McMahon BA, Atta MG. HIV-associated nephropathy: links, risks and management. HIV AIDS (Auckl) 2018; 10:73-81. [PMID: 29872351 PMCID: PMC5975615 DOI: 10.2147/hiv.s141978] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Despite the decreased incidence of human immunodeficiency virus (HIV)-associated nephropathy due to the widespread use of combined active antiretroviral therapy, it remains one of the leading causes of end-stage renal disease (ESRD) in HIV-1 seropositive patients. Patients usually present with low CD4 count, high viral load and heavy proteinuria, with the pathologic findings of collapsing focal segmental glomerulosclerosis. Increased susceptibility exists in individuals with African descent, largely due to polymorphism in APOL1 gene. Other clinical risk factors include high viral load and low CD4 count. Advanced kidney disease and nephrotic range proteinuria have been associated with progression to ESRD. Improvement in kidney function has been observed after initiation of combined active antiretroviral therapy. Other treatment options, when clinically indicated, are inhibition of the renin-angiotensin system and corticosteroids. Further routine management approaches for patients with chronic kidney disease should be implemented. In patients with progression to ESRD, kidney transplant should be pursued, provided that viral load control is adequate. Screening for the presence of kidney disease upon detection of HIV-1 seropositivity in high-risk populations is recommended.
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Affiliation(s)
- Laura Palau
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Steven Menez
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Tessa Novick
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Marco Delsante
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Blaithin A McMahon
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mohamed G Atta
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
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32
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Cyrus C, Al-Mueilo S, Vatte C, Chathoth S, Li YR, Qutub H, Al Ali R, Al-Muhanna F, Lanktree MB, Alkharsah KR, Al-Rubaish A, Kim-Mozeleski B, Keating B, Al Ali A. Assessing known chronic kidney disease associated genetic variants in Saudi Arabian populations. BMC Nephrol 2018; 19:88. [PMID: 29665793 PMCID: PMC5905143 DOI: 10.1186/s12882-018-0890-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 04/05/2018] [Indexed: 01/13/2023] Open
Abstract
Background Genome wide association studies of patients with European descent have identified common variants associated with risk of reduced estimated glomerular filtration rate (eGFR). A panel of eight variants were selected to evaluate their association and prevalence in a Saudi Arabian patient cohort with chronic kidney disease (CKD). Methods Eight genetic variants in four genes (SHROOM3, MYH9, SLC7A9, and CST3) were genotyped in 160 CKD patients and 189 ethnicity-matched healthy controls. Genetic variants were tested for association with the development of CKD (eGFR < 60 ml/min/1.73m2) and effects were compared with results obtained from 133,413 participants in the CKD genetics consortium. Multivariable regression was used to evaluate the role of these eight variants in improving prediction of CKD development. Results All eight variants were present in Saudi populations with minor allele frequency ranging from 16 to 46%. The risk variant in all four genes demonstrated the same direction of effect as observed in European populations. One variant, rs4821480, in MYH9 was significantly associated with increased risk of development of CKD (OR = 1.69, 95% CI 1.22–2.36, P = 0.002), but the additional variants were not statistically significant given our modest sample size. Conclusions CKD risk variants identified in European populations are present in Saudis. We did not find evidence to suggest heterogeneity of effect size compared to previously published estimates in European populations. Multivariable logistic regression analysis showed a statistically significant improvement in predicting the CKD using models with either FGF23 and vitamin D or FGF23, vitamin D level, and MYH9 genotypes (AUC = 0.93, 95% CI 0.90–0.95, P < 0.0001). Electronic supplementary material The online version of this article (10.1186/s12882-018-0890-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cyril Cyrus
- Institute for Research and Medical Consultation, Imam Abdulrahman bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia.
