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Usuzaki T, Ishikuro M, Kikuya M, Murakami K, Noda A, Ueno F, Metoki H, Obara T, Kuriyama S. Child-parent associations of hematocrit in trios of Japanese adulthood confirmed by the random family method: The TMM BirThree Cohort Study. Sci Rep 2024; 14:19047. [PMID: 39152204 PMCID: PMC11329627 DOI: 10.1038/s41598-024-69752-2] [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: 02/05/2024] [Accepted: 08/08/2024] [Indexed: 08/19/2024] Open
Abstract
To examine child-parent associations of HCT among Japanese adults and their parents. Factors associated with hematocrit (HCT) were analyzed in 3,574 sons and 7,203 daughters using Pearson's correlation coefficient and Student's t-test. Multiple linear regression analysis, adjusted by the factors identified by univariate analyses and by living with parents, was performed on 242 son-parent trios and 587 daughter-parent trios. When a child-parent association was observed in the multiple linear regression analysis, it was validated using the random family method (RFM). In univariate analyses, the son's HCT was associated with age (correlation coefficient = -0.072), white blood cell (WBC) (0.19), alanine aminotransferase (ALT) (0.20), triglyceride (0.11), and estimated glomerular filtration rate (eGFR) (- 0.087). The daughter's HCT was associated with WBC (0.014), ALT (0.18), and eGFR (- 0.17). In multiple linear regression analysis, the son's HCT was associated with the son's WBC (coefficient = 3.48 × 10-4), the son's eGFR (0.031), the father's HCT (0.11), and the mother's HCT (0.17). RFM confirmed the association between the son's and father's HCT (p = 0.0070) and between the son's and mother's HCT (p = 0.0011). The daughter's HCT was associated with WBC (2.6 × 10-4), ALT (0.037), and the mother's HCT (0.14). RFM confirmed the association between the daughter's and mother's HCT (p = 0.00043). Child-parent association of HCT was confirmed between son-father, son-mother, and daughter-mother relationships, and differed depending on the sex of the child and the parents.
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Affiliation(s)
- Takuma Usuzaki
- Department of Diagnostic Radiology, Tohoku University Hospital, Sendai, Japan
| | - Mami Ishikuro
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan
- Division of Molecular Epidemiology, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masahiro Kikuya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan
- Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan
| | - Keiko Murakami
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan
| | - Aoi Noda
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan
- Division of Molecular Epidemiology, Graduate School of Medicine, Tohoku University, Sendai, Japan
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Fumihiko Ueno
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan
| | - Hirohito Metoki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan
- Division of Public Health, Hygiene and Epidemiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan.
- Division of Molecular Epidemiology, Graduate School of Medicine, Tohoku University, Sendai, Japan.
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan.
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan
- Division of Molecular Epidemiology, Graduate School of Medicine, Tohoku University, Sendai, Japan
- Division of Disaster Public Health, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
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Taniguchi J, Masuda T, Iwatani Y, Yamamoto K, Sakai N, Okada Y, Watanabe M. Rigorous evaluation of genetic and epigenetic effects on clinical laboratory measurements using Japanese monozygotic twins. Clin Genet 2024; 105:159-172. [PMID: 37899590 DOI: 10.1111/cge.14443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/10/2023] [Accepted: 10/09/2023] [Indexed: 10/31/2023]
Abstract
The investigation of environmental effects on clinical measurements using individual samples is challenging because their genetic and environmental factors are different. However, using monozygotic twins (MZ) makes it possible to investigate the influence of environmental factors as they have the same genetic factors within pairs because the difference in the clinical traits within the MZ mostly reflect the influence of environmental factors. We hypothesized that the within-pair differences in the traits that are strongly affected by genetic factors become larger after genetic risk score (GRS) correction. Using 278 Japanese MZ pairs, we compared the change in within-pair differences in each of the 45 normalized clinical measurements before and after GRS correction, and we also attempted to correct for the effects of genetic factors to identify Cytosine-phosphodiester-Guanine (CpG) sites in DNA sequences with epigenetic effects that are regulated by genetic factors. Five traits were classified into the high heritability group, which was strongly affected by genetic factors. CpG sites could be classified into three groups: regulated only by environmental factors, regulated by environmental factors masked by genetic factors, and regulated only by genetic factors. Our method has the potential to identify trait-related methylation sites that have not yet been discovered.
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Affiliation(s)
- Jumpei Taniguchi
- Department of Clinical Laboratory and Biomedical Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Tatsuo Masuda
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshinori Iwatani
- Department of Clinical Laboratory and Biomedical Sciences, Osaka University Graduate School of Medicine, Suita, Japan
- Center for Twin Research, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Norio Sakai
- Center for Twin Research, Osaka University Graduate School of Medicine, Suita, Japan
- Child Healthcare and Genetic Science Laboratory, Division of Health Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mikio Watanabe
- Department of Clinical Laboratory and Biomedical Sciences, Osaka University Graduate School of Medicine, Suita, Japan
- Center for Twin Research, Osaka University Graduate School of Medicine, Suita, Japan
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3
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Vellani V, Garrett N, Gaule A, Patil KR, Sharot T. Quantifying the heritability of belief formation. Sci Rep 2022; 12:11833. [PMID: 35821231 PMCID: PMC9276818 DOI: 10.1038/s41598-022-15492-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 06/24/2022] [Indexed: 11/09/2022] Open
Abstract
Individual differences in behaviour, traits and mental-health are partially heritable. Traditionally, studies have focused on quantifying the heritability of high-order characteristics, such as happiness or education attainment. Here, we quantify the degree of heritability of lower-level mental processes that likely contribute to complex traits and behaviour. In particular, we quantify the degree of heritability of cognitive and affective factors that contribute to the generation of beliefs about risk, which drive behavior in domains ranging from finance to health. Monozygotic and dizygotic twin pairs completed a belief formation task. We first show that beliefs about risk are associated with vividness of imagination, affective evaluation and learning abilities. We then demonstrate that the genetic contribution to individual differences in these processes range between 13.5 and 39%, with affect evaluation showing a particular robust heritability component. These results provide clues to which mental factors may be driving the heritability component of beliefs formation, which in turn contribute to the heritability of complex traits.
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Affiliation(s)
- Valentina Vellani
- Affective Brain Lab, Department of Experimental Psychology, University College London, London, WC1H 0AP, UK.
- The Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London, London, WC1B 5EH, UK.
| | - Neil Garrett
- School of Psychology, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Anne Gaule
- Developmental Risk and Resilience Unit, Department of Experimental Psychology, University College London, London, WC1H 0AP, UK
| | - Kaustubh R Patil
- Institute of Neuroscience and Medicine (INM-7), Forschungszentrum Jülich, Jülich, Germany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tali Sharot
- Affective Brain Lab, Department of Experimental Psychology, University College London, London, WC1H 0AP, UK.
- The Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London, London, WC1B 5EH, UK.
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Pavlova LE, Panchenko AV, Timina MF, Gvozdik TE, Kovalenko VV, Agumava AA, Panchenko AV. Genetic Homogeneity of the Population of Male Rhesus Macaques by the Polymorphisms of Genes oprm1, npy, maoa, crh, 5-htt as Determined by Cluster Analysis of Blood Count Data. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422030097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Krayem I, Sohrabi Y, Javorková E, Volkova V, Strnad H, Havelková H, Vojtíšková J, Aidarova A, Holáň V, Demant P, Lipoldová M. Genetic Influence on Frequencies of Myeloid-Derived Cell Subpopulations in Mouse. Front Immunol 2022; 12:760881. [PMID: 35154069 PMCID: PMC8826059 DOI: 10.3389/fimmu.2021.760881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Differences in frequencies of blood cell subpopulations were reported to influence the course of infections, atopic and autoimmune diseases, and cancer. We have discovered a unique mouse strain B10.O20 containing extremely high frequency of myeloid-derived cells (MDC) in spleen. B10.O20 carries 3.6% of genes of the strain O20 on the C57BL/10 genetic background. It contains much higher frequency of CD11b+Gr1+ cells in spleen than both its parents. B10.O20 carries O20-derived segments on chromosomes 1, 15, 17, and 18. Their linkage with frequencies of blood cell subpopulations in spleen was tested in F2 hybrids between B10.O20 and C57BL/10. We found 3 novel loci controlling MDC frequencies: Mydc1, 2, and 3 on chromosomes 1, 15, and 17, respectively, and a locus controlling relative spleen weight (Rsw1) that co-localizes with Mydc3 and also influences proportion of white and red pulp in spleen. Mydc1 controls numbers of CD11b+Gr1+ cells. Interaction of Mydc2 and Mydc3 regulates frequency of CD11b+Gr1+ cells and neutrophils (Gr1+Siglec-F- cells from CD11b+ cells). Interestingly, Mydc3/Rsw1 is orthologous with human segment 6q21 that was shown previously to determine counts of white blood cells. Bioinformatics analysis of genomic sequence of the chromosomal segments bearing these loci revealed polymorphisms between O20 and C57BL/10 that change RNA stability and genes’ functions, and we examined expression of relevant genes. This identified potential candidate genes Smap1, Vps52, Tnxb, and Rab44. Definition of genetic control of MDC can help to personalize therapy of diseases influenced by these cells.
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Affiliation(s)
- Imtissal Krayem
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Yahya Sohrabi
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Eliška Javorková
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czechia.,Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Valeriya Volkova
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Hynek Strnad
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Helena Havelková
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Jarmila Vojtíšková
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Aigerim Aidarova
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Vladimír Holáň
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czechia.,Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Peter Demant
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Marie Lipoldová
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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6
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Kachuri L, Jeon S, DeWan AT, Metayer C, Ma X, Witte JS, Chiang CWK, Wiemels JL, de Smith AJ. Genetic determinants of blood-cell traits influence susceptibility to childhood acute lymphoblastic leukemia. Am J Hum Genet 2021; 108:1823-1835. [PMID: 34469753 PMCID: PMC8546033 DOI: 10.1016/j.ajhg.2021.08.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/06/2021] [Indexed: 01/07/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Despite overlap between genetic risk loci for ALL and hematologic traits, the etiological relevance of dysregulated blood-cell homeostasis remains unclear. We investigated this question in a genome-wide association study (GWAS) of childhood ALL (2,666 affected individuals, 60,272 control individuals) and a multi-trait GWAS of nine blood-cell indices in the UK Biobank. We identified 3,000 blood-cell-trait-associated (p < 5.0 × 10-8) variants, explaining 4.0% to 23.9% of trait variation and including 115 loci associated with blood-cell ratios (LMR, lymphocyte-to-monocyte ratio; NLR, neutrophil-to-lymphocyte ratio; PLR, platelet-to-lymphocyte ratio). ALL susceptibility was genetically correlated with lymphocyte counts (rg = 0.088, p = 4.0 × 10-4) and PLR (rg = -0.072, p = 0.0017). In Mendelian randomization analyses, genetically predicted increase in lymphocyte counts was associated with increased ALL risk (odds ratio [OR] = 1.16, p = 0.031) and strengthened after accounting for other cell types (OR = 1.43, p = 8.8 × 10-4). We observed positive associations with increasing LMR (OR = 1.22, p = 0.0017) and inverse effects for NLR (OR = 0.67, p = 3.1 × 10-4) and PLR (OR = 0.80, p = 0.002). Our study shows that a genetically induced shift toward higher lymphocyte counts, overall and in relation to monocytes, neutrophils, and platelets, confers an increased susceptibility to childhood ALL.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Soyoung Jeon
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Andrew T DeWan
- Center for Perinatal, Pediatric, and Environmental Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA; Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA
| | - Catherine Metayer
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.
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Ebel ER, Kuypers FA, Lin C, Petrov DA, Egan ES. Common host variation drives malaria parasite fitness in healthy human red cells. eLife 2021; 10:e69808. [PMID: 34553687 PMCID: PMC8497061 DOI: 10.7554/elife.69808] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/22/2021] [Indexed: 12/11/2022] Open
Abstract
The replication of Plasmodium falciparum parasites within red blood cells (RBCs) causes severe disease in humans, especially in Africa. Deleterious alleles like hemoglobin S are well-known to confer strong resistance to malaria, but the effects of common RBC variation are largely undetermined. Here, we collected fresh blood samples from 121 healthy donors, most with African ancestry, and performed exome sequencing, detailed RBC phenotyping, and parasite fitness assays. Over one-third of healthy donors unknowingly carried alleles for G6PD deficiency or hemoglobinopathies, which were associated with characteristic RBC phenotypes. Among non-carriers alone, variation in RBC hydration, membrane deformability, and volume was strongly associated with P. falciparum growth rate. Common genetic variants in PIEZO1, SPTA1/SPTB, and several P. falciparum invasion receptors were also associated with parasite growth rate. Interestingly, we observed little or negative evidence for divergent selection on non-pathogenic RBC variation between Africans and Europeans. These findings suggest a model in which globally widespread variation in a moderate number of genes and phenotypes modulates P. falciparum fitness in RBCs.
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Affiliation(s)
- Emily R Ebel
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States
| | - Frans A Kuypers
- Children's Hospital Oakland Research InstituteOaklandUnited States
| | - Carrie Lin
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Elizabeth S Egan
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States
- Department of Microbiology & Immunology, Stanford University School of MedicineStanfordUnited States
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8
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Comprehensive Transcriptomic Comparison between Porcine CD8 - and CD8 + Gamma Delta T Cells Revealed Distinct Immune Phenotype. Animals (Basel) 2021; 11:ani11082165. [PMID: 34438623 PMCID: PMC8388496 DOI: 10.3390/ani11082165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/13/2021] [Accepted: 07/21/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary This study was conducted to comprehensively understand the functional mechanisms of CD8+/− porcine gamma delta (γδ) T cells related to the immune system using RNA-sequencing technology. In total, 646 upregulated and 561 downregulated differentially expressed genes (DEGs) for CD8+ were identified and functional annotation was performed. A cytokine–cytokine receptor interaction and T cell receptor (TCR) signaling pathway were enriched in the upregulated DEG group, whereas the B cell receptor signaling pathway was enriched in the downregulated DEG group. Chemokine-related genes (CXCR3, CCR5, CCL4, CCL5), interferon gamma (IFNG), and CD40 ligand (CD40LG) identified in the cytokine–cytokine receptor interaction and TCR signaling pathway may affect the inter-regulation of immune signaling. Our results are expected to contribute to the understanding of mechanisms of porcine γδ T cells. Abstract We aimed to comprehensively understand the functional mechanisms of immunity, especially of the CD8+/− subsets of gamma delta (γδ) T cells, using an RNA-sequencing analysis. Herein, γδ T cells were obtained from bronchial lymph node tissues of 38-day-old (after weaning 10-day: D10) and 56-day-old (after weaning 28-day: D28) weaned pigs and sorted into CD8+ and CD8− groups. Differentially expressed genes (DEGs) were identified based on the CD8 groups at D10 and D28 time points. We confirmed 1699 DEGs between D10 CD8+ versus D10 CD8− groups and 1784 DEGs between D28 CD8+ versus D28 CD8− groups; 646 upregulated and 561 downregulated DEGs were common. The common upregulated DEGs were enriched in the cytokine–cytokine receptor interaction and T cell receptor (TCR) signaling pathway, and the common downregulated DEGs were enriched in the B cell receptor signaling pathway. Further, chemokine-related genes, interferon gamma, and CD40 ligand were involved in the cytokine–cytokine receptor interaction and TCR signaling pathway, which are associated with inter-regulation in immunity. We expect our results to form the basic data required for understanding the mechanisms of γδ T cells in pigs; however, further studies are required in order to reveal the dynamic changes in γδ T cells under pathogenic infections, such as those by viruses.