| | - Samir Al-Mueilo
- King Fahd Hospital of the University, Imam Abdulrahman bin Faisal University , Alkhobar, Saudi Arabia
| | - Chittibabu Vatte
- Institute for Research and Medical Consultation, Imam Abdulrahman bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Shahanas Chathoth
- Institute for Research and Medical Consultation, Imam Abdulrahman bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Yun R Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hatem Qutub
- King Fahd Hospital of the University, Imam Abdulrahman bin Faisal University , Alkhobar, Saudi Arabia.,Al-Omran Scientific Chair for hematological diseases, King Faisal University, Al Hassa, Saudi Arabia
| | - Rudaynah Al Ali
- King Fahd Hospital of the University, Imam Abdulrahman bin Faisal University , Alkhobar, Saudi Arabia
| | - Fahad Al-Muhanna
- King Fahd Hospital of the University, Imam Abdulrahman bin Faisal University , Alkhobar, Saudi Arabia
| | - Matthew B Lanktree
- Nephrology Division, Department of Medicine, McMaster University, Hamilton, ON, L8N 4A6, Canada
| | - Khaled Riyad Alkharsah
- Institute for Research and Medical Consultation, Imam Abdulrahman bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Abdullah Al-Rubaish
- King Fahd Hospital of the University, Imam Abdulrahman bin Faisal University , Alkhobar, Saudi Arabia
| | - Brian Kim-Mozeleski
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brendan Keating
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amein Al Ali
- Institute for Research and Medical Consultation, Imam Abdulrahman bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia.,Al-Omran Scientific Chair for hematological diseases, King Faisal University, Al Hassa, Saudi Arabia
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Population genetic evidence for positive and purifying selection acting at the human IFN-γ locus in Africa. Genes Immun 2018; 20:143-157. [PMID: 29599512 DOI: 10.1038/s41435-018-0016-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/22/2018] [Accepted: 01/26/2018] [Indexed: 01/09/2023]
Abstract
Despite its critical role in the defense against microbial infection and tumor development, little is known about the range of nucleotide and haplotype variation at IFN-γ, or the evolutionary forces that have shaped patterns of diversity at this locus. To address this gap in knowledge, we examined sequence data from the IFN-γ gene in 1461 individuals from 15 worldwide populations. Our analyses uncovered novel patterns of variation in distinct African populations, including an excess of high frequency-derived alleles, unusually long haplotype structure surrounding the IFN-γ gene, and a "star-like" genealogy of African-specific haplotypes carrying variants previously associated with infectious disease. We also inferred a deep time to coalescence of variation at IFN-γ (~ 0.8 million years ago) and ancient ages for common polymorphisms predating the evolution of modern humans. Taken together, these results are congruent with a model of positive selection on standing variation in African populations. Furthermore, we inferred that common variants in intron 3 of IFN-γ are the likely targets of selection. In addition, we observed a paucity of non-synonymous substitutions relative to synonymous changes in the exons of IFN-γ in African and non-African populations, suggestive of strong purifying selection. Therefore, we contend that positive and purifying selection have influenced levels of diversity in different regions of IFN-γ, implying that these distinct genic regions are, or have been, functionally important. Overall, this study provides additional insights into the evolutionary events that have contributed to the frequency and distribution of alleles having a role in human health and disease.
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Kidney disease in the setting of HIV infection: conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference. Kidney Int 2018; 93:545-559. [PMID: 29398134 DOI: 10.1016/j.kint.2017.11.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/23/2017] [Accepted: 11/08/2017] [Indexed: 12/12/2022]
Abstract
HIV-positive individuals are at increased risk for kidney disease, including HIV-associated nephropathy, noncollapsing focal segmental glomerulosclerosis, immune-complex kidney disease, and comorbid kidney disease, as well as kidney injury resulting from prolonged exposure to antiretroviral therapy or from opportunistic infections. Clinical guidelines for kidney disease prevention and treatment in HIV-positive individuals are largely extrapolated from studies in the general population, and do not fully incorporate existing knowledge of the unique HIV-related pathways and genetic factors that contribute to the risk of kidney disease in this population. We convened an international panel of experts in nephrology, renal pathology, and infectious diseases to define the pathology of kidney disease in the setting of HIV infection; describe the role of genetics in the natural history, diagnosis, and treatment of kidney disease in HIV-positive individuals; characterize the renal risk-benefit of antiretroviral therapy for HIV treatment and prevention; and define best practices for the prevention and management of kidney disease in HIV-positive individuals.