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Hu Y, Bien SA, Nishimura KK, Haessler J, Hodonsky CJ, Baldassari AR, Highland HM, Wang Z, Preuss M, Sitlani CM, Wojcik GL, Tao R, Graff M, Huckins LM, Sun Q, Chen MH, Mousas A, Auer PL, Lettre G, Tang W, Qi L, Thyagarajan B, Buyske S, Fornage M, Hindorff LA, Li Y, Lin D, Reiner AP, North KE, Loos RJF, Raffield LM, Peters U, Avery CL, Kooperberg C. Multi-ethnic genome-wide association analyses of white blood cell and platelet traits in the Population Architecture using Genomics and Epidemiology (PAGE) study. BMC Genomics 2021; 22:432. [PMID: 34107879 PMCID: PMC8191001 DOI: 10.1186/s12864-021-07745-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 05/26/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Circulating white blood cell and platelet traits are clinically linked to various disease outcomes and differ across individuals and ancestry groups. Genetic factors play an important role in determining these traits and many loci have been identified. However, most of these findings were identified in populations of European ancestry (EA), with African Americans (AA), Hispanics/Latinos (HL), and other races/ethnicities being severely underrepresented. RESULTS We performed ancestry-combined and ancestry-specific genome-wide association studies (GWAS) for white blood cell and platelet traits in the ancestrally diverse Population Architecture using Genomics and Epidemiology (PAGE) Study, including 16,201 AA, 21,347 HL, and 27,236 EA participants. We identified six novel findings at suggestive significance (P < 5E-8), which need confirmation, and independent signals at six previously established regions at genome-wide significance (P < 2E-9). We confirmed multiple previously reported genome-wide significant variants in the single variant association analysis and multiple genes using PrediXcan. Evaluation of loci reported from a Euro-centric GWAS indicated attenuation of effect estimates in AA and HL compared to EA populations. CONCLUSIONS Our results highlighted the potential to identify ancestry-specific and ancestry-agnostic variants in participants with diverse backgrounds and advocate for continued efforts in improving inclusion of racially/ethnically diverse populations in genetic association studies for complex traits.
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Affiliation(s)
- Yao Hu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Katherine K Nishimura
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jeffrey Haessler
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chani J Hodonsky
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Antoine R Baldassari
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | | | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- The Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Quan Sun
- Department of Biostatistics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ming-Huei Chen
- The Framingham Heart Study, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA
| | - Abdou Mousas
- Montreal Heart Institute, Montreal, Quebec, Canada
| | - Paul L Auer
- School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montreal, Quebec, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Weihong Tang
- School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Lihong Qi
- School of Medicine, University of California Davis, Davis, CA, USA
| | | | - Steve Buyske
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, NJ, USA
| | - Myriam Fornage
- Brown Foundation Institute for Molecular Medicine, the University of Texas Health Science Center, Houston, TX, USA
| | - Lucia A Hindorff
- Division of Genomic Medicine, NIH National Human Genome Research Institute, Bethesda, MD, USA
| | - Yun Li
- Department of Biostatistics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Danyu Lin
- Department of Biostatistics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexander P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura M Raffield
- Department of Genetics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christy L Avery
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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10
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Hu Y, Stilp AM, McHugh CP, Rao S, Jain D, Zheng X, Lane J, Méric de Bellefon S, Raffield LM, Chen MH, Yanek LR, Wheeler M, Yao Y, Ren C, Broome J, Moon JY, de Vries PS, Hobbs BD, Sun Q, Surendran P, Brody JA, Blackwell TW, Choquet H, Ryan K, Duggirala R, Heard-Costa N, Wang Z, Chami N, Preuss MH, Min N, Ekunwe L, Lange LA, Cushman M, Faraday N, Curran JE, Almasy L, Kundu K, Smith AV, Gabriel S, Rotter JI, Fornage M, Lloyd-Jones DM, Vasan RS, Smith NL, North KE, Boerwinkle E, Becker LC, Lewis JP, Abecasis GR, Hou L, O'Connell JR, Morrison AC, Beaty TH, Kaplan R, Correa A, Blangero J, Jorgenson E, Psaty BM, Kooperberg C, Walton RT, Kleinstiver BP, Tang H, Loos RJF, Soranzo N, Butterworth AS, Nickerson D, Rich SS, Mitchell BD, Johnson AD, Auer PL, Li Y, Mathias RA, Lettre G, Pankratz N, Laurie CC, Laurie CA, Bauer DE, Conomos MP, Reiner AP. Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program. Am J Hum Genet 2021; 108:874-893. [PMID: 33887194 DOI: 10.1016/j.ajhg.2021.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Whole-genome sequencing (WGS), a powerful tool for detecting novel coding and non-coding disease-causing variants, has largely been applied to clinical diagnosis of inherited disorders. Here we leveraged WGS data in up to 62,653 ethnically diverse participants from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program and assessed statistical association of variants with seven red blood cell (RBC) quantitative traits. We discovered 14 single variant-RBC trait associations at 12 genomic loci, which have not been reported previously. Several of the RBC trait-variant associations (RPN1, ELL2, MIDN, HBB, HBA1, PIEZO1, and G6PD) were replicated in independent GWAS datasets imputed to the TOPMed reference panel. Most of these discovered variants are rare/low frequency, and several are observed disproportionately among non-European Ancestry (African, Hispanic/Latino, or East Asian) populations. We identified a 3 bp indel p.Lys2169del (g.88717175_88717177TCT[4]) (common only in the Ashkenazi Jewish population) of PIEZO1, a gene responsible for the Mendelian red cell disorder hereditary xerocytosis (MIM: 194380), associated with higher mean corpuscular hemoglobin concentration (MCHC). In stepwise conditional analysis and in gene-based rare variant aggregated association analysis, we identified several of the variants in HBB, HBA1, TMPRSS6, and G6PD that represent the carrier state for known coding, promoter, or splice site loss-of-function variants that cause inherited RBC disorders. Finally, we applied base and nuclease editing to demonstrate that the sentinel variant rs112097551 (nearest gene RPN1) acts through a cis-regulatory element that exerts long-range control of the gene RUVBL1 which is essential for hematopoiesis. Together, these results demonstrate the utility of WGS in ethnically diverse population-based samples and gene editing for expanding knowledge of the genetic architecture of quantitative hematologic traits and suggest a continuum between complex trait and Mendelian red cell disorders.
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Affiliation(s)
- Yao Hu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98105, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Shuquan Rao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - John Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | | | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Yao Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Chunyan Ren
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Jai Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94601, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Nancy Heard-Costa
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nancy Min
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Lynette Ekunwe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mary Cushman
- Department of Medicine, Larner College of Medicine at the University of Vermont, Burlington, VT 05405, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia and Department of Genetics University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kousik Kundu
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK
| | - Albert V Smith
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | | | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | | | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Departments of Cardiology and Preventive Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98105, USA; Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98105, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lewis C Becker
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Lifang Hou
- Northwestern University, Chicago, IL 60208, USA
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Terri H Beaty
- School of Public Health, John Hopkins University, Baltimore, MD 21205, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94601, USA
| | - Bruce M Psaty
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98105, USA; Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98105, USA
| | - Russell T Walton
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole Soranzo
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Department of Human Genetics, Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge CB1 8RN, UK
| | - Debbie Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53205, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MA 21205, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; Faculté de Médecine, Université de Montréal, Montréal, QC H1T 1C8, Canada
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA.
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11
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Choudhuri A, Trompouki E, Abraham BJ, Colli LM, Kock KH, Mallard W, Yang ML, Vinjamur DS, Ghamari A, Sporrij A, Hoi K, Hummel B, Boatman S, Chan V, Tseng S, Nandakumar SK, Yang S, Lichtig A, Superdock M, Grimes SN, Bowman TV, Zhou Y, Takahashi S, Joehanes R, Cantor AB, Bauer DE, Ganesh SK, Rinn J, Albert PS, Bulyk ML, Chanock SJ, Young RA, Zon LI. Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits. Nat Genet 2020; 52:1333-1345. [PMID: 33230299 DOI: 10.1038/s41588-020-00738-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/14/2020] [Indexed: 12/13/2022]
Abstract
Genome-wide association studies identify genomic variants associated with human traits and diseases. Most trait-associated variants are located within cell-type-specific enhancers, but the molecular mechanisms governing phenotypic variation are less well understood. Here, we show that many enhancer variants associated with red blood cell (RBC) traits map to enhancers that are co-bound by lineage-specific master transcription factors (MTFs) and signaling transcription factors (STFs) responsive to extracellular signals. The majority of enhancer variants reside on STF and not MTF motifs, perturbing DNA binding by various STFs (BMP/TGF-β-directed SMADs or WNT-induced TCFs) and affecting target gene expression. Analyses of engineered human blood cells and expression quantitative trait loci verify that disrupted STF binding leads to altered gene expression. Our results propose that the majority of the RBC-trait-associated variants that reside on transcription-factor-binding sequences fall in STF target sequences, suggesting that the phenotypic variation of RBC traits could stem from altered responsiveness to extracellular stimuli.
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Affiliation(s)
- Avik Choudhuri
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Eirini Trompouki
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,CIBSS Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Leandro M Colli
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, MD, USA.,Department of Medical Imaging, Hematology, and Medical Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Kian Hong Kock
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
| | - William Mallard
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Min-Lee Yang
- Division of Cardiovascular Medicine, Department of Internal Medicine and Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Divya S Vinjamur
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alireza Ghamari
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Audrey Sporrij
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Karen Hoi
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Barbara Hummel
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Sonja Boatman
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Victoria Chan
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Sierra Tseng
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Satish K Nandakumar
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Song Yang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Asher Lichtig
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Michael Superdock
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Seraj N Grimes
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Summer Institute in Biomedical Informatics, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Teresa V Bowman
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yi Zhou
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | | | - Roby Joehanes
- Hebrew Senior Life, Harvard Medical School, Boston, MA, USA.,Framingham Heart Study, National Heart, Blood, and Lung Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alan B Cantor
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Santhi K Ganesh
- Division of Cardiovascular Medicine, Department of Internal Medicine and Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - John Rinn
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Paul S Albert
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA.,The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Summer Institute in Biomedical Informatics, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leonard I Zon
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. .,Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA.
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12
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Semenova EA, Miyamoto-Mikami E, Akimov EB, Al-Khelaifi F, Murakami H, Zempo H, Kostryukova ES, Kulemin NA, Larin AK, Borisov OV, Miyachi M, Popov DV, Boulygina EA, Takaragawa M, Kumagai H, Naito H, Pushkarev VP, Dyatlov DA, Lekontsev EV, Pushkareva YE, Andryushchenko LB, Elrayess MA, Generozov EV, Fuku N, Ahmetov II. The association of HFE gene H63D polymorphism with endurance athlete status and aerobic capacity: novel findings and a meta-analysis. Eur J Appl Physiol 2020; 120:665-673. [PMID: 31970519 PMCID: PMC7042188 DOI: 10.1007/s00421-020-04306-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/16/2020] [Indexed: 12/04/2022]
Abstract
PURPOSE Iron is an important component of the oxygen-binding proteins and may be critical to optimal athletic performance. Previous studies have suggested that the G allele of C/G rare variant (rs1799945), which causes H63D amino acid replacement, in the HFE is associated with elevated iron indexes and may give some advantage in endurance-oriented sports. The aim of the present study was to investigate the association between the HFE H63D polymorphism and elite endurance athlete status in Japanese and Russian populations, aerobic capacity and to perform a meta-analysis using current findings and three previous studies. METHODS The study involved 315 international-level endurance athletes (255 Russian and 60 Japanese) and 809 healthy controls (405 Russian and 404 Japanese). Genotyping was performed using micro-array analysis or by PCR. VO2max in 46 male Russian endurance athletes was determined using gas analysis system. RESULTS The frequency of the iron-increasing CG/GG genotypes was significantly higher in Russian (38.0 vs 24.9%; OR 1.85, P = 0.0003) and Japanese (13.3 vs 5.0%; OR 2.95, P = 0.011) endurance athletes compared to ethnically matched controls. The meta-analysis using five cohorts (two French, Japanese, Spanish, and Russian; 586 athletes and 1416 controls) showed significant prevalence of the CG/GG genotypes in endurance athletes compared to controls (OR 1.96, 95% CI 1.58-2.45; P = 1.7 × 10-9). Furthermore, the HFE G allele was associated with high V̇O2max in male athletes [CC: 61.8 (6.1), CG/GG: 66.3 (7.8) ml/min/kg; P = 0.036]. CONCLUSIONS We have shown that the HFE H63D polymorphism is strongly associated with elite endurance athlete status, regardless ethnicities and aerobic capacity in Russian athletes.
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Affiliation(s)
- Ekaterina A. Semenova
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Department of Biochemistry, Kazan Federal University, Kazan, Russia
| | - Eri Miyamoto-Mikami
- Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
| | | | - Fatima Al-Khelaifi
- Anti Doping Laboratory Qatar, Sports City, Doha, Qatar
- UCL-Medical School, Royal Free Campus, London, UK
| | - Haruka Murakami
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, NIBIOHN, Tokyo, Japan
| | - Hirofumi Zempo
- Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
- Faculty of Health and Nutrition, Tokyo Seiei College, Tokyo, Japan
| | - Elena S. Kostryukova
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Nikolay A. Kulemin
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Andrey K. Larin
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Oleg V. Borisov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Motohiko Miyachi
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, NIBIOHN, Tokyo, Japan
| | - Daniil V. Popov
- Laboratory of Exercise Physiology, Institute for Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | | | - Mizuki Takaragawa
- Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
| | - Hiroshi Kumagai
- Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
- Research Fellow of Japanese Society for the Promotion of Science, Tokyo, Japan
| | - Hisashi Naito
- Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
| | - Vladimir P. Pushkarev
- Medical Genetic Centre “Progen”, Moscow, Russia
- Moscow Center of Advanced Sport Technologies, Moscow, Russia
- Department of the Theory of Physical Culture and Biomechanics, Ural State University of Physical Culture, Chelyabinsk, Russia
| | - Dmitry A. Dyatlov
- Department of the Theory of Physical Culture and Biomechanics, Ural State University of Physical Culture, Chelyabinsk, Russia
| | - Eugene V. Lekontsev
- Methodical and Analytical Department, Regional Center for Sports Training, Chelyabinsk, Russia
- Research Institute of Olympic Sports, Ural State University of Physical Culture, Chelyabinsk, Russia
| | - Yuliya E. Pushkareva
- Department of Pediatrics, South Ural State Medical University, Chelyabinsk, Russia
| | | | | | - Edward V. Generozov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Noriyuki Fuku
- Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
| | - Ildus I. Ahmetov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Department of Physical Education, Plekhanov Russian University of Economics, Moscow, Russia
- Laboratory of Molecular Genetics, Kazan State Medical University, Kazan, Russia
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Byrom St, Liverpool, L3 5AF UK
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13
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Critchley WR, Reid A, Morris J, Naish JH, Stone JP, Ball AL, Major T, Clark D, Waldron N, Fortune C, Lagan J, Lewis GA, Ainslie M, Schelbert EB, Davis DM, Schmitt M, Fildes JE, Miller CA. The effect of 1.5 T cardiac magnetic resonance on human circulating leucocytes. Eur Heart J 2019; 39:305-312. [PMID: 29165554 DOI: 10.1093/eurheartj/ehx646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/20/2017] [Indexed: 12/25/2022] Open
Abstract
Aims Investigators have proposed that cardiovascular magnetic resonance (CMR) should have restrictions similar to those of ionizing imaging techniques. We aimed to investigate the acute effect of 1.5 T CMR on leucocyte DNA integrity, cell counts, and function in vitro, and in a large cohort of patients in vivo. Methods and results In vitro study: peripheral blood mononuclear cells (PBMCs) were isolated from healthy volunteers, and histone H2AX phosphorylation (γ-H2AX) expression, leucocyte counts, and functional parameters were quantified using flow cytometry under the following conditions: (i) immediately following PBMC isolation, (ii) after standing on the benchside as a temperature and time control, (iii) after a standard CMR scan. In vivo study: blood samples were taken from 64 consecutive consenting patients immediately before and after a standard clinical scan. Samples were analysed for γ-H2AX expression and leucocyte counts. CMR was not associated with a significant change in γ-H2AX expression in vitro or in vivo, although there were significant inter-patient variations. In vitro cell integrity and function did not change with CMR. There was a significant reduction in circulating T cells in vivo following CMR. Conclusion 1.5 T CMR was not associated with DNA damage in vitro or in vivo. Histone H2AX phosphorylation expression varied markedly between individuals; therefore, small studies using γ-H2AX as a marker of DNA damage should be interpreted with caution. Cardiovascular magnetic resonance was not associated with loss of leucocyte viability or function in vitro. Cardiovascular magnetic resonance was associated with a statistically significant reduction in viable leucocytes in vivo.
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Affiliation(s)
- William R Critchley
- Manchester Collaborative Centre for Inflammation Research (MCCIR), Division of Infection, Immunity and Respiratory Research, School of Biology, Medicine and Health, Manchester Academic Health Science Centre, Room 2.12 Core Technology Facility, Grafton Street, University of Manchester, M13 9NT Manchester, UK.,The Transplant Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Anna Reid
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK.,Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 3rd Floor-Core Technology Facility, 46 Grafton Street, M13 9PL Manchester UK
| | - Julie Morris
- Department of Medical Statistics, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Josephine H Naish
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 3rd Floor-Core Technology Facility, 46 Grafton Street, M13 9PL Manchester UK
| | - John P Stone
- Manchester Collaborative Centre for Inflammation Research (MCCIR), Division of Infection, Immunity and Respiratory Research, School of Biology, Medicine and Health, Manchester Academic Health Science Centre, Room 2.12 Core Technology Facility, Grafton Street, University of Manchester, M13 9NT Manchester, UK.,The Transplant Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Alexandra L Ball
- Manchester Collaborative Centre for Inflammation Research (MCCIR), Division of Infection, Immunity and Respiratory Research, School of Biology, Medicine and Health, Manchester Academic Health Science Centre, Room 2.12 Core Technology Facility, Grafton Street, University of Manchester, M13 9NT Manchester, UK.,The Transplant Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Triin Major
- Manchester Collaborative Centre for Inflammation Research (MCCIR), Division of Infection, Immunity and Respiratory Research, School of Biology, Medicine and Health, Manchester Academic Health Science Centre, Room 2.12 Core Technology Facility, Grafton Street, University of Manchester, M13 9NT Manchester, UK.,The Transplant Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - David Clark
- Wythenshawe Alliance Medical Cardiac MRI Unit, Wythenshawe Hospital, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Nick Waldron
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Christien Fortune
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 3rd Floor-Core Technology Facility, 46 Grafton Street, M13 9PL Manchester UK
| | - Jakub Lagan
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK.,Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 3rd Floor-Core Technology Facility, 46 Grafton Street, M13 9PL Manchester UK
| | - Gavin A Lewis
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK.,Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 3rd Floor-Core Technology Facility, 46 Grafton Street, M13 9PL Manchester UK
| | - Mark Ainslie
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Erik B Schelbert
- Department of Medicine, University of Pittsburgh School of Medicine, 3550 Terrace St, Pittsburgh, PA 15213, USA.,Cardiovascular Magnetic Resonance Center, UPMC, 200 Lothrop St., Pittsburgh, PA 15213, USA
| | - Daniel M Davis
- Manchester Collaborative Centre for Inflammation Research (MCCIR), Division of Infection, Immunity and Respiratory Research, School of Biology, Medicine and Health, Manchester Academic Health Science Centre, Room 2.12 Core Technology Facility, Grafton Street, University of Manchester, M13 9NT Manchester, UK
| | - Matthias Schmitt
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - James E Fildes
- Manchester Collaborative Centre for Inflammation Research (MCCIR), Division of Infection, Immunity and Respiratory Research, School of Biology, Medicine and Health, Manchester Academic Health Science Centre, Room 2.12 Core Technology Facility, Grafton Street, University of Manchester, M13 9NT Manchester, UK.,The Transplant Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Christopher A Miller
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK.,Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 3rd Floor-Core Technology Facility, 46 Grafton Street, M13 9PL Manchester UK.,Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biology, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, M13 9PT Manchester, UK
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14
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Ma X, Jia C, Fu D, Chu M, Ding X, Wu X, Guo X, Pei J, Bao P, Liang C, Yan P. Analysis of Hematological Traits in Polled Yak by Genome-Wide Association Studies Using Individual SNPs and Haplotypes. Genes (Basel) 2019; 10:E463. [PMID: 31212963 PMCID: PMC6627507 DOI: 10.3390/genes10060463] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 12/21/2022] Open
Abstract
Yak (Bos grunniens) is an important domestic animal living in high-altitude plateaus. Due to inadequate disease prevention, each year, the yak industry suffers significant economic losses. The identification of causal genes that affect blood- and immunity-related cells could provide preliminary reference guidelines for the prevention of diseases in the population of yaks. The genome-wide association studies (GWASs) utilizing a single-marker or haplotype method were employed to analyze 15 hematological traits in the genome of 315 unrelated yaks. Single-marker GWASs identified a total of 43 significant SNPs, including 35 suggestive and eight genome-wide significant SNPs, associated with nine traits. Haplotype analysis detected nine significant haplotype blocks, including two genome-wide and seven suggestive blocks, associated with seven traits. The study provides data on the genetic variability of hematological traits in the yak. Five essential genes (GPLD1, EDNRA,APOB, HIST1H1E, and HIST1H2BI) were identified, which affect the HCT, HGB, RBC, PDW, PLT, and RDWSD traits and can serve as candidate genes for regulating hematological traits. The results provide a valuable reference to be used in the analysis of blood properties and immune diseases in the yak.
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Affiliation(s)
- Xiaoming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Congjun Jia
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Donghai Fu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Xuezhi Ding
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Jie Pei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Chunnian Liang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
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15
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Tarr IS, McCann EP, Benyamin B, Peters TJ, Twine NA, Zhang KY, Zhao Q, Zhang ZH, Rowe DB, Nicholson GA, Bauer D, Clark SJ, Blair IP, Williams KL. Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression. Sci Rep 2019; 9:8254. [PMID: 31164693 PMCID: PMC6547746 DOI: 10.1038/s41598-019-44765-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/23/2019] [Indexed: 12/02/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterised by the loss of upper and lower motor neurons. ALS exhibits high phenotypic variability including age and site of onset, and disease duration. To uncover epigenetic and transcriptomic factors that may modify an ALS phenotype, we used a cohort of Australian monozygotic twins (n = 3 pairs) and triplets (n = 1 set) that are discordant for ALS and represent sporadic ALS and the two most common types of familial ALS, linked to C9orf72 and SOD1. Illumina Infinium HumanMethylation450K BeadChip, EpiTYPER and RNA-Seq analyses in these ALS-discordant twins/triplets and control twins (n = 2 pairs), implicated genes with consistent longitudinal differential DNA methylation and/or gene expression. Two identified genes, RAD9B and C8orf46, showed significant differential methylation in an extended cohort of >1000 ALS cases and controls. Combined longitudinal methylation-transcription analysis within a single twin set implicated CCNF, DPP6, RAMP3, and CCS, which have been previously associated with ALS. Longitudinal transcriptome data showed an 8-fold enrichment of immune function genes and under-representation of transcription and protein modification genes in ALS. Examination of these changes in a large Australian sporadic ALS cohort suggest a broader role in ALS. Furthermore, we observe that increased methylation age is a signature of ALS in older patients.
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Affiliation(s)
- Ingrid S Tarr
- Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Emily P McCann
- Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Beben Benyamin
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, School of Health Sciences, University of South Australia, Adelaide, Australia.,South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Timothy J Peters
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Natalie A Twine
- Health and Biosecurity Business Unit, Commonwealth Scientific and Industrial Research Organisation, Sydney, New South Wales, Australia
| | - Katharine Y Zhang
- Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Qiongyi Zhao
- Queensland Brain Institute, University of Queensland, Queensland, Australia
| | - Zong-Hong Zhang
- Queensland Brain Institute, University of Queensland, Queensland, Australia
| | - Dominic B Rowe
- Department of Clinical Medicine, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Garth A Nicholson
- ANZAC Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Molecular Medicine Laboratory, Concord Hospital, Sydney, New South Wales, Australia
| | - Denis Bauer
- Health and Biosecurity Business Unit, Commonwealth Scientific and Industrial Research Organisation, Sydney, New South Wales, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,St Vincent's Clinical School, UNSW Sydney, New South Wales, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia.
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16
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Ittermann T, Feig MA, Petersmann A, Radke D, Greinacher A, Völzke H, Thiele T. Mean platelet volume is more important than age for defining reference intervals of platelet counts. PLoS One 2019; 14:e0213658. [PMID: 30870494 PMCID: PMC6417788 DOI: 10.1371/journal.pone.0213658] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/26/2019] [Indexed: 12/11/2022] Open
Abstract
Background Platelet count is known to be associated with sex, age and mean platelet volume (MPV). Sex and age were proposed for adjustment of platelet count reference intervals, but MPV is currently not used for further adjustment. We investigated the association of MPV, age and sex with platelet counts and established individualized reference ranges respecting MPV. Methods The association of platelet count with age, sex and MPV was assessed in healthy participants (n = 3,033 individuals; 1,542 women) in the cross-sectional population-based cohort Study of Health in Pomerania. Reference intervals respecting age, sex, and MPV were estimated using quantile regressions for the 2.5th and 97.5th percentile. Results Women had higher platelet counts than men (239 vs. 207 x109/L, p<0.001). Platelet counts correlated with age (p<0.001) and MPV (p<0.001). Quantile regression of lower and upper platelet count limits correlated less with age in female (p = 0.047 for 2.5th percentile; p = 0.906 for 97.5th percentile) and male subjects (p = 0.029 for 2.5th percentile; p = 0.195 for 97.5th percentile) compared to MPV (p<0.001 for upper and lower limit for both sexes). After adjustment for MPV, age did no longer correlate with the 2.5th (p = 0.165) or 97.5th percentile (p = 0.999) of platelet count. In contrast, after adjustment for age, MPV levels still significantly correlated with 2.5th, 50th and 97.5th percentile (p<0.001). Conclusion MPV and sex have a stronger association with platelet count than age. MPV should be considered to adjust platelet count reference intervals and needs to be respected as confounder for platelet counts in epidemiological studies and clinical practice.
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Affiliation(s)
- Till Ittermann
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- * E-mail:
| | - Martin A. Feig
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Astrid Petersmann
- Institute for Clinical Chemistry and Laboratory Medicine; University Medicine Greifswald, Greifswald, Germany
| | - Dörte Radke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Andreas Greinacher
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Thomas Thiele
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
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17
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Yan G, Guo T, Xiao S, Zhang F, Xin W, Huang T, Xu W, Li Y, Zhang Z, Huang L. Imputation-Based Whole-Genome Sequence Association Study Reveals Constant and Novel Loci for Hematological Traits in a Large-Scale Swine F 2 Resource Population. Front Genet 2018; 9:401. [PMID: 30405681 PMCID: PMC6204663 DOI: 10.3389/fgene.2018.00401] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 09/03/2018] [Indexed: 11/13/2022] Open
Abstract
The whole-genome sequences of progenies with low-density single-nucleotide polymorphism (SNP) genotypes can be imputed with high accuracy based on the deep-coverage sequences of key ancestors. With this imputation technology, a more powerful genome-wide association study (GWAS) can be carried out using imputed whole-genome variants and the phenotypes of interest to overcome the shortcomings of low-power detection and the large confidence interval derived from low-density SNP markers in classic association studies. In this study, 19 ancestors of a large-scale swine F2 White Duroc × Erhualian population were deeply sequenced for their genome with an average coverage of 25×. Considering 98 pigs from 10 different breeds with high-quality deep sequenced genomes, we imputed the whole genomic variants of 1020 F2 pigs genotyped by the PorcineSNP60 BeadChip with high accuracy and obtained 14,851,440 sequence variants after quality control. Based on this, 87 novel quantitative traits loci (QTLs) for 18 hematological traits at three different physiological stages of the F2 pigs were identified, among which most of the novel QTLs have been repeated in two of the three stages. Literature mining pinpointed that the FGF14 and LCLAT1 genes at SSC11 and SSC3 may affect the MCH at day 240 and MCV at day 18, respectively. The present study shows that combining high-quality imputed genomic variants and correlated phenomic traits into GWAS can improve the capability to detect QTL considerably. The large number of different QTLs for hematological traits identified at multiple growth stages implies the complexity and time specificity of these traits.
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Affiliation(s)
- Guorong Yan
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Tianfu Guo
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Feng Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Wenshui Xin
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Tao Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Wenwu Xu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yiping Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Zhiyan Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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18
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Jo Hodonsky C, Schurmann C, Schick UM, Kocarnik J, Tao R, van Rooij FJ, Wassel C, Buyske S, Fornage M, Hindorff LA, Floyd JS, Ganesh SK, Lin DY, North KE, Reiner AP, Loos RJ, Kooperberg C, Avery CL. Generalization and fine mapping of red blood cell trait genetic associations to multi-ethnic populations: The PAGE Study. Am J Hematol 2018; 93:10.1002/ajh.25161. [PMID: 29905378 PMCID: PMC6300146 DOI: 10.1002/ajh.25161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022]
Abstract
Red blood cell (RBC) traits provide insight into a wide range of physiological states and exhibit moderate to high heritability, making them excellent candidates for genetic studies to inform underlying biologic mechanisms. Previous RBC trait genome-wide association studies were performed primarily in European- or Asian-ancestry populations, missing opportunities to inform understanding of RBC genetic architecture in diverse populations and reduce intervals surrounding putative functional SNPs through fine-mapping. Here, we report the first fine-mapping of six correlated (Pearson's r range: |0.04 - 0.92|) RBC traits in up to 19,036 African Americans and 19,562 Hispanic/Latinos participants of the Population Architecture using Genomics and Epidemiology (PAGE) consortium. Trans-ethnic meta-analysis of race/ethnic- and study-specific estimates for approximately 11,000 SNPs flanking 13 previously identified association signals as well as 150,000 additional array-wide SNPs was performed using inverse-variance meta-analysis after adjusting for study and clinical covariates. Approximately half of previously reported index SNP-RBC trait associations generalized to the trans-ethnic study population (p<1.7x10-4 ); previously unreported independent association signals within the ABO region reinforce the potential for multiple functional variants affecting the same locus. Trans-ethnic fine-mapping did not reveal additional signals at the HFE locus independent of the known functional variants. Finally, we identified a potential novel association in the Hispanic/Latino study population at the HECTD4/RPL6 locus for RBC count (p=1.9x10-7 ). The identification of a previously unknown association, generalization of a large proportion of known association signals, and refinement of known association signals all exemplify the benefits of genetic studies in diverse populations. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Chani Jo Hodonsky
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ursula M Schick
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jonathan Kocarnik
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Frank Ja van Rooij
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3000, the Netherlands
| | - Christina Wassel
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT
| | - Steve Buyske
- Department of Statistics and Biostatistics, Hill Center, Rutgers, The State University of New Jersey, 110 Frelinghuysen Rd. Piscataway, NY
| | - Myriam Fornage
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National institutes of Health, Bethesda, MD
| | - James S Floyd
- Departments of Medicine, University of Washington, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Santhi K Ganesh
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI
| | - Dan-Yu Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC
| | - Kari E North
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Ruth Jf Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC
- Carolina Population Center, University of North Carolina, Chapel Hill, NC
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19
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Anabire NG, Aryee PA, Addo F, Anaba F, Kanwugu ON, Ankrah J, Awandare GA, Helegbe GK. Evaluation of hematological indices of childhood illnesses in Tamale Metropolis of Ghana. J Clin Lab Anal 2018; 32:e22582. [PMID: 29862574 DOI: 10.1002/jcla.22582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 05/13/2018] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Although hematological indices cannot in entirety be used to diagnose diseases or defects, the appropriate interpretation of these indices could complement diagnostics such as microscopy and serology for numerous illnesses in children. This study sought to evaluate distinct hematological indices characterizing different childhood illnesses. METHODS Full blood counts from 150 children (age range from 1 to 15 year) presenting different disease conditions at the Tamale Central Hospital were assessed. The hematological indices were compared between disease categories, and relationships between disease indicators were determined. RESULTS The prevalence of the diagnosed childhood illness were: 50.7% malaria, 20.0% diarrhea, 13.3% typhoid fever, 10.0% Sickle Cell Disease (SCD), and 6.0% malaria-typhoid co-infection. Fever was diagnosed in a majority (66.0%) of the children, but was independent of each disease group, (χ2 = 9.18, P = .057). Of the 24 hematological indices analyzed, eight; red blood cell (RBC) (P < .001), hemoglobin (Hb) (P < .001), mean cell volume (MCV) (P = .002), mean cell hemoglobin (MCH) (P < .001; lowest and below normal range for SCD), red cell distribution width (RDW_CV) (P < .001), eosinophil percentage [EOS (%)] (P = .001), eosinophil number [EOS#] (P = .002), and platelets (PLT) (P = .001; lowest for malaria) differed significantly across the different disease groups. Levels of Hb and/or MCV were below the normal reference ranges for most of the diagnosed diseases. In addition, low PLT and MCH were respectively distinct for children with malaria and SCD. CONCLUSION Hematological indices including Hb, MCV and PLT, or MCH may be useful indices that could incite further diagnostic tests for malaria or SCD among children in Ghana.