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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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Kruzel-Davila E, Wasser WG, Skorecki K. APOL1 Nephropathy: A Population Genetics and Evolutionary Medicine Detective Story. Semin Nephrol 2017; 37:490-507. [PMID: 29110756 DOI: 10.1016/j.semnephrol.2017.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Common DNA sequence variants rarely have a high-risk association with a common disease. When such associations do occur, evolutionary forces must be sought, such as in the association of apolipoprotein L1 (APOL1) gene risk variants with nondiabetic kidney diseases in populations of African ancestry. The variants originated in West Africa and provided pathogenic resistance in the heterozygous state that led to high allele frequencies owing to an adaptive evolutionary selective sweep. However, the homozygous state is disadvantageous and is associated with a markedly increased risk of a spectrum of kidney diseases encompassing hypertension-attributed kidney disease, focal segmental glomerulosclerosis, human immunodeficiency virus nephropathy, sickle cell nephropathy, and progressive lupus nephritis. This scientific success story emerged with the help of the tools developed over the past 2 decades in human genome sequencing and population genomic databases. In this introductory article to a timely issue dedicated to illuminating progress in this area, we describe this unique population genetics and evolutionary medicine detective story. We emphasize the paradox of the inheritance mode, the missing heritability, and unresolved associations, including cardiovascular risk and diabetic nephropathy. We also highlight how genetic epidemiology elucidates mechanisms and how the principles of evolution can be used to unravel conserved pathways affected by APOL1 that may lead to novel therapies. The APOL1 gene provides a compelling example of a common variant association with common forms of nondiabetic kidney disease occurring in a continental population isolate with subsequent global admixture. Scientific collaboration using multiple experimental model systems and approaches should further clarify pathomechanisms further, leading to novel therapies.
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Affiliation(s)
| | - Walter G Wasser
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel; Department of Nephrology, Mayanei HaYeshua Medical Center, Bnei Brak, Israel
| | - Karl Skorecki
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel; Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute Technion-Israel Institute of Technology, Rambam Health Care Campus, Haifa, Israel.
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Stanifer JW, Karia F, Maro V, Kilonzo K, Qin X, Patel UD, Hauser ER. APOL1 risk alleles among individuals with CKD in Northern Tanzania: A pilot study. PLoS One 2017; 12:e0181811. [PMID: 28732083 PMCID: PMC5521837 DOI: 10.1371/journal.pone.0181811] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/09/2017] [Indexed: 01/13/2023] Open
Abstract
INTRODUCTION In sub-Saharan Africa, approximately 100 million people have CKD, yet genetic risk factors are not well-understood. Despite the potential importance of understanding APOL1 risk allele status among individuals with CKD, little genetic research has been conducted. Therefore, we conducted a pilot study evaluating the feasibility of and willingness to participate in genetic research on kidney disease, and we estimated APOL1 risk allele frequencies among individuals with CKD. METHODS In 2014, we conducted a community-based field study evaluating CKD epidemiology in northern Tanzania. We assessed for CKD using urine albumin and serum creatinine to estimate GFR. We invited participants with CKD to enroll in an additional genetic study. We obtained dried-blood spots on filter cards, from which we extracted DNA using sterile punch biopsies. We genotyped for two single nucleotide polymorphisms (SNPs) defining the APOL1 G1 risk allele and an insertion/deletion polymorphism defining the G2 risk allele. Genotyping was performed in duplicate. RESULTS We enrolled 481 participant, 57 (12%) of whom had CKD. Among these, enrollment for genotyping was high (n = 48; 84%). We extracted a median of 19.4 ng of DNA from each dried-blood spot sample, and we genotyped the two APOL1 G1 SNPs and the APOL1 G2 polymorphism. Genotyping quality was high, with all duplicated samples showing perfect concordance. The frequency of APOL1 risk variants ranged from 7.0% to 11.0%, which was similar to previously-reported frequencies from the general population of northern Tanzania (p>0.2). DISCUSSION In individuals with CKD from northern Tanzania, we demonstrated feasibility of genotyping APOL1 risk alleles. We successfully genotyped three risk variants from DNA extracted from filter cards, and we demonstrated a high enrollment for participation. In this population, more extensive genetic studies of kidney disease may be well-received and will be feasible.
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Affiliation(s)
- John W. Stanifer
- Department of Medicine, Duke University; Durham, NC United States of America
- Duke Global Health Institute, Duke University; Durham, NC United States of America
- Duke Clinical Research Institute, Duke University; Durham, NC United States of America
| | - Francis Karia
- Kilimanjaro Christian Medical College; Moshi, Tanzania
| | - Venance Maro
- Kilimanjaro Christian Medical College; Moshi, Tanzania
| | | | - Xuejun Qin
- Duke Molecular Physiology Institute, Duke University School of Medicine; Durham NC United States of America
| | - Uptal D. Patel
- Department of Medicine, Duke University; Durham, NC United States of America
| | - Elizabeth R. Hauser
- Department of Medicine, Duke University; Durham, NC United States of America
- Duke Molecular Physiology Institute, Duke University School of Medicine; Durham NC United States of America
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine; Durham, NC United States of America
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Cooper A, Ilboudo H, Alibu VP, Ravel S, Enyaru J, Weir W, Noyes H, Capewell P, Camara M, Milet J, Jamonneau V, Camara O, Matovu E, Bucheton B, MacLeod A. APOL1 renal risk variants have contrasting resistance and susceptibility associations with African trypanosomiasis. eLife 2017; 6. [PMID: 28537557 PMCID: PMC5495568 DOI: 10.7554/elife.25461] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/22/2017] [Indexed: 12/17/2022] Open
Abstract
Reduced susceptibility to infectious disease can increase the frequency of otherwise deleterious alleles. In populations of African ancestry, two apolipoprotein-L1 (APOL1) variants with a recessive kidney disease risk, named G1 and G2, occur at high frequency. APOL1 is a trypanolytic protein that confers innate resistance to most African trypanosomes, but not Trypanosoma brucei rhodesiense or T.b. gambiense, which cause human African trypanosomiasis. In this case-control study, we test the prevailing hypothesis that these APOL1 variants reduce trypanosomiasis susceptibility, resulting in their positive selection in sub-Saharan Africa. We demonstrate a five-fold dominant protective association for G2 against T.b. rhodesiense infection. Furthermore, we report unpredicted strong opposing associations with T.b. gambiense disease outcome. G2 associates with faster progression of T.b. gambiense trypanosomiasis, while G1 associates with asymptomatic carriage and undetectable parasitemia. These results implicate both forms of human African trypanosomiasis in the selection and persistence of otherwise detrimental APOL1 kidney disease variants. DOI:http://dx.doi.org/10.7554/eLife.25461.001 African-Americans have a greater risk of developing chronic kidney disease than Americans with European ancestry. Much of this increased risk is explained by two versions of a gene called APOL1 that are common in people with African ancestry. These two versions of the gene, known as G1 and G2, suddenly became much more common in people in sub-Saharan Africa in the last 10,000 years. One theory for their rapid spread is that they might protect against a deadly parasitic disease known as African sleeping sickness. This disease is caused by two related parasites of a species known as Trypanosoma brucei, one of which is found in East Africa, while the other affects West Africa. Laboratory studies have shown that blood from individuals who carry the G1 and G2 variants is better at killing the East African parasites. However, it is not clear if these gene versions help people living in the rural communities, where African sleeping sickness is common, to fight off the disease. Now, Cooper, Ilboudo et al. show that G1 and G2 do indeed influence how susceptible individuals in these communities are to African sleeping sickness. Individuals with the G2 version were five-times less likely to get the disease from the East African parasite. Neither version could protect individuals from infection with the West African parasite, but infected individuals with the G1 version had fewer parasites in their blood and were less likely to become severely ill. The ability of the G1 version to control the disease and prolong life could explain why this gene version has become so common amongst people in West Africa. Unexpectedly, the experiments also revealed that people with the G2 version were more likely to become severely unwell when they were infected by the West African parasite. This indicates that whether this gene variant is helpful or harmful depends on where an individual lives. The next step following on from this work will be to investigate exactly how the G1 version reduces the severity of the West African disease. This may aid the development of new drugs for African sleeping sickness and kidney disease. DOI:http://dx.doi.org/10.7554/eLife.25461.002
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Affiliation(s)
- Anneli Cooper
- Wellcome Trust Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Hamidou Ilboudo