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Affiliation(s)
- Nsoh Godwin Anabire
- Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, University for development studies, Tamale, Ghana.,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.,Department of Biochemistry, Cell & Molecular Biology, University of Ghana, Accra, Ghana
| | - Paul Armah Aryee
- Department of Nutritional Sciences, School of Allied Health Sciences, University for Development Studies, Tamale, Ghana
| | - Francis Addo
- Department of Applied Chemistry & Biochemistry, University for Development Studies, Navrongo, Ghana
| | - Frank Anaba
- Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, University for development studies, Tamale, Ghana
| | - Osman Nabayire Kanwugu
- Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, University for development studies, Tamale, Ghana
| | - Jacob Ankrah
- Department of Hematology, Tamale Central Hospital, Tamale, Ghana
| | - Gordon Akanzuwine Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.,Department of Biochemistry, Cell & Molecular Biology, University of Ghana, Accra, Ghana
| | - Gideon Kofi Helegbe
- Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, University for development studies, Tamale, Ghana.,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
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20
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Botzman M, Gat-Viks I. Significant common environmental effects on leukocyte subpopulations. PLoS One 2018; 13:e0196193. [PMID: 29689083 PMCID: PMC5915319 DOI: 10.1371/journal.pone.0196193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 04/09/2018] [Indexed: 11/19/2022] Open
Abstract
Major efforts are invested in the analysis of phenotypic variation in a population of individuals. While many of these studies focus on the genetic basis of phenotypic variation via measurements of DNA polymorphic sites, the environmental effects are still elusive. Here we propose a methodology, called CCCE ('Cell Composition Common Environment'), to identify environmental effects on the composition of immune cell functionalities. Specifically, CCCE is focused on the common experiences that are shared between siblings (the 'common environment'), designed to correct for cell subpopulation heterogeneity, and is based on a multicolor flow cytometry analysis across a large cohort of human monozygotic and dizygotic twins. We demonstrate that the CCCE methodology can provide insights on the relations between common environmental effects and the heterogenic functions of several immune cell types, such as NK cells effector functions and coagulation-related capabilities of monocytes. The software described in this article is available at http://csgi.tau.ac.il/CCCE.
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Affiliation(s)
- Maya Botzman
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Irit Gat-Viks
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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21
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Charles BA, Hsieh MM, Adeyemo AA, Shriner D, Ramos E, Chin K, Srivastava K, Zakai NA, Cushman M, McClure LA, Howard V, Flegel WA, Rotimi CN, Rodgers GP. Analyses of genome wide association data, cytokines, and gene expression in African-Americans with benign ethnic neutropenia. PLoS One 2018; 13:e0194400. [PMID: 29596498 PMCID: PMC5875757 DOI: 10.1371/journal.pone.0194400] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/04/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Benign ethnic neutropenia (BEN) is a hematologic condition associated with people of African ancestry and specific Middle Eastern ethnic groups. Prior genetic association studies in large population showed that rs2814778 in Duffy Antigen Receptor for Chemokines (DARC) gene, specifically DARC null red cell phenotype, was associated with BEN. However, the mechanism of this red cell phenotype leading to low white cell count remained elusive. METHODS We conducted an extreme phenotype design genome-wide association study (GWAS), analyzed ~16 million single nucleotide polymorphisms (SNP) in 1,178 African-Americans individuals from the Reasons for Geographic and Racial Differences in Stroke (REGARDS) study and replicated from 819 African-American participants in the Atherosclerosis Risk in Communities (ARIC) study. Conditional analyses on rs2814778 were performed to identify additional association signals on chromosome 1q22. In a separate cohort of healthy individuals with and without BEN, whole genome gene expression from peripheral blood neutrophils were analyzed for DARC. RESULTS We confirmed that rs2814778 in DARC was associated with BEN (p = 4.09×10-53). Conditioning on rs2814778 abolished other significant chromosome 1 associations. Inflammatory cytokines (IL-2, 6, and 10) in participants in the Howard University Family Study (HUFS) and Multi-Ethnic Study in Atherosclerosis (MESA) showed similar levels in individuals homozygous for the rs2814778 allele compared to others, indicating cytokine sink hypothesis played a minor role in leukocyte homeostasis. Gene expression in neutrophils of individuals with and without BEN was also similar except for low DARC expression in BEN, suggesting normal function. BEN neutrophils had slightly activated profiles in leukocyte migration and hematopoietic stem cell mobilization pathways (expression fold change <2). CONCLUSIONS These results in humans support the notion of DARC null erythroid progenitors preferentially differentiating to myeloid cells, leading to activated DARC null neutrophils egressing from circulation to the spleen, and causing relative neutropenia. Collectively, these human data sufficiently explained the mechanism DARC null red cell phenotype causing BEN and further provided a biologic basis that BEN is clinically benign.
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Affiliation(s)
- Bashira A. Charles
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Matthew M. Hsieh
- Molecular and Clinical Hematology Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, United States of America
| | - Adebowale A. Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Edward Ramos
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
- National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, Maryland, United States of America
| | - Kyung Chin
- Molecular and Clinical Hematology Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, United States of America
| | - Kshitij Srivastava
- Warren Grant Magnuson Clinical Center, NIH, Bethesda, Maryland, United States of America
| | - Neil A. Zakai
- Departments of Pathology and Medicine, University of Vermont Larner College of Medicine, Burlington, Vermont, United States of America
| | - Mary Cushman
- Departments of Pathology and Medicine, University of Vermont Larner College of Medicine, Burlington, Vermont, United States of America
| | - Leslie A. McClure
- School of Public Health, University of Alabama, Birmingham, Alabama, United States of America
- Department of Epidemiology and Biostatistics, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Virginia Howard
- School of Public Health, University of Alabama, Birmingham, Alabama, United States of America
| | - Willy A. Flegel
- Warren Grant Magnuson Clinical Center, NIH, Bethesda, Maryland, United States of America
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
- * E-mail: (CNR); (GPR)
| | - Griffin P. Rodgers
- Molecular and Clinical Hematology Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, United States of America
- * E-mail: (CNR); (GPR)
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Abstract
Recent progress in both conceptual and technological approaches to human immunology have rejuvenated a field that has long been in the shadow of the inbred mouse model. This is a healthy development both for the clinical relevance of immunology and for the fact that it is a way to gain access to the wealth of phenomenology in the many human diseases that involve the immune system. This is where we are likely to discover new immunological mechanisms and principals, especially those involving genetic heterogeneity or environmental influences that are difficult to model effectively in inbred mice. We also suggest that there are likely to be novel immunological mechanisms in long-lived, less fecund mammals such as human beings since they must remain healthy far longer than short-lived rodents in order for the species to survive.
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Affiliation(s)
- Mark M Davis
- Department of Microbiology and Immunology, The Howard Hughes Medical Institute, and the Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Petter Brodin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17121 Solna, Sweden.,Department of Neonatology, Karolinska University Hospital, 17176 Solna, Sweden
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23
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Siraj N, Issac J, Anwar M, Mehari Y, Russom S, Kahsay S, Frezghi H. Establishment of hematological reference intervals for healthy adults in Asmara. BMC Res Notes 2018; 11:55. [PMID: 29357920 PMCID: PMC5778762 DOI: 10.1186/s13104-018-3142-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 01/09/2018] [Indexed: 11/16/2022] Open
Abstract
Objectives Clinical laboratory reference intervals used in a specific area should be derived from the local population as they are influenced by many factors. The purpose of this quantitative cross sectional study was to establish hematological reference intervals for healthy adults in Asmara and to determine whether the currently used reference interval do represent the adult population in the city. In addition, the established reference intervals were compared to findings from similar studies conducted in selected countries in Africa. Results There was a significant difference between males and females in the reference intervals for erythrocyte count, hemoglobin, hematocrit, mean cell volume, mean cell hemoglobin, mean cell hemoglobin concentration and differential white blood cell count. All the evaluated hematological analytes were found to be higher in males than in females except for platelet count. The out of range percentage for the parameters extends from 3.5 to 46.7%; with red blood cell count having the lowest while mean cell volume having the highest out of range percentage. The results indicated that the currently used reference interval does not represent the population in Asmara and are different from those obtained elsewhere in Africa. Electronic supplementary material The online version of this article (10.1186/s13104-018-3142-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nejat Siraj
- Department of Clinical Laboratory Sciences, School of Allied Health Professions, Asmara College of Health Sciences (ACHS), P.O. Box 8566, Asmara, Eritrea.
| | - John Issac
- Department of Clinical Laboratory Sciences, School of Allied Health Professions, Asmara College of Health Sciences (ACHS), P.O. Box 8566, Asmara, Eritrea
| | - Mohammed Anwar
- Department of Clinical Laboratory Sciences, School of Allied Health Professions, Asmara College of Health Sciences (ACHS), P.O. Box 8566, Asmara, Eritrea
| | - Yohannes Mehari
- Department of Clinical Laboratory Sciences, School of Allied Health Professions, Asmara College of Health Sciences (ACHS), P.O. Box 8566, Asmara, Eritrea
| | - Shushan Russom
- Department of Clinical Laboratory Sciences, School of Allied Health Professions, Asmara College of Health Sciences (ACHS), P.O. Box 8566, Asmara, Eritrea
| | - Semere Kahsay
- Department of Clinical Laboratory Sciences, School of Allied Health Professions, Asmara College of Health Sciences (ACHS), P.O. Box 8566, Asmara, Eritrea
| | - Haben Frezghi
- Department of Clinical Laboratory Sciences, School of Allied Health Professions, Asmara College of Health Sciences (ACHS), P.O. Box 8566, Asmara, Eritrea
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24
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Couvy-Duchesne B, Davenport TA, Martin NG, Wright MJ, Hickie IB. Validation and psychometric properties of the Somatic and Psychological HEalth REport (SPHERE) in a young Australian-based population sample using non-parametric item response theory. BMC Psychiatry 2017; 17:279. [PMID: 28764680 PMCID: PMC5540428 DOI: 10.1186/s12888-017-1420-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 07/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Somatic and Psychological HEalth REport (SPHERE) is a 34-item self-report questionnaire that assesses symptoms of mental distress and persistent fatigue. As it was developed as a screening instrument for use mainly in primary care-based clinical settings, its validity and psychometric properties have not been studied extensively in population-based samples. METHODS We used non-parametric Item Response Theory to assess scale validity and item properties of the SPHERE-34 scales, collected through four waves of the Brisbane Longitudinal Twin Study (N = 1707, mean age = 12, 51% females; N = 1273, mean age = 14, 50% females; N = 1513, mean age = 16, 54% females, N = 1263, mean age = 18, 56% females). We estimated the heritability of the new scores, their genetic correlation, and their predictive ability in a sub-sample (N = 1993) who completed the Composite International Diagnostic Interview. RESULTS After excluding items most responsible for noise, sex or wave bias, the SPHERE-34 questionnaire was reduced to 21 items (SPHERE-21), comprising a 14-item scale for anxiety-depression and a 10-item scale for chronic fatigue (3 items overlapping). These new scores showed high internal consistency (alpha > 0.78), moderate three months reliability (ICC = 0.47-0.58) and item scalability (Hi > 0.23), and were positively correlated (phenotypic correlations r = 0.57-0.70; rG = 0.77-1.00). Heritability estimates ranged from 0.27 to 0.51. In addition, both scores were associated with later DSM-IV diagnoses of MDD, social anxiety and alcohol dependence (OR in 1.23-1.47). Finally, a post-hoc comparison showed that several psychometric properties of the SPHERE-21 were similar to those of the Beck Depression Inventory. CONCLUSIONS The scales of SPHERE-21 measure valid and comparable constructs across sex and age groups (from 9 to 28 years). SPHERE-21 scores are heritable, genetically correlated and show good predictive ability of mental health in an Australian-based population sample of young people.
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Affiliation(s)
- Baptiste Couvy-Duchesne
- Queensland Brain Institute, the University of Queensland, Brisbane, Australia. .,Centre for Advanced Imaging, the University of Queensland, Brisbane, Australia. .,Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
| | - Tracey A. Davenport
- 0000 0004 1936 834Xgrid.1013.3Brain and Mind Centre, The University of Sydney, Sydney, Australia
| | - Nicholas G. Martin
- 0000 0001 2294 1395grid.1049.cGenetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Margaret J. Wright
- 0000 0000 9320 7537grid.1003.2Queensland Brain Institute, the University of Queensland, Brisbane, Australia
| | - Ian B. Hickie
- 0000 0004 1936 834Xgrid.1013.3Brain and Mind Centre, The University of Sydney, Sydney, Australia
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25
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Common variants of T-cells contribute differently to phenotypic variation in sarcoidosis. Sci Rep 2017; 7:5623. [PMID: 28717140 PMCID: PMC5514043 DOI: 10.1038/s41598-017-05754-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 06/02/2017] [Indexed: 12/30/2022] Open
Abstract
The involvement of the immune system, particularly the role of T-cells, in sarcoidosis is unclear. The existence of higher CD4+ T-cells and increased CD4/CD8 ratio may indicate a pathogenic role of T-cells in the disease. In this study, we quantified the contribution of T-cells associated variants and of CD4/CD8 ratio in sarcoidosis phenotypes, Löfgren’s syndrome (LS) and non- Löfgren’s syndrome (non-LS). We employed a polygenic-based approach using genome-wide association studies results on relative levels of T-cells in healthy individuals to measure the genetic contribution of T-cells in sarcoidosis entities. Results revealed that the genetic architecture of LS is highly influenced by genetic variants associated with CD8+ T-cells and CD4/CD8 ratio, explaining up to 7.94% and 6.49% of LS variation, respectively; whereas, the genetic architecture of non-LS is minimally influenced by T-cells, explaining a phenotypic variation of <1%. Moreover, pleiotropy assessment between T-cells and LS/non-LS associated-variants led to the discovery of highly scored pathway maps that shared common factors related to antigen presentation and T-cell regulatory mechanisms. Differences in significant polygenic scores, presence of pleiotropy, and distinct genetic factors provide further insights on how genetic variants and genes associated with relative levels of T-cell subtypes contribute differently to sarcoidosis phenotypes.