- Centre International de Recherche-Développement sur l'Elevage en zone Subhumide, Bobo-Dioulasso, Burkina Faso.,TrypanoGEN, H3Africa Consortium, Makerere University, Kampala, Uganda
| | - V Pius Alibu
- TrypanoGEN, H3Africa Consortium, Makerere University, Kampala, Uganda.,College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Sophie Ravel
- Unité Mixte de Recherche IRD-CIRAD 177, Institut de Recherche pour le Développement, Montpellier, France
| | - John Enyaru
- TrypanoGEN, H3Africa Consortium, Makerere University, Kampala, Uganda.,College of Natural Sciences, Makerere University, Kampala, Uganda
| | - William Weir
- Wellcome Trust Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Harry Noyes
- Wellcome Trust Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.,TrypanoGEN, H3Africa Consortium, Makerere University, Kampala, Uganda.,Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Paul Capewell
- Wellcome Trust Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Mamadou Camara
- TrypanoGEN, H3Africa Consortium, Makerere University, Kampala, Uganda.,Programme National de Lutte contre la Trypanosomiase Humaine Africaine, Conakry, Guinea
| | - Jacqueline Milet
- Unité Mixte de Recherche IRD-CIRAD 177, Institut de Recherche pour le Développement, Montpellier, France
| | - Vincent Jamonneau
- Centre International de Recherche-Développement sur l'Elevage en zone Subhumide, Bobo-Dioulasso, Burkina Faso.,TrypanoGEN, H3Africa Consortium, Makerere University, Kampala, Uganda.,Unité Mixte de Recherche IRD-CIRAD 177, Institut de Recherche pour le Développement, Montpellier, France
| | - Oumou Camara
- Programme National de Lutte contre la Trypanosomiase Humaine Africaine, Conakry, Guinea
| | - Enock Matovu
- TrypanoGEN, H3Africa Consortium, Makerere University, Kampala, Uganda.,College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Bruno Bucheton
- TrypanoGEN, H3Africa Consortium, Makerere University, Kampala, Uganda.,Unité Mixte de Recherche IRD-CIRAD 177, Institut de Recherche pour le Développement, Montpellier, France.,Programme National de Lutte contre la Trypanosomiase Humaine Africaine, Conakry, Guinea
| | - Annette MacLeod
- Wellcome Trust Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.,TrypanoGEN, H3Africa Consortium, Makerere University, Kampala, Uganda
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A co-evolutionary arms race: trypanosomes shaping the human genome, humans shaping the trypanosome genome. Parasitology 2017; 142 Suppl 1:S108-19. [PMID: 25656360 PMCID: PMC4413828 DOI: 10.1017/s0031182014000602] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Trypanosoma brucei is the causative agent of African sleeping sickness in humans and one of several pathogens that cause the related veterinary disease Nagana. A complex co-evolution has occurred between these parasites and primates that led to the emergence of trypanosome-specific defences and counter-measures. The first line of defence in humans and several other catarrhine primates is the trypanolytic protein apolipoprotein-L1 (APOL1) found within two serum protein complexes, trypanosome lytic factor 1 and 2 (TLF-1 and TLF-2). Two sub-species of T. brucei have evolved specific mechanisms to overcome this innate resistance, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense. In T. b. rhodesiense, the presence of the serum resistance associated (SRA) gene, a truncated variable surface glycoprotein (VSG), is sufficient to confer resistance to lysis. The resistance mechanism of T. b. gambiense is more complex, involving multiple components: reduction in binding affinity of a receptor for TLF, increased cysteine protease activity and the presence of the truncated VSG, T. b. gambiense-specific glycoprotein (TgsGP). In a striking example of co-evolution, evidence is emerging that primates are responding to challenge by T. b. gambiense and T. b. rhodesiense, with several populations of humans and primates displaying resistance to infection by these two sub-species.
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Sex, Ethnicity, and CVD Among Women of African Descent: An Approach for the New Era of Genomic Research. Glob Heart 2017; 12:69-71. [PMID: 28351700 DOI: 10.1016/j.gheart.2017.01.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/13/2017] [Indexed: 01/13/2023] Open
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Fan S, Hansen MEB, Lo Y, Tishkoff SA. Going global by adapting local: A review of recent human adaptation. Science 2017; 354:54-59. [PMID: 27846491 DOI: 10.1126/science.aaf5098] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The spread of modern humans across the globe has led to genetic adaptations to diverse local environments. Recent developments in genomic technologies, statistical analyses, and expanded sampled populations have led to improved identification and fine-mapping of genetic variants associated with adaptations to regional living conditions and dietary practices. Ongoing efforts in sequencing genomes of indigenous populations, accompanied by the growing availability of "-omics" and ancient DNA data, promises a new era in our understanding of recent human evolution and the origins of variable traits and disease risks.
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Affiliation(s)
- Shaohua Fan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yancy Lo
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.,Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA. .,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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Galinsky KJ, Loh PR, Mallick S, Patterson NJ, Price AL. Population Structure of UK Biobank and Ancient Eurasians Reveals Adaptation at Genes Influencing Blood Pressure. Am J Hum Genet 2016; 99:1130-1139. [PMID: 27773431 PMCID: PMC5097941 DOI: 10.1016/j.ajhg.2016.09.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/21/2016] [Indexed: 01/11/2023] Open
Abstract
Analyzing genetic differences between closely related populations can be a powerful way to detect recent adaptation. The very large sample size of the UK Biobank is ideal for using population differentiation to detect selection and enables an analysis of the UK population structure at fine resolution. In this study, analyses of 113,851 UK Biobank samples showed that population structure in the UK is dominated by five principal components (PCs) spanning six clusters: Northern Ireland, Scotland, northern England, southern England, and two Welsh clusters. Analyses of ancient Eurasians revealed that populations in the northern UK have higher levels of Steppe ancestry and that UK population structure cannot be explained as a simple mixture of Celts and Saxons. A scan for unusual population differentiation along the top PCs identified a genome-wide-significant signal of selection at the coding variant rs601338 in FUT2 (p = 9.16 × 10-9). In addition, by combining evidence of unusual differentiation within the UK with evidence from ancient Eurasians, we identified genome-wide-significant (p = 5 × 10-8) signals of recent selection at two additional loci: CYP1A2-CSK and F12. We detected strong associations between diastolic blood pressure in the UK Biobank and both the variants with selection signals at CYP1A2-CSK (p = 1.10 × 10-19) and the variants with ancient Eurasian selection signals at the ATXN2-SH2B3 locus (p = 8.00 × 10-33), implicating recent adaptation related to blood pressure.
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Affiliation(s)
- Kevin J Galinsky
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Swapan Mallick
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nick J Patterson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alkes L Price
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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Pharmacogenomic implications of the evolutionary history of infectious diseases in Africa. THE PHARMACOGENOMICS JOURNAL 2016; 17:112-120. [PMID: 27779243 PMCID: PMC5380847 DOI: 10.1038/tpj.2016.78] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/06/2016] [Accepted: 07/19/2016] [Indexed: 12/20/2022]
Abstract
As the common birthplace of all human populations, modern humans have lived longer on the African continent than in any other geographical region of the world. This long history, along with the evolutionary need to adapt to environmental challenges such as exposure to infectious agents, has led to greater genetic variation in Africans. The vast genetic variation in Africans also extends to genes involved in the absorption, distribution, metabolism and excretion of pharmaceuticals. Ongoing cataloging of these clinically relevant variants reveals huge allele-frequency differences within and between African populations. Here, we examine Africa's large burden of infectious disease, discuss key examples of known genetic variation modulating disease risk, and provide examples of clinically relevant variants critical for establishing dosing guidelines. We propose that a more systematic characterization of the genetic diversity of African ancestry populations is required if the current benefits of precision medicine are to be extended to these populations.
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45
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Rotimi CN, Tekola-Ayele F, Baker JL, Shriner D. The African diaspora: history, adaptation and health. Curr Opin Genet Dev 2016; 41:77-84. [PMID: 27644073 DOI: 10.1016/j.gde.2016.08.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 06/30/2016] [Accepted: 08/02/2016] [Indexed: 01/13/2023]
Abstract
The trans-Atlantic slave trade brought millions of Africans to the New World. Advances in genomics are providing novel insights into the history and health of Africans and the diasporan populations. Recent examples reviewed here include the unraveling of substantial hunter-gatherer and 'Eurasian' admixtures across sub-Saharan Africa, expanding our understanding of ancestral African genetics; the global ubiquity of mixed ancestry; the revealing of African ancestry in Latin Americans that likely derived from the slave trade; and understanding of the ancestral backgrounds of APOL1 and LPL found to influence kidney disease and lipid levels, respectively, providing specific insights into disease etiology and health disparities.
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Affiliation(s)
- Charles N Rotimi
- Center for Research on Genomics and Global Health National Human Genome Research Institute, Building 12A, Room 4047 12 South Drive, Bethesda, MD 20892, USA.