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26
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Abstract
The last decade has witnessed an explosion in the depth, variety, and amount of human genetic data that can be generated. This revolution in technical and analytical capacities has enabled the genetic investigation of human traits and disease in thousands to now millions of participants. Investigators have taken advantage of these advancements to gain insight into platelet biology and the platelet's role in human disease. To do so, large human genetics studies have examined the association of genetic variation with two quantitative traits measured in many population and patient based cohorts: platelet count (PLT) and mean platelet volume (MPV). This article will review the many human genetic strategies-ranging from genome-wide association study (GWAS), Exomechip, whole exome sequencing (WES), to whole genome sequencing (WGS)-employed to identify genes and variants that contribute to platelet traits. Additionally, we will discuss how these investigations have examined and interpreted the functional implications of these newly identified genetic factors and whether they also impart risk to human disease. The depth and size of genetic, phenotypic, and other -omic data are primed to continue their growth in the coming years and provide unprecedented opportunities to gain critical insights into platelet biology and how platelets contribute to disease.
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Affiliation(s)
- John D Eicher
- a Population Sciences Branch , National Heart Lung and Blood Institute, The Framingham Heart Study , Framingham , MA , USA
| | - Guillaume Lettre
- b Department of Medicine , Université de Montréal , Montréal , Québec , Canada.,c Montreal Heart Institute , Montréal , Québec , Canada
| | - Andrew D Johnson
- a Population Sciences Branch , National Heart Lung and Blood Institute, The Framingham Heart Study , Framingham , MA , USA
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27
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Jain D, Hodonsky CJ, Schick UM, Morrison JV, Minnerath S, Brown L, Schurmann C, Liu Y, Auer PL, Laurie CA, Taylor KD, Browning BL, Papanicolaou G, Browning SR, Loos RJF, North KE, Thyagarajan B, Laurie CC, Thornton TA, Sofer T, Reiner AP. Genome-wide association of white blood cell counts in Hispanic/Latino Americans: the Hispanic Community Health Study/Study of Latinos. Hum Mol Genet 2017; 26:1193-1204. [PMID: 28158719 DOI: 10.1093/hmg/ddx024] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/11/2017] [Indexed: 12/13/2022] Open
Abstract
Circulating white blood cell (WBC) counts (neutrophils, monocytes, lymphocytes, eosinophils, basophils) differ by ethnicity. The genetic factors underlying basal WBC traits in Hispanics/Latinos are unknown. We performed a genome-wide association study of total WBC and differential counts in a large, ethnically diverse US population sample of Hispanics/Latinos ascertained by the Hispanic Community Health Study and Study of Latinos (HCHS/SOL). We demonstrate that several previously known WBC-associated genetic loci (e.g. the African Duffy antigen receptor for chemokines null variant for neutrophil count) are generalizable to WBC traits in Hispanics/Latinos. We identified and replicated common and rare germ-line variants at FLT3 (a gene often somatically mutated in leukemia) associated with monocyte count. The common FLT3 variant rs76428106 has a large allele frequency differential between African and non-African populations. We also identified several novel genetic loci involving or regulating hematopoietic transcription factors (CEBPE-SLC7A7, CEBPA and CRBN-TRNT1) associated with basophil count. The minor allele of the CEBPE variant associated with lower basophil count has been previously associated with Amerindian ancestry and higher risk of acute lymphoblastic leukemia in Hispanics. Together, these data suggest that germline genetic variation affecting transcriptional and signaling pathways that underlie WBC development and lineage specification can contribute to inter-individual as well as ethnic differences in peripheral blood cell counts (normal hematopoiesis) in addition to susceptibility to leukemia (malignant hematopoiesis).
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Affiliation(s)
- Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Chani J Hodonsky
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC 27514, USA
| | - Ursula M Schick
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
| | - Jean V Morrison
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Sharon Minnerath
- Department of Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lisa Brown
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongmei Liu
- Department of Epidemiology and Prevention, School of Medicine, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Paul L Auer
- Department of Biostatistics, Joseph J. Zilber School of Public Health, University of Wisconsin Milwaukee, Milwaukee, WI 53201, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences at Harbor-UCLA Medical Center, Torrance, CA 90502, USA.,Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Brian L Browning
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - George Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung and Blood Institute, Bethesda, MD 20824, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC 27514, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Bharat Thyagarajan
- Department of Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
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28
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Hodonsky CJ, Jain D, Schick UM, Morrison JV, Brown L, McHugh CP, Schurmann C, Chen DD, Liu YM, Auer PL, Laurie CA, Taylor KD, Browning BL, Li Y, Papanicolaou G, Rotter JI, Kurita R, Nakamura Y, Browning SR, Loos RJF, North KE, Laurie CC, Thornton TA, Pankratz N, Bauer DE, Sofer T, Reiner AP. Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos. PLoS Genet 2017; 13:e1006760. [PMID: 28453575 PMCID: PMC5428979 DOI: 10.1371/journal.pgen.1006760] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 05/12/2017] [Accepted: 04/12/2017] [Indexed: 01/13/2023] Open
Abstract
Prior GWAS have identified loci associated with red blood cell (RBC) traits in populations of European, African, and Asian ancestry. These studies have not included individuals with an Amerindian ancestral background, such as Hispanics/Latinos, nor evaluated the full spectrum of genomic variation beyond single nucleotide variants. Using a custom genotyping array enriched for Amerindian ancestral content and 1000 Genomes imputation, we performed GWAS in 12,502 participants of Hispanic Community Health Study and Study of Latinos (HCHS/SOL) for hematocrit, hemoglobin, RBC count, RBC distribution width (RDW), and RBC indices. Approximately 60% of previously reported RBC trait loci generalized to HCHS/SOL Hispanics/Latinos, including African ancestral alpha- and beta-globin gene variants. In addition to the known 3.8kb alpha-globin copy number variant, we identified an Amerindian ancestral association in an alpha-globin regulatory region on chromosome 16p13.3 for mean corpuscular volume and mean corpuscular hemoglobin. We also discovered and replicated three genome-wide significant variants in previously unreported loci for RDW (SLC12A2 rs17764730, PSMB5 rs941718), and hematocrit (PROX1 rs3754140). Among the proxy variants at the SLC12A2 locus we identified rs3812049, located in a bi-directional promoter between SLC12A2 (which encodes a red cell membrane ion-transport protein) and an upstream anti-sense long-noncoding RNA, LINC01184, as the likely causal variant. We further demonstrate that disruption of the regulatory element harboring rs3812049 affects transcription of SLC12A2 and LINC01184 in human erythroid progenitor cells. Together, these results reinforce the importance of genetic study of diverse ancestral populations, in particular Hispanics/Latinos.
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Affiliation(s)
- Chani J. Hodonsky
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC, United States of America
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Ursula M. Schick
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Jean V. Morrison
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Lisa Brown
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Caitlin P. McHugh
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
- New York Genome Center, New York, NY, United States of America
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Diane D. Chen
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, United States of America
| | - Yong Mei Liu
- School of Medicine, Wake Forest University, Winston-Salem, NC, United States of America
| | - Paul L. Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin Milwaukee, Milwaukee, WI, United States of America
| | - Cecilia A. Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA United States of America
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA United States of America
| | - Brian L. Browning
- Department of Medicine, University of Washington, Seattle, WA United States of America
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States of America
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, United States of America
| | - George Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD, United States of America
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA United States of America
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA United States of America
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
- Comprehensive Human Sciences, Tsukuba University, Tsukuba, Ibaraki, Japan
| | - Sharon R. Browning
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kari E. North
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC, United States of America
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Cathy C. Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Nathan Pankratz
- Division of Laboratory Medicine & Pathology, University of Minnesota, Minneapolis, MN, United States of America
| | - Daniel E. Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States of America
- Department of Pediatrics, Harvard Medical School and Harvard Stem Cell Institute, Harvard University, Boston, MA, United States of America
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Alex P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- * E-mail:
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29
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van Rooij FJ, Qayyum R, Smith AV, Zhou Y, Trompet S, Tanaka T, Keller MF, Chang LC, Schmidt H, Yang ML, Chen MH, Hayes J, Johnson AD, Yanek LR, Mueller C, Lange L, Floyd JS, Ghanbari M, Zonderman AB, Jukema JW, Hofman A, van Duijn CM, Desch KC, Saba Y, Ozel AB, Snively BM, Wu JY, Schmidt R, Fornage M, Klein RJ, Fox CS, Matsuda K, Kamatani N, Wild PS, Stott DJ, Ford I, Slagboom PE, Yang J, Chu AY, Lambert AJ, Uitterlinden AG, Franco OH, Hofer E, Ginsburg D, Hu B, Keating B, Schick UM, Brody JA, Li JZ, Chen Z, Zeller T, Guralnik JM, Chasman DI, Peters LL, Kubo M, Becker DM, Li J, Eiriksdottir G, Rotter JI, Levy D, Grossmann V, Patel KV, Chen CH, Ridker PM, Tang H, Launer LJ, Rice KM, Li-Gao R, Ferrucci L, Evans MK, Choudhuri A, Trompouki E, Abraham BJ, Yang S, Takahashi A, Kamatani Y, Kooperberg C, Harris TB, Jee SH, Coresh J, Tsai FJ, Longo DL, Chen YT, Felix JF, Yang Q, Psaty BM, Boerwinkle E, Becker LC, Mook-Kanamori DO, Wilson JG, Gudnason V, O'Donnell CJ, Dehghan A, Cupples LA, Nalls MA, Morris AP, Okada Y, Reiner AP, Zon LI, Ganesh SK, Ganesh SK. Genome-wide Trans-ethnic Meta-analysis Identifies Seven Genetic Loci Influencing Erythrocyte Traits and a Role for RBPMS in Erythropoiesis. Am J Hum Genet 2017; 100:51-63. [PMID: 28017375 DOI: 10.1016/j.ajhg.2016.11.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 11/16/2016] [Indexed: 11/26/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified loci for erythrocyte traits in primarily European ancestry populations. We conducted GWAS meta-analyses of six erythrocyte traits in 71,638 individuals from European, East Asian, and African ancestries using a Bayesian approach to account for heterogeneity in allelic effects and variation in the structure of linkage disequilibrium between ethnicities. We identified seven loci for erythrocyte traits including a locus (RBPMS/GTF2E2) associated with mean corpuscular hemoglobin and mean corpuscular volume. Statistical fine-mapping at this locus pointed to RBPMS at this locus and excluded nearby GTF2E2. Using zebrafish morpholino to evaluate loss of function, we observed a strong in vivo erythropoietic effect for RBPMS but not for GTF2E2, supporting the statistical fine-mapping at this locus and demonstrating that RBPMS is a regulator of erythropoiesis. Our findings show the utility of trans-ethnic GWASs for discovery and characterization of genetic loci influencing hematologic traits.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Santhi K Ganesh
- Division of Cardiovascular Medicine, Department of Internal Medicine, Department of Human Genetics, University of Michigan, 1500 E. Medical Center Drive, Ann Arbor, MI 48109, USA.
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30
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Zhuang WV, Murabito JM, Lunetta KL. Phenotypically Enriched Genotypic Imputation in Genetic Association Tests. Hum Hered 2016; 81:35-45. [PMID: 27576319 DOI: 10.1159/000446986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 05/20/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In longitudinal epidemiological studies there may be individuals with rich phenotype data who die or are lost to follow-up before providing DNA for genetic studies. Often, the genotypic and phenotypic data of the relatives are available. Two strategies for analyzing the incomplete data are to exclude ungenotyped subjects from analysis (the complete-case method, CC) and to include phenotyped but ungenotyped individuals in analysis by using relatives' genotypes for genotype imputation (GI). In both strategies, the information in the phenotypic data was not used to handle the missing-genotype problem. METHODS We propose a phenotypically enriched genotypic imputation (PEGI) method that uses the EM (expectation-maximization)-based maximum likelihood method to incorporate observed phenotypes into genotype imputation. RESULTS Our simulations with genotypes missing completely at random show that, for a single-nucleotide polymorphism (SNP) with moderate to strong effect on a phenotype, PEGI improves power more than GI without excess type I errors. Using the Framingham Heart Study data set, we compare the ability of the PEGI, GI, and CC to detect the associations between 5 SNPs and age at natural menopause. CONCLUSION The PEGI method may improve power to detect an association over both CC and GI under many circumstances.
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Affiliation(s)
- Wei Vivian Zhuang
- Department of Biostatistics, Boston University School of Public Health, Boston, Mass., USA
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31
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Lin BD, Hottenga JJ, Abdellaoui A, Dolan CV, de Geus EJC, Kluft C, Boomsma DI, Willemsen G. Causes of variation in the neutrophil-lymphocyte and platelet-lymphocyte ratios: a twin-family study. Biomark Med 2016; 10:1061-1072. [PMID: 27690543 DOI: 10.2217/bmm-2016-0147] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
AIM Neutrophil-lymphocyte ratio (NLR) and platelet-lymphocyte ratio (PLR) are biomarkers for disease development, for whom little is known about causes of variation in the general population. MATERIALS & METHODS We estimated the heritability of PLR and NLR and examined their association with gender, demographic, lifestyle and environmental factors in a Dutch nonpatient twin family population (n = 8108). RESULTS Heritability was estimated at 64% for PLR and 36% for NLR. Men had on average higher NLR, but lower PLR levels than women. PLR and NLR increased significantly with age, decreased in colder months and showed small but significant sex- and age-specific associations with body composition and smoking. CONCLUSION NLR and PLR levels are heritable and influenced by age, sex and environmental factors, such as seasonal conditions and lifestyle.
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Affiliation(s)
- Bochao D Lin
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,EMGO+ Institute for Health & Care Research, VU Medical Center, Amsterdam, The Netherlands
| | - Abdel Abdellaoui
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Conor V Dolan
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Eco J C de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,EMGO+ Institute for Health & Care Research, VU Medical Center, Amsterdam, The Netherlands
| | | | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,EMGO+ Institute for Health & Care Research, VU Medical Center, Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,EMGO+ Institute for Health & Care Research, VU Medical Center, Amsterdam, The Netherlands
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32
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Prabhu SB, Rathore DK, Nair D, Chaudhary A, Raza S, Kanodia P, Sopory S, George A, Rath S, Bal V, Tripathi R, Ramji S, Batra A, Aggarwal KC, Chellani HK, Arya S, Agarwal N, Mehta U, Natchu UCM, Wadhwa N, Bhatnagar S. Comparison of Human Neonatal and Adult Blood Leukocyte Subset Composition Phenotypes. PLoS One 2016; 11:e0162242. [PMID: 27610624 PMCID: PMC5017693 DOI: 10.1371/journal.pone.0162242] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/21/2016] [Indexed: 12/26/2022] Open
Abstract
The human peripheral leukocyte subset composition depends on genotype variation and pre-natal and post-natal environmental influence diversity. We quantified this composition in adults and neonates, and compared the median values and dispersal ranges of various subsets in them. We confirmed higher frequencies of monocytes and regulatory T cells (Tregs), similar frequencies of neutrophils, and lower frequencies of CD8 T cells, NKT cells, B1 B cells and gamma-delta T cells in neonatal umbilical cord blood. Unlike previous reports, we found higher frequencies of eosinophils and B cells, higher CD4:CD8 ratios, lower frequencies of T cells and iNKT cells, and similar frequencies of CD4 T cells and NK cells in neonates. We characterized monocyte subsets and dendritic cell (DC) subsets in far greater detail than previously reported, using recently described surface markers and gating strategies and observed that neonates had lower frequencies of patrolling monocytes and lower myeloid dendritic cell (mDC):plasmacytoid DC (pDC) ratios. Our data contribute to South Asian reference values for these parameters. We found that dispersal ranges differ between different leukocyte subsets, suggesting differential determination of variation. Further, some subsets were more dispersed in adults than in neonates suggesting influences of postnatal sources of variation, while some show the opposite pattern suggesting influences of developmental process variation. Together, these data and analyses provide interesting biological possibilities for future exploration.