| | - Fasil Tekola-Ayele
- Center for Research on Genomics and Global Health National Human Genome Research Institute, Building 12A, Room 4047 12 South Drive, Bethesda, MD 20892, USA
| | - Jennifer L Baker
- Center for Research on Genomics and Global Health National Human Genome Research Institute, Building 12A, Room 4047 12 South Drive, Bethesda, MD 20892, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health National Human Genome Research Institute, Building 12A, Room 4047 12 South Drive, Bethesda, MD 20892, USA
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Pinto JC, Oliveira S, Teixeira S, Martins D, Fehn AM, Aço T, Gayà-Vidal M, Rocha J. Food and pathogen adaptations in the Angolan Namib desert: Tracing the spread of lactase persistence and human African trypanosomiasis resistance into southwestern Africa. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 161:436-447. [PMID: 27402285 DOI: 10.1002/ajpa.23042] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/11/2016] [Accepted: 06/12/2016] [Indexed: 01/13/2023]
Abstract
OBJECTIVES We investigated the frequency distribution and haplotype diversity of human African trypanosomiasis (HAT) resistance and lactase persistence (LP) variants in populations from the Angolan Namib to trace the spread of these genetic adaptations into southwestern Africa. MATERIALS AND METHODS We resequenced two fragments of the LCT enhancer and the APOL1 gene and genotyped flanking short tandem repeat loci in six groups with different subsistence traditions living in the Angolan Namib, and in a comparative dataset including other populations from Africa and Europe. LP in the Angolan Namib is represented by the -14010*C allele, which is associated with a predominant haplotype that is shared with other southern and eastern African populations. While LP was found to be more frequent in foragers than in pastoralists, the frequencies of the two APOL1 variants associated with HAT-resistance (G1 and G2) did not differ between the two groups. The G1 allele is mostly associated with a single widespread haplotype. The G2 allele is linked to several haplotypes that are molecularly related to haplotypes found in other African Bantu-speaking populations. The putatively archaic G3 variant displayed more intra-allelic diversity in Africa than in Europe. DISCUSSION The LP adaptation was carried to southern Africa by non-Bantu speaking pastoralists from eastern Africa, but an obvious link between its presence in southern Angola and groups speaking languages of the Khoe-Kwadi family, as previously found in other areas, could not be confirmed. The presence of APOL1 variants G1 and G2 is linked to the Bantu expansions. Our results suggest that the G3 variant was retained in modern humans by incomplete lineage sorting.
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Affiliation(s)
- Joana C Pinto
- CIBIO/InBIO: Research Centre in Biodiversity and Genetic Resources, Vairão, 4485-661, Portugal
| | - Sandra Oliveira
- CIBIO/InBIO: Research Centre in Biodiversity and Genetic Resources, Vairão, 4485-661, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, 4169-007, Portugal
| | - Sérgio Teixeira
- CIBIO/InBIO: Research Centre in Biodiversity and Genetic Resources, Vairão, 4485-661, Portugal
| | - Dayana Martins
- ISCED/Huíla-Instituto Superior de Ciências da Educação, Lubango, Angola
| | - Anne-Maria Fehn
- CIBIO/InBIO: Research Centre in Biodiversity and Genetic Resources, Vairão, 4485-661, Portugal.,Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Teresa Aço
- Centro de Estudos do Deserto (CEDO), Namibe, Angola
| | - Magdalena Gayà-Vidal
- CIBIO/InBIO: Research Centre in Biodiversity and Genetic Resources, Vairão, 4485-661, Portugal
| | - Jorge Rocha
- CIBIO/InBIO: Research Centre in Biodiversity and Genetic Resources, Vairão, 4485-661, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, 4169-007, Portugal.
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Reiner AP, Susztak K. APOL1 Variants: From Parasites to Kidney Function to Cardiovascular Disease. Arterioscler Thromb Vasc Biol 2016; 36:219-20. [PMID: 26819463 DOI: 10.1161/atvbaha.115.306794] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Alex P Reiner
- From the Fred Hutchinson Cancer Research Center, WHI Clinical Coordinating Center/Public Health Sciences (A.P.R.), and Renal Electrolyte and Hypertension Division, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (K.S.).
| | - Katalin Susztak
- From the Fred Hutchinson Cancer Research Center, WHI Clinical Coordinating Center/Public Health Sciences (A.P.R.), and Renal Electrolyte and Hypertension Division, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (K.S.).
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48
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FSGS: Diagnosis and Diagnostic Work-Up. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4632768. [PMID: 27314022 PMCID: PMC4894996 DOI: 10.1155/2016/4632768] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/03/2016] [Indexed: 01/13/2023]
Abstract
Focal segmental glomerulosclerosis is a histologic lesion, rather than a clinical disease. FSGS is common cause of nephrotic syndrome in both adults and children worldwide. In the United States it is the most common primary glomerular disease resulting in end-stage renal disease and recent reports have suggested that its incidence might be on the rise. Currently the incidence is estimated to be 7 per million. The podocyte is the cellular target cell in FSGS and in recent years substantial insight in the pathogenesis and genetics of FSGS have accumulated. Furthermore the discovery of potential novel biomarkers to diagnose FSGS and monitor disease activity has renewed interest in this disease. In this review article we will focus on the clinical presentation and diagnosis of FSGS.