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Affiliation(s)
- Savit B. Prabhu
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- National Institute of Immunology, New Delhi, India
- * E-mail:
| | - Deepak K. Rathore
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Deepa Nair
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Anita Chaudhary
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Saimah Raza
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | | | - Shailaja Sopory
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Anna George
- National Institute of Immunology, New Delhi, India
| | - Satyajit Rath
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- National Institute of Immunology, New Delhi, India
| | - Vineeta Bal
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- National Institute of Immunology, New Delhi, India
| | - Reva Tripathi
- Department of Obstetrics & Gynecology, Maulana Azad Medical College, New Delhi, India
| | - Siddharth Ramji
- Department of Neonatology, Maulana Azad Medical College, New Delhi, India
| | - Aruna Batra
- Department of Obstetrics & Gynecology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Kailash C. Aggarwal
- Department of Pediatrics, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Harish K. Chellani
- Department of Pediatrics, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Sugandha Arya
- Department of Pediatrics, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Nidhi Agarwal
- Department of Obstetrics and Gynecology, Gurgaon Civil Hospital, Gurgaon, India
| | - Umesh Mehta
- Department of Pediatrics, Gurgaon Civil Hospital, Gurgaon, India
| | - Uma Chandra Mouli Natchu
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Nitya Wadhwa
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Shinjini Bhatnagar
- Pediatric Biology Center, Translational Health Science and Technology Institute, Faridabad, Haryana, India
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33
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Pankratz N, Schick UM, Zhou Y, Zhou W, Ahluwalia TS, Allende ML, Auer PL, Bork-Jensen J, Brody JA, Chen MH, Clavo V, Eicher JD, Grarup N, Hagedorn EJ, Hu B, Hunker K, Johnson AD, Leusink M, Lu Y, Lyytikäinen LP, Manichaikul A, Marioni RE, Nalls MA, Pazoki R, Smith AV, van Rooij FJA, Yang ML, Zhang X, Zhang Y, Asselbergs FW, Boerwinkle E, Borecki IB, Bottinger EP, Cushman M, de Bakker PIW, Deary IJ, Dong L, Feitosa MF, Floyd JS, Franceschini N, Franco OH, Garcia ME, Grove ML, Gudnason V, Hansen T, Harris TB, Hofman A, Jackson RD, Jia J, Kähönen M, Launer LJ, Lehtimäki T, Liewald DC, Linneberg A, Liu Y, Loos RJF, Nguyen VM, Numans ME, Pedersen O, Psaty BM, Raitakari OT, Rich SS, Rivadeneira F, Di Sant AMR, Rotter JI, Starr JM, Taylor KD, Thuesen BH, Tracy RP, Uitterlinden AG, Wang J, Wang J, Dehghan A, Huo Y, Cupples LA, Wilson JG, Proia RL, Zon LI, O’Donnell CJ, Reiner AP, Ganesh SK. Meta-analysis of rare and common exome chip variants identifies S1PR4 and other loci influencing blood cell traits. Nat Genet 2016; 48:867-76. [PMID: 27399967 PMCID: PMC5145000 DOI: 10.1038/ng.3607] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 06/03/2016] [Indexed: 12/15/2022]
Abstract
Hematologic measures such as hematocrit and white blood cell (WBC) count are heritable and clinically relevant. We analyzed erythrocyte and WBC phenotypes in 52,531 individuals (37,775 of European ancestry, 11,589 African Americans, and 3,167 Hispanic Americans) from 16 population-based cohorts with Illumina HumanExome BeadChip genotypes. We then performed replication analyses of new discoveries in 18,018 European-American women and 5,261 Han Chinese. We identified and replicated four new erythrocyte trait-locus associations (CEP89, SHROOM3, FADS2, and APOE) and six new WBC loci for neutrophil count (S1PR4), monocyte count (BTBD8, NLRP12, and IL17RA), eosinophil count (IRF1), and total WBC count (MYB). The association of a rare missense variant in S1PR4 supports the role of sphingosine-1-phosphate signaling in leukocyte trafficking and circulating neutrophil counts. Loss-of-function experiments for S1pr4 in mouse and s1pr4 in zebrafish demonstrated phenotypes consistent with the association observed in humans and altered kinetics of neutrophil recruitment and resolution in response to tissue injury.
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Affiliation(s)
- Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Ursula M Schick
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yi Zhou
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
| | - Wei Zhou
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Biology, University of Michigan, Ann Arbor, MI, USA
| | - Tarunveer Singh Ahluwalia
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center, Gentofte, Denmark
| | - Maria Laura Allende
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Paul L Auer
- School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jette Bork-Jensen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ming-Huei Chen
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA
| | - Vinna Clavo
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - John D Eicher
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elliott J Hagedorn
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
| | - Bella Hu
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
| | - Kristina Hunker
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Andrew D Johnson
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Maarten Leusink
- Division Pharmacoepidemiology & Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories and University of Tampere School of Medicine, Tampere, Finland
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Raha Pazoki
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Albert Vernon Smith
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Frank J A van Rooij
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Min-Lee Yang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoling Zhang
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Yan Zhang
- Department of Cardiology, Peking University First Hospital, Beijing, China
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht, Netherlands
- Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, Utrecht, Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, United Kingdom
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ingrid B Borecki
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mary Cushman
- Department of Medicine, Division of Hematology/Oncology, University of Vermont, Burlington, VT, USA
| | - Paul I W de Bakker
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Liguang Dong
- Jin Ding Street Community Healthy Center, Peking University Shougang Hospital, Beijing, China
| | - Mary F Feitosa
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Nora Franceschini
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Melissa E Garcia
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Megan L Grove
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes, and Metabolism, Ohio State University, Columbus, OH, USA
| | - Jia Jia
- Department of Cardiology, Peking University First Hospital, Beijing, China
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and University of Tampere School of Medicine, Tampere, Finland
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and University of Tampere School of Medicine, Tampere, Finland
| | - David C Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Allan Linneberg
- Research Centre for Prevention and Health, Capital Region of Denmark, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yongmei Liu
- Center for Human Genetics, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vy M Nguyen
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
| | - Mattijs E Numans
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
- Public Health and Primary Care, Leiden University Medical Centre, Leiden, Netherlands
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
- Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Amanda M Rosa Di Sant
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Torrance, CA, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Geriatric Medicine unit, University of Edinburgh, Edinburgh, UK
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Torrance, CA, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Colchester, VT, USA
- Department of Biochemistry, University of Vermont College of Medicine, Colchester, VT, USA
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jiansong Wang
- Chronic Diseases Research Center, Peking University Shougang Hospital, Beijing, China
| | - Judy Wang
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Yong Huo
- Department of Cardiology, Peking University First Hospital, Beijing, China
| | - L Adrienne Cupples
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Richard L Proia
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Leonard I Zon
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
| | - Christopher J O’Donnell
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA
- Cardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung, and Blood Institute, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
- Cardiology Section, Department of Medicine, Boston Veteran’s Administration Healthcare, Boston, MA, USA
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| | - Santhi K Ganesh
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
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34
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Chami N, Chen MH, Slater AJ, Eicher JD, Evangelou E, Tajuddin SM, Love-Gregory L, Kacprowski T, Schick UM, Nomura A, Giri A, Lessard S, Brody JA, Schurmann C, Pankratz N, Yanek LR, Manichaikul A, Pazoki R, Mihailov E, Hill WD, Raffield LM, Burt A, Bartz TM, Becker DM, Becker LC, Boerwinkle E, Bork-Jensen J, Bottinger EP, O'Donoghue ML, Crosslin DR, de Denus S, Dubé MP, Elliott P, Engström G, Evans MK, Floyd JS, Fornage M, Gao H, Greinacher A, Gudnason V, Hansen T, Harris TB, Hayward C, Hernesniemi J, Highland HM, Hirschhorn JN, Hofman A, Irvin MR, Kähönen M, Lange E, Launer LJ, Lehtimäki T, Li J, Liewald DCM, Linneberg A, Liu Y, Lu Y, Lyytikäinen LP, Mägi R, Mathias RA, Melander O, Metspalu A, Mononen N, Nalls MA, Nickerson DA, Nikus K, O'Donnell CJ, Orho-Melander M, Pedersen O, Petersmann A, Polfus L, Psaty BM, Raitakari OT, Raitoharju E, Richard M, Rice KM, Rivadeneira F, Rotter JI, Schmidt F, Smith AV, Starr JM, Taylor KD, Teumer A, Thuesen BH, Torstenson ES, Tracy RP, Tzoulaki I, Zakai NA, Vacchi-Suzzi C, van Duijn CM, van Rooij FJA, Cushman M, Deary IJ, Velez Edwards DR, Vergnaud AC, Wallentin L, Waterworth DM, White HD, Wilson JG, Zonderman AB, Kathiresan S, Grarup N, Esko T, Loos RJF, Lange LA, Faraday N, Abumrad NA, Edwards TL, Ganesh SK, Auer PL, Johnson AD, Reiner AP, Lettre G. Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits. Am J Hum Genet 2016; 99:8-21. [PMID: 27346685 PMCID: PMC5005438 DOI: 10.1016/j.ajhg.2016.05.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/03/2016] [Indexed: 11/24/2022] Open
Abstract
Red blood cell (RBC) traits are important heritable clinical biomarkers and modifiers of disease severity. To identify coding genetic variants associated with these traits, we conducted meta-analyses of seven RBC phenotypes in 130,273 multi-ethnic individuals from studies genotyped on an exome array. After conditional analyses and replication in 27,480 independent individuals, we identified 16 new RBC variants. We found low-frequency missense variants in MAP1A (rs55707100, minor allele frequency [MAF] = 3.3%, p = 2 × 10(-10) for hemoglobin [HGB]) and HNF4A (rs1800961, MAF = 2.4%, p < 3 × 10(-8) for hematocrit [HCT] and HGB). In African Americans, we identified a nonsense variant in CD36 associated with higher RBC distribution width (rs3211938, MAF = 8.7%, p = 7 × 10(-11)) and showed that it is associated with lower CD36 expression and strong allelic imbalance in ex vivo differentiated human erythroblasts. We also identified a rare missense variant in ALAS2 (rs201062903, MAF = 0.2%) associated with lower mean corpuscular volume and mean corpuscular hemoglobin (p < 8 × 10(-9)). Mendelian mutations in ALAS2 are a cause of sideroblastic anemia and erythropoietic protoporphyria. Gene-based testing highlighted three rare missense variants in PKLR, a gene mutated in Mendelian non-spherocytic hemolytic anemia, associated with HGB and HCT (SKAT p < 8 × 10(-7)). These rare, low-frequency, and common RBC variants showed pleiotropy, being also associated with platelet, white blood cell, and lipid traits. Our association results and functional annotation suggest the involvement of new genes in human erythropoiesis. We also confirm that rare and low-frequency variants play a role in the architecture of complex human traits, although their phenotypic effect is generally smaller than originally anticipated.
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Affiliation(s)
- Nathalie Chami
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
| | - Ming-Huei Chen
- Population Sciences Branch, National Heart, Lung, and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, USA
| | - Andrew J Slater
- Genetics Target Sciences, GlaxoSmithKline, Research Triangle Park, NC 27709, USA; OmicSoft Corporation, Cary, NC 27513, USA
| | - John D Eicher
- Population Sciences Branch, National Heart, Lung, and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, USA
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina 45110, Greece
| | - Salman M Tajuddin
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Latisha Love-Gregory
- Department of Medicine, Center of Human Nutrition, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Tim Kacprowski
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine, Greifswald and Ernst-Mortiz-Arndt University Greifswald, Greifswald 17475, Germany; DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald QA, Germany
| | - Ursula M Schick
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10069, USA
| | - Akihiro Nomura
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Cardiovascular Medicine, Kanazawa University, Graduate School of Medical Science, Kanazawa, Ishikawa 9200942, Japan
| | - Ayush Giri
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA
| | - Samuel Lessard
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
| | - Jennifer A Brody
- Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10069, USA; The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10069, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55454, USA
| | - Lisa R Yanek
- Department of Medicine/Division of General Internal Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Raha Pazoki
- Department of Epidemiology, Erasmus, MC Rotterdam 3000, the Netherlands
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - W David Hill
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Amber Burt
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Traci M Bartz
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Diane M Becker
- Department of Medicine/Division of General Internal Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Lewis C Becker
- Department of Medicine/Divisions of Cardiology and General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jette Bork-Jensen
- The Novo Nordisk Foundation, Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2100, Denmark
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10069, USA
| | - Michelle L O'Donoghue
- TIMI Study Group, Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Simon de Denus
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; Faculty of Pharmacy, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Marie-Pierre Dubé
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Gunnar Engström
- Department of Clinical Sciences, Malmö, Lund University, Malmö 221 00, Sweden; Skåne University Hospital, Malmö 222 41, Sweden
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - James S Floyd
- Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - He Gao
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Andreas Greinacher
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald 17475, Germany
| | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Torben Hansen
- The Novo Nordisk Foundation, Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2100, Denmark
| | - Tamara B Harris
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Intramural Research Program, NIH, Bethesda, MD 20892, USA
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jussi Hernesniemi
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33014, Finland; University of Tampere, School of Medicine, Tampere 33014, Finland
| | - Heather M Highland
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Joel N Hirschhorn
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus, MC Rotterdam 3000, the Netherlands; Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere 33521, Finland; Department of Clinical Physiology, University of Tampere School of Medicine, Tampere 33014, Finland
| | - Ethan Lange
- Departments of Genetics and Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lenore J Launer
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Intramural Research Program, NIH, Bethesda, MD 20892, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33014, Finland
| | - Jin Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, School of Medicine, Palo Alto, CA 94305, USA
| | - David C M Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Allan Linneberg
- Research Centre for Prevention and Health, The Capital Region of Denmark, Copenhagen 2600, Denmark; Department of Clinical Experimental Research, Rigshospitalet, Glostrup 2100, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Yongmei Liu
- Center for Human Genetics, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10069, USA; The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10069, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33014, Finland
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Rasika A Mathias
- Department of Medicine, Divisions of Allergy and Clinical Immunology and General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Olle Melander
- Department of Clinical Sciences, Malmö, Lund University, Malmö 221 00, Sweden; Skåne University Hospital, Malmö 222 41, Sweden
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33014, Finland
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Kjell Nikus
- University of Tampere, School of Medicine, Tampere 33014, Finland; Department of Cardiology, Heart Center, Tampere University Hospital, Tampere 33521, Finland
| | - Chris J O'Donnell
- Population Sciences Branch, National Heart, Lung, and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, USA; Cardiology Section and Center for Population Genomics, Boston Veteran's Administration (VA) Healthcare, Boston, MA 02118, USA
| | - Marju Orho-Melander
- Department of Clinical Sciences, Malmö, Lund University, Malmö 221 00, Sweden; Skåne University Hospital, Malmö 222 41, Sweden
| | - Oluf Pedersen
- The Novo Nordisk Foundation, Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2100, Denmark
| | - Astrid Petersmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald 17475, Germany
| | - Linda Polfus
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine Epidemiology and Health Services, University of Washington, Seattle, WA 98101, USA; Group Health Research Institute, Group Health Cooperative, Seattle, WA 98101, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20521, Finland; Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20520, Finland
| | - Emma Raitoharju
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33014, Finland
| | - Melissa Richard
- Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus, MC Rotterdam 3000, the Netherlands; Department of Internal Medicine, Erasmus MC, Rotterdam 3000, the Netherlands; Netherlands Consortium for Healthy Ageing (NCHA), Rotterdam 3015, the Netherlands
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Torrance, CA 90502, USA; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Frank Schmidt
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine, Greifswald and Ernst-Mortiz-Arndt University Greifswald, Greifswald 17475, Germany
| | - Albert Vernon Smith
- Icelandic Heart Association, 201 Kopavogur, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Alzheimer Scotland Research Centre, Edinburgh EH8 9JZ, UK
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Torrance, CA 90502, USA; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald 17475, Germany
| | - Betina H Thuesen
- Research Centre for Prevention and Health, The Capital Region of Denmark, Copenhagen 2600, Denmark
| | - Eric S Torstenson
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA
| | - Russell P Tracy
- Departments of Pathology and Laboratory Medicine and Biochemistry, University of Vermont College of Medicine, Colchester, VT 05446, USA
| | - Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina 45110, Greece
| | - Neil A Zakai
- Departments of Medicine and Pathology, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Caterina Vacchi-Suzzi
- Department of Family Population and Preventive Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | | | | | - Mary Cushman
- Departments of Medicine and Pathology, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Digna R Velez Edwards
- Vanderbilt Epidemiology Center, Department of Obstetrics & Gynecology, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
| | - Anne-Claire Vergnaud
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Lars Wallentin
- Department of Medical Sciences, Cardiology and Uppsala Clinical Research Center, Uppsala University, Uppsala 751 85, Sweden
| | - Dawn M Waterworth
- Genetics Target Sciences, GlaxoSmithKline, King of Prussia, PA 19406, USA
| | - Harvey D White
- Green Lane Cardiovascular Service, Auckland City Hospital and University of Auckland, Auckland 1142, New Zealand
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Sekar Kathiresan
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Niels Grarup
- The Novo Nordisk Foundation, Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2100, Denmark
| | - Tõnu Esko
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10069, USA; The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10069, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10069, USA
| | - Leslie A Lange
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Nauder Faraday
- Department of Anesthesiology & Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nada A Abumrad
- Department of Medicine, Center of Human Nutrition, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA
| | - Santhi K Ganesh
- Departments of Internal Medicine and Human Genetics, University of Michigan, Ann Arbor, MI 48108, USA
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53205, USA
| | - Andrew D Johnson
- Population Sciences Branch, National Heart, Lung, and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Guillaume Lettre
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Montreal Heart Institute, Montréal, QC H1T 1C8, Canada.
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35
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McLachlan S, Giambartolomei C, White J, Charoen P, Wong A, Finan C, Engmann J, Shah T, Hersch M, Podmore C, Cavadino A, Jefferis BJ, Dale CE, Hypponen E, Morris RW, Casas JP, Kumari M, Ben-Shlomo Y, Gaunt TR, Drenos F, Langenberg C, Kuh D, Kivimaki M, Rueedi R, Waeber G, Hingorani AD, Price JF, Walker AP. Replication and Characterization of Association between ABO SNPs and Red Blood Cell Traits by Meta-Analysis in Europeans. PLoS One 2016; 11:e0156914. [PMID: 27280446 PMCID: PMC4900668 DOI: 10.1371/journal.pone.0156914] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/20/2016] [Indexed: 01/07/2023] Open
Abstract
Red blood cell (RBC) traits are routinely measured in clinical practice as important markers of health. Deviations from the physiological ranges are usually a sign of disease, although variation between healthy individuals also occurs, at least partly due to genetic factors. Recent large scale genetic studies identified loci associated with one or more of these traits; further characterization of known loci and identification of new loci is necessary to better understand their role in health and disease and to identify potential molecular mechanisms. We performed meta-analysis of Metabochip association results for six RBC traits—hemoglobin concentration (Hb), hematocrit (Hct), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), mean corpuscular volume (MCV) and red blood cell count (RCC)—in 11 093 Europeans from seven studies of the UCL-LSHTM-Edinburgh-Bristol (UCLEB) Consortium. We identified 394 non-overlapping SNPs in five loci at genome-wide significance: 6p22.1-6p21.33 (with HFE among others), 6q23.2 (with HBS1L among others), 6q23.3 (contains no genes), 9q34.3 (only ABO gene) and 22q13.1 (with TMPRSS6 among others), replicating previous findings of association with RBC traits at these loci and extending them by imputation to 1000 Genomes. We further characterized associations between ABO SNPs and three traits: hemoglobin, hematocrit and red blood cell count, replicating them in an independent cohort. Conditional analyses indicated the independent association of each of these traits with ABO SNPs and a role for blood group O in mediating the association. The 15 most significant RBC-associated ABO SNPs were also associated with five cardiometabolic traits, with discordance in the direction of effect between groups of traits, suggesting that ABO may act through more than one mechanism to influence cardiometabolic risk.
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Affiliation(s)
- Stela McLachlan
- Centre for Population Health Sciences, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Claudia Giambartolomei
- Department of Psychiatry, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, The Leon and Norma Hess Center for Science and Medicine, New York, New York, United States of America
| | - Jon White
- University College London Genetics Institute, Department of Genetics, Environment and Evolution, London, United Kingdom
| | - Pimphen Charoen
- Department of Non-communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing at UCL, London, United Kingdom
| | - Chris Finan
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Jorgen Engmann
- Genetic Epidemiology Group, Institute of Cardiovascular Science, University College London, London, United Kingdom
- Farr Institute of Health Informatics Research, Department of Epidemiology & Public Health, University College London, London, United Kingdom
| | - Tina Shah
- Genetic Epidemiology Group, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Micha Hersch
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Clara Podmore
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Alana Cavadino
- Centre for Environmental and Preventive Medicine, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, United Kingdom
- Population, Policy and Practice, UCL Institute of Child Health, University College London, London, United Kingdom
| | - Barbara J. Jefferis
- Department of Primary Care & Population Health, UCL Institute of Epidemiology & Health Care, University College London, London, United Kingdom
| | - Caroline E. Dale
- Farr Institute of Health Informatics Research, Department of Epidemiology & Public Health, University College London, London, United Kingdom
| | - Elina Hypponen
- Population, Policy and Practice, UCL Institute of Child Health, University College London, London, United Kingdom
- Centre for Population Health Research, School of Health Sciences and Sansom Institute of Health Research, University of South Australia, Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Richard W. Morris
- Department of Primary Care & Population Health, UCL Institute of Epidemiology & Health Care, University College London, London, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Juan P. Casas
- Institute of Health Informatics, University College London, London, United Kingdom
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, United Kingdom
- Department of Epidemiology & Public Health, UCL Institute of Epidemiology & Health Care, University College London, London, United Kingdom
| | - Yoav Ben-Shlomo
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Tom R. Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Fotios Drenos
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Institute of Health Informatics, University College London, London, United Kingdom
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing at UCL, London, United Kingdom
| | - Mika Kivimaki
- Department of Epidemiology & Public Health, UCL Institute of Epidemiology & Health Care, University College London, London, United Kingdom
| | - Rico Rueedi
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gerard Waeber
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Aroon D. Hingorani
- Institute of Cardiovascular Science, University College London, London, United Kingdom
- Farr Institute of Health Informatics Research, Department of Epidemiology & Public Health, University College London, London, United Kingdom
| | - Jacqueline F. Price
- Centre for Population Health Sciences, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Ann P. Walker
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, United Kingdom
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Gutierrez-Arcelus M, Rich SS, Raychaudhuri S. Autoimmune diseases - connecting risk alleles with molecular traits of the immune system. Nat Rev Genet 2016; 17:160-74. [PMID: 26907721 PMCID: PMC4896831 DOI: 10.1038/nrg.2015.33] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome-wide strategies have driven the discovery of more than 300 susceptibility loci for autoimmune diseases. However, for almost all loci, understanding of the mechanisms leading to autoimmunity remains limited, and most variants that are likely to be causal are in non-coding regions of the genome. A critical next step will be to identify the in vivo and ex vivo immunophenotypes that are affected by risk variants. To do this, key cell types and cell states that are implicated in autoimmune diseases will need to be defined. Functional genomic annotations from these cell types and states can then be used to resolve candidate genes and causal variants. Together with longitudinal studies, this approach may yield pivotal insights into how autoimmunity is triggered.
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Affiliation(s)
- Maria Gutierrez-Arcelus
- Division of Genetics, and Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
- Partners Center for Personalized Genetic Medicine, Boston, Massachusetts 02115, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Soumya Raychaudhuri
- Division of Genetics, and Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
- Partners Center for Personalized Genetic Medicine, Boston, Massachusetts 02115, USA
- Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PL, UK
- Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm SE-171 77, Sweden
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37
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Schick UM, Jain D, Hodonsky CJ, Morrison JV, Davis JP, Brown L, Sofer T, Conomos MP, Schurmann C, McHugh CP, Nelson SC, Vadlamudi S, Stilp A, Plantinga A, Baier L, Bien SA, Gogarten SM, Laurie CA, Taylor KD, Liu Y, Auer PL, Franceschini N, Szpiro A, Rice K, Kerr KF, Rotter JI, Hanson RL, Papanicolaou G, Rich SS, Loos RJF, Browning BL, Browning SR, Weir BS, Laurie CC, Mohlke KL, North KE, Thornton TA, Reiner AP. Genome-wide Association Study of Platelet Count Identifies Ancestry-Specific Loci in Hispanic/Latino Americans. Am J Hum Genet 2016; 98:229-42. [PMID: 26805783 PMCID: PMC4746331 DOI: 10.1016/j.ajhg.2015.12.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/07/2015] [Indexed: 12/23/2022] Open
Abstract
Platelets play an essential role in hemostasis and thrombosis. We performed a genome-wide association study of platelet count in 12,491 participants of the Hispanic Community Health Study/Study of Latinos by using a mixed-model method that accounts for admixture and family relationships. We discovered and replicated associations with five genes (ACTN1, ETV7, GABBR1-MOG, MEF2C, and ZBTB9-BAK1). Our strongest association was with Amerindian-specific variant rs117672662 (p value = 1.16 × 10(-28)) in ACTN1, a gene implicated in congenital macrothrombocytopenia. rs117672662 exhibited allelic differences in transcriptional activity and protein binding in hematopoietic cells. Our results underscore the value of diverse populations to extend insights into the allelic architecture of complex traits.
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Affiliation(s)
- Ursula M Schick
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA; Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Chani J Hodonsky
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Jean V Morrison
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - James P Davis
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lisa Brown
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Claudia Schurmann
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | | | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Anna Plantinga
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Leslie Baier
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, NIH, 445 North 5(th) Street, Phoenix, AZ 85004, USA
| | - Stephanie A Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
| | | | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA; Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Yongmei Liu
- School of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin Milwaukee, Milwaukee, WI 53201, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Adam Szpiro
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Ken Rice
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Kathleen F Kerr
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, NIH, 445 North 5(th) Street, Phoenix, AZ 85004, USA
| | - George Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Division of Endocrinology, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brian L Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA.
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38
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Couvy-Duchesne B, Ebejer JL, Gillespie NA, Duffy DL, Hickie IB, Thompson PM, Martin NG, de Zubicaray GI, McMahon KL, Medland SE, Wright MJ. Head Motion and Inattention/Hyperactivity Share Common Genetic Influences: Implications for fMRI Studies of ADHD. PLoS One 2016; 11:e0146271. [PMID: 26745144 PMCID: PMC4712830 DOI: 10.1371/journal.pone.0146271] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/15/2015] [Indexed: 11/18/2022] Open
Abstract
Head motion (HM) is a well known confound in analyses of functional MRI (fMRI) data. Neuroimaging researchers therefore typically treat HM as a nuisance covariate in their analyses. Even so, it is possible that HM shares a common genetic influence with the trait of interest. Here we investigate the extent to which this relationship is due to shared genetic factors, using HM extracted from resting-state fMRI and maternal and self report measures of Inattention and Hyperactivity-Impulsivity from the Strengths and Weaknesses of ADHD Symptoms and Normal Behaviour (SWAN) scales. Our sample consisted of healthy young adult twins (N = 627 (63% females) including 95 MZ and 144 DZ twin pairs, mean age 22, who had mother-reported SWAN; N = 725 (58% females) including 101 MZ and 156 DZ pairs, mean age 25, with self reported SWAN). This design enabled us to distinguish genetic from environmental factors in the association between head movement and ADHD scales. HM was moderately correlated with maternal reports of Inattention (r = 0.17, p-value = 7.4E-5) and Hyperactivity-Impulsivity (r = 0.16, p-value = 2.9E-4), and these associations were mainly due to pleiotropic genetic factors with genetic correlations [95% CIs] of rg = 0.24 [0.02, 0.43] and rg = 0.23 [0.07, 0.39]. Correlations between self-reports and HM were not significant, due largely to increased measurement error. These results indicate that treating HM as a nuisance covariate in neuroimaging studies of ADHD will likely reduce power to detect between-group effects, as the implicit assumption of independence between HM and Inattention or Hyperactivity-Impulsivity is not warranted. The implications of this finding are problematic for fMRI studies of ADHD, as failing to apply HM correction is known to increase the likelihood of false positives. We discuss two ways to circumvent this problem: censoring the motion contaminated frames of the RS-fMRI scan or explicitly modeling the relationship between HM and Inattention or Hyperactivity-Impulsivity.
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Affiliation(s)
- Baptiste Couvy-Duchesne
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Psychology, University of Queensland, Brisbane, Australia
- Centre for Advanced Imaging, University of Queensland, Brisbane, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Jane L. Ebejer
- Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, Virginia, United States of America
| | - Nathan A. Gillespie
- Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, Virginia, United States of America
| | - David L. Duffy
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Ian B. Hickie
- Brain & Mind Research Institute, University of Sydney, Sydney, Australia
| | - Paul M. Thompson
- Imaging Genetics Center, Keck School of Medicine, University of Southern California, Marina del Rey, California, United States of America
| | | | - Greig I. de Zubicaray
- School of Psychology, University of Queensland, Brisbane, Australia
- Institute of Health Biomedical Innovation, Queensland Institute of Technology, Brisbane, Australia
| | - Katie L. McMahon
- Centre for Advanced Imaging, University of Queensland, Brisbane, Australia
| | | | - Margaret J. Wright
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
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Vasquez LJ, Mann AL, Chen L, Soranzo N. From GWAS to function: lessons from blood cells. ISBT SCIENCE SERIES 2016; 11:211-219. [PMID: 27347004 PMCID: PMC4916502 DOI: 10.1111/voxs.12217] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Haematopoiesis, or the process of formation of mature blood cells from committed progenitors, represents an accessible and well-studied paradigm of cell differentiation and lineage specification. Genetic association studies provide a powerful approach to discover new genes, biological pathways and mechanisms underlying haematopoietic development. Here, we highlight recent findings of genomewide association studies (GWAS) linking 145 genomic loci to traits affecting the formation of red and white cells and platelets in European and other ancestries. We present strategies to address the main challenges in GWAS discoveries, particularly to find functional and regulatory effects of genetic variants, and to identify genes through which these genetic variants affect haematological phenotypes. We argue that studies of haematological trait variation provide an ideal paradigm for understanding the function of GWAS-associated variants owing to the accessible nature of cells, simple cellular phenotype and focused efforts to characterize the genetic and epigenetic factors influencing the regulatory landscape in highly pure mature cell populations.