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Dummer PD, Limou S, Rosenberg AZ, Heymann J, Nelson G, Winkler CA, Kopp JB. APOL1 Kidney Disease Risk Variants: An Evolving Landscape. Semin Nephrol 2016. [PMID: 26215860 DOI: 10.1016/j.semnephrol.2015.04.008] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Apolipoprotein L1 (APOL1) genetic variants account for much of the excess risk of chronic and end-stage kidney disease, which results in a significant global health disparity for persons of African ancestry. We estimate the lifetime risk of kidney disease in APOL1 dual-risk allele individuals to be at least 15%. Experimental evidence suggests a direct role of APOL1 in pore formation, cellular injury, and programmed cell death in renal injury. The APOL1 BH3 motif, often associated with cell death, is unlikely to play a role in APOL1-induced cytotoxicity because it is not conserved within the APOL family and is dispensable for cell death in vitro. We discuss two models for APOL1 trypanolytic activity: one involving lysosome permeabilization and another involving colloid-osmotic swelling of the cell body, as well as their relevance to human pathophysiology. Experimental evidence from human cell culture models suggests that both mechanisms may be operative. A systems biology approach whereby APOL1-associated perturbations in gene and protein expression in affected individuals are correlated with molecular pathways may be productive to elucidate APOL1 function in vivo.
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Affiliation(s)
- Patrick D Dummer
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Sophie Limou
- Molecular Epidemiology Genetics Section, Center for Cancer Research, National Cancer Institute, Frederick MD
| | - Avi Z Rosenberg
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD; Department of Pathology Johns Hopkins University, Baltimore, MD
| | - Jurgen Heymann
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - George Nelson
- Molecular Epidemiology Genetics Section, Center for Cancer Research, National Cancer Institute, Frederick MD
| | - Cheryl A Winkler
- Molecular Epidemiology Genetics Section, Center for Cancer Research, National Cancer Institute, Frederick MD
| | - Jeffrey B Kopp
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.
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50
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Abstract
African trypanosomes, except Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense, which cause human African trypanosomiasis, are lysed by the human serum protein apolipoprotein L1 (ApoL1). These two subspecies can resist human ApoL1 because they express the serum resistance proteins T. b. gambiense glycoprotein (TgsGP) and serum resistance-associated protein (SRA), respectively. Whereas in T. b. rhodesiense, SRA is necessary and sufficient to inhibit ApoL1, in T. b. gambiense, TgsGP cannot protect against high ApoL1 uptake, so different additional mechanisms contribute to limit this uptake. Here we report a complex interplay between trypanosomes and an ApoL1 variant, revealing important insights into innate human immunity against these parasites. Using whole-genome sequencing, we characterized an atypical T. b. gambiense infection in a patient in Ghana. We show that the infecting trypanosome has diverged from the classical T. b. gambiense strains and lacks the TgsGP defense mechanism against human serum. By sequencing the ApoL1 gene of the patient and subsequent in vitro mutagenesis experiments, we demonstrate that a homozygous missense substitution (N264K) in the membrane-addressing domain of this ApoL1 variant knocks down the trypanolytic activity, allowing the trypanosome to avoid ApoL1-mediated immunity. Most African trypanosomes are lysed by the ApoL1 protein in human serum. Only the subspecies Trypanosoma b. gambiense and T. b. rhodesiense can resist lysis by ApoL1 because they express specific serum resistance proteins. We here report a complex interplay between trypanosomes and an ApoL1 variant characterized by a homozygous missense substitution (N264K) in the domain that we hypothesize interacts with the endolysosomal membranes of trypanosomes. The N264K substitution knocks down the lytic activity of ApoL1 against T. b. gambiense strains lacking the TgsGP defense mechanism and against T. b. rhodesiense if N264K is accompanied by additional substitutions in the SRA-interacting domain. Our data suggest that populations with high frequencies of the homozygous N264K ApoL1 variant may be at increased risk of contracting human African trypanosomiasis.
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