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Affiliation(s)
- L J Vasquez
- Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton UK
| | - A L Mann
- Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton UK
| | - L Chen
- Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton UK; Department of Haematology University of Cambridge Cambridge Biomedical Campus Cambridge UK
| | - N Soranzo
- Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton UK; Department of Haematology University of Cambridge Cambridge Biomedical Campus Cambridge UK
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40
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Influence of Genetic Variants in EGF and Other Genes on Hematological Traits in Korean Populations by a Genome-Wide Approach. BIOMED RESEARCH INTERNATIONAL 2015; 2015:914965. [PMID: 26064965 PMCID: PMC4430676 DOI: 10.1155/2015/914965] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/31/2015] [Accepted: 03/31/2015] [Indexed: 01/11/2023]
Abstract
Hematological traits are important health indicators and are used as diagnostic clinical parameters for human disorders. Recently, genome-wide association studies (GWAS) identified many genetic loci associated with hematological traits in diverse ethnic groups. However, additional GWAS are necessary to elucidate the breadth of genetic variation and the underlying genetic architecture represented by hematological metrics. To identify additional genetic loci influencing hematological traits (such as hematocrit, hemoglobin concentration, white blood cell count, red blood cell count, and platelet count), we conducted GWAS and meta-analyses on data from 12,509 Korean individuals grouped into population-based cohorts. Of interest is EGF, a factor plays a role in the proliferation and differentiation of hematopoietic progenitor cells. We identified a novel EGF variant, which associated with platelet count in our study (Pcombined = 2.44 × 10−15). Our study also replicated 16 genetic associations related to five hematological traits with genome-wide significance (P < 5 × 10−8) that were previously established in other ethnic groups. Of these, variants influencing platelet count are distributed across several genes and have pleiotropic effects in coronary artery disease and dyslipidemia. Our findings may aid in elucidating molecular mechanisms underlying not only hematopoiesis but also inflammatory and cardiovascular diseases.
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41
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Roederer M, Quaye L, Mangino M, Beddall MH, Mahnke Y, Chattopadhyay P, Tosi I, Napolitano L, Terranova Barberio M, Menni C, Villanova F, Di Meglio P, Spector TD, Nestle FO. The genetic architecture of the human immune system: a bioresource for autoimmunity and disease pathogenesis. Cell 2015; 161:387-403. [PMID: 25772697 PMCID: PMC4393780 DOI: 10.1016/j.cell.2015.02.046] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/22/2014] [Accepted: 02/04/2015] [Indexed: 01/22/2023]
Abstract
Despite recent discoveries of genetic variants associated with autoimmunity and infection, genetic control of the human immune system during homeostasis is poorly understood. We undertook a comprehensive immunophenotyping approach, analyzing 78,000 immune traits in 669 female twins. From the top 151 heritable traits (up to 96% heritable), we used replicated GWAS to obtain 297 SNP associations at 11 genetic loci, explaining up to 36% of the variation of 19 traits. We found multiple associations with canonical traits of all major immune cell subsets and uncovered insights into genetic control for regulatory T cells. This data set also revealed traits associated with loci known to confer autoimmune susceptibility, providing mechanistic hypotheses linking immune traits with the etiology of disease. Our data establish a bioresource that links genetic control elements associated with normal immune traits to common autoimmune and infectious diseases, providing a shortcut to identifying potential mechanisms of immune-related diseases.
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Affiliation(s)
- Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA.
| | - Lydia Quaye
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK; NIHR Biomedical Research Centre at Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Margaret H Beddall
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Yolanda Mahnke
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Pratip Chattopadhyay
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Isabella Tosi
- Cutaneous Medicine Unit, St. John's Institute of Dermatology, King's College London, London SE1 9RT, UK; NIHR Biomedical Research Centre at Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Luca Napolitano
- Cutaneous Medicine Unit, St. John's Institute of Dermatology, King's College London, London SE1 9RT, UK
| | | | - Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Federica Villanova
- Cutaneous Medicine Unit, St. John's Institute of Dermatology, King's College London, London SE1 9RT, UK; NIHR Biomedical Research Centre at Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Paola Di Meglio
- Cutaneous Medicine Unit, St. John's Institute of Dermatology, King's College London, London SE1 9RT, UK
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK.
| | - Frank O Nestle
- Cutaneous Medicine Unit, St. John's Institute of Dermatology, King's College London, London SE1 9RT, UK; NIHR Biomedical Research Centre at Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
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Brodin P, Jojic V, Gao T, Bhattacharya S, Angel CJL, Furman D, Shen-Orr S, Dekker CL, Swan GE, Butte AJ, Maecker HT, Davis MM. Variation in the human immune system is largely driven by non-heritable influences. Cell 2015; 160:37-47. [PMID: 25594173 DOI: 10.1016/j.cell.2014.12.020] [Citation(s) in RCA: 702] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/20/2014] [Accepted: 11/14/2014] [Indexed: 12/31/2022]
Abstract
There is considerable heterogeneity in immunological parameters between individuals, but its sources are largely unknown. To assess the relative contribution of heritable versus non-heritable factors, we have performed a systems-level analysis of 210 healthy twins between 8 and 82 years of age. We measured 204 different parameters, including cell population frequencies, cytokine responses, and serum proteins, and found that 77% of these are dominated (>50% of variance) and 58% almost completely determined (>80% of variance) by non-heritable influences. In addition, some of these parameters become more variable with age, suggesting the cumulative influence of environmental exposure. Similarly, the serological responses to seasonal influenza vaccination are also determined largely by non-heritable factors, likely due to repeated exposure to different strains. Lastly, in MZ twins discordant for cytomegalovirus infection, more than half of all parameters are affected. These results highlight the largely reactive and adaptive nature of the immune system in healthy individuals.
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Affiliation(s)
- Petter Brodin
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institutet, 17121 Solna, Sweden; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Vladimir Jojic
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tianxiang Gao
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sanchita Bhattacharya
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Cesar J Lopez Angel
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - David Furman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Shai Shen-Orr
- Department of Immunology, Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Cornelia L Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Gary E Swan
- Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Atul J Butte
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA; Center for Pediatric Bioinformatics, Lucille Packard Children's Hospital, Stanford University, Stanford, CA 94304, USA
| | - Holden T Maecker
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA; Human Immune Monitoring Center, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94304, USA.
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Van 't Erve TJ, Wagner BA, Martin SM, Knudson CM, Blendowski R, Keaton M, Holt T, Hess JR, Buettner GR, Ryckman KK, Darbro BW, Murray JC, Raife TJ. The heritability of hemolysis in stored human red blood cells. Transfusion 2015; 55:1178-85. [PMID: 25644965 DOI: 10.1111/trf.12992] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 11/14/2014] [Accepted: 11/16/2014] [Indexed: 11/28/2022]
Abstract
BACKGROUND The transfusion of red blood cells (RBCs) with maximum therapeutic efficacy is a major goal in transfusion medicine. One of the criteria used in determining stored RBC quality is end-of-storage hemolysis. Between donors, a wide range of hemolysis is observed under identical storage conditions. Here, a potential mechanism for this wide range is investigated. We hypothesize that the magnitude of hemolysis is a heritable trait. Also, we investigated correlations between hemolysis and RBC metabolites; this will establish pathways influencing hemolysis as future targets for genetic analysis. STUDY DESIGN AND METHODS Units of RBCs from identical and nonidentical twins were collected and stored under standard conditions for 56 days. Hemolysis, adenosine triphosphate (ATP), and total glutathione (tGSH) were measured throughout storage. Nontargeted metabolic analyses were performed on RBCs that had been stored for 28 days. Heritability was determined by comparing values between identical and nonidentical twins. RESULTS Hemolysis was found to be heritable (mean > 45%) throughout the storage period. Potential correlations were observed between hemolysis and metabolites from the purine metabolism, lysolipid, and glycolysis pathways. These also exhibited heritability (>20%). No correlation was found with ATP or tGSH. CONCLUSION The susceptibility of RBCs to lysis during storage is partly determined by inheritance. We have also uncovered several pathways that are candidate targets for future genomewide association studies. These findings will aid in the design of better storage solutions and the development of donor screening tools that minimize hemolysis during storage.
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Affiliation(s)
- Thomas J Van 't Erve
- Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, Iowa
| | - Brett A Wagner
- Free Radical and Radiation Biology Program, Radiation Oncology, University of Iowa, Iowa City, Iowa
| | - Sean M Martin
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - C Michael Knudson
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Robyn Blendowski
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | | | | | - John R Hess
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Garry R Buettner
- Free Radical and Radiation Biology Program, Radiation Oncology, University of Iowa, Iowa City, Iowa.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
| | - Kelli K Ryckman
- Department of Epidemiology, College of Public Health, University of Iowa
| | - Benjamin W Darbro
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Thomas J Raife
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa
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Oh JH, Kim YK, Moon S, Kim YJ, Kim BJ. Genome-wide association study identifies candidate Loci associated with platelet count in koreans. Genomics Inform 2014; 12:225-30. [PMID: 25705162 PMCID: PMC4330258 DOI: 10.5808/gi.2014.12.4.225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/08/2014] [Accepted: 11/09/2014] [Indexed: 11/20/2022] Open
Abstract
Platelets are derived from the fragments that are formed from the cytoplasm of bone marrow megakaryocytes-small irregularly shaped anuclear cells. Platelets respond to vascular damage, contracts blood vessels, and attaches to the damaged region, thereby stopping bleeding, together with the action of blood coagulation factors. Platelet activation is known to affect genes associated with vascular risk factors, as well as with arteriosclerosis and myocardial infarction. Here, we performed a genome-wide association study with 352,228 single-nucleotide polymorphisms typed in 8,842 subjects of the Korea Association Resource (KARE) project and replicated the results in 7,861 subjects from an independent population. We identified genetic associations between platelet count and common variants nearby chromosome 4p16.1 (p = 1.46 × 10-10, in the KIAA0232 gene), 6p21 (p = 1.36 × 10-7, in the BAK1 gene), and 12q24.12 (p = 1.11 × 10-15, in the SH2B3 gene). Our results illustrate the value of large-scale discovery and a focus for several novel research avenues.
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Affiliation(s)
- Ji Hee Oh
- Division of Structural and Functional Genomics, National Institute of Health, Cheongwon 363-951, Korea
| | - Yun Kyoung Kim
- Division of Structural and Functional Genomics, National Institute of Health, Cheongwon 363-951, Korea
| | - Sanghoon Moon
- Division of Structural and Functional Genomics, National Institute of Health, Cheongwon 363-951, Korea
| | - Young Jin Kim
- Division of Structural and Functional Genomics, National Institute of Health, Cheongwon 363-951, Korea
| | - Bong-Jo Kim
- Division of Structural and Functional Genomics, National Institute of Health, Cheongwon 363-951, Korea
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45
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Chronic idiopathic neutrophilia in two twins. Case Rep Hematol 2014; 2014:785454. [PMID: 25431700 PMCID: PMC4241303 DOI: 10.1155/2014/785454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 10/21/2014] [Indexed: 11/17/2022] Open
Abstract
Neutrophilia in adults refers to an alteration in the total number of blood neutrophils that is in excess of about 7500 cells/μL. This definition is restrictive in childhood as neutrophil count is age-dependent. Chronic Idiopathic Neutrophilia (CIN) refers to a condition that persists for many years in individuals who appear otherwise healthy. CIN is rarely mentioned in scientific literature and in academic books of hematology; only few words are dedicated to this topic. We report a case study of two twins with CIN followed from the first year of life to 24 years of age. To the best of our knowledge this is the first case report of two twins with CIN followed through a long period of time. We believe that our observation may contribute to better understand and characterize this hematologic abnormality.
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46
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Abstract
This thesis explores the contribution of twin studies, particularly those studies originating from the Danish Twin Registry, to the understanding of the aetiology of asthma. First, it is explored how twin studies have established the contribution of genetic and environmental factors to the variation in the susceptibility to asthma, and to the variation in several aspects of the clinical expression of the disease such as its age at onset, its symptomatology, its intermediate phenotypes, and its relationship with other atopic diseases. Next, it is explored how twin studies have corroborated theories explaining asthma's recent increase in prevalence, and last, how these fit with the explanations of the epidemiological trends in other common chronic diseases of modernity.
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47
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Castillo-Fernandez JE, Spector TD, Bell JT. Epigenetics of discordant monozygotic twins: implications for disease. Genome Med 2014; 6:60. [PMID: 25484923 PMCID: PMC4254430 DOI: 10.1186/s13073-014-0060-z] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/25/2014] [Indexed: 12/13/2022] Open
Abstract
Monozygotic (MZ) twins share nearly all of their genetic variants and many similar environments before and after birth. However, they can also show phenotypic discordance for a wide range of traits. Differences at the epigenetic level may account for such discordances. It is well established that epigenetic states can contribute to phenotypic variation, including disease. Epigenetic states are dynamic and potentially reversible marks involved in gene regulation, which can be influenced by genetics, environment, and stochastic events. Here, we review advances in epigenetic studies of discordant MZ twins, focusing on disease. The study of epigenetics and disease using discordant MZ twins offers the opportunity to control for many potential confounders encountered in general population studies, such as differences in genetic background, early-life environmental exposure, age, gender, and cohort effects. Recently, analysis of disease-discordant MZ twins has been successfully used to study epigenetic mechanisms in aging, cancer, autoimmune disease, psychiatric, neurological, and multiple other traits. Epigenetic aberrations have been found in a range of phenotypes, and challenges have been identified, including sampling time, tissue specificity, validation, and replication. The results have relevance for personalized medicine approaches, including the identification of prognostic, diagnostic, and therapeutic targets. The findings also help to identify epigenetic markers of environmental risk and molecular mechanisms involved in disease and disease progression, which have implications both for understanding disease and for future medical research.
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Affiliation(s)
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, SE1 7EH UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, SE1 7EH UK
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48
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Bielczyk-Maczyńska E, Serbanovic-Canic J, Ferreira L, Soranzo N, Stemple DL, Ouwehand WH, Cvejic A. A loss of function screen of identified genome-wide association study Loci reveals new genes controlling hematopoiesis. PLoS Genet 2014; 10:e1004450. [PMID: 25010335 PMCID: PMC4091788 DOI: 10.1371/journal.pgen.1004450] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 05/02/2014] [Indexed: 01/01/2023] Open
Abstract
The formation of mature cells by blood stem cells is very well understood at the cellular level and we know many of the key transcription factors that control fate decisions. However, many upstream signalling and downstream effector processes are only partially understood. Genome wide association studies (GWAS) have been particularly useful in providing new directions to dissect these pathways. A GWAS meta-analysis identified 68 genetic loci controlling platelet size and number. Only a quarter of those genes, however, are known regulators of hematopoiesis. To determine function of the remaining genes we performed a medium-throughput genetic screen in zebrafish using antisense morpholino oligonucleotides (MOs) to knock down protein expression, followed by histological analysis of selected genes using a wide panel of different hematopoietic markers. The information generated by the initial knockdown was used to profile phenotypes and to position candidate genes hierarchically in hematopoiesis. Further analysis of brd3a revealed its essential role in differentiation but not maintenance and survival of thrombocytes. Using the from-GWAS-to-function strategy we have not only identified a series of genes that represent novel regulators of thrombopoiesis and hematopoiesis, but this work also represents, to our knowledge, the first example of a functional genetic screening strategy that is a critical step toward obtaining biologically relevant functional data from GWA study for blood cell traits.
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Affiliation(s)
- Ewa Bielczyk-Maczyńska
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Jovana Serbanovic-Canic
- MRC Centre for Developmental and Biomedical Genetics, University of Sheffield, Sheffield, United Kingdom
- Department of Cardiovascular Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Lauren Ferreira
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nicole Soranzo
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Derek L. Stemple
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Ana Cvejic
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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49
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Stadhouders R, Aktuna S, Thongjuea S, Aghajanirefah A, Pourfarzad F, van Ijcken W, Lenhard B, Rooks H, Best S, Menzel S, Grosveld F, Thein SL, Soler E. HBS1L-MYB intergenic variants modulate fetal hemoglobin via long-range MYB enhancers. J Clin Invest 2014; 124:1699-710. [PMID: 24614105 DOI: 10.1172/jci71520] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 01/09/2014] [Indexed: 01/21/2023] Open
Abstract
Genetic studies have identified common variants within the intergenic region (HBS1L-MYB) between GTP-binding elongation factor HBS1L and myeloblastosis oncogene MYB on chromosome 6q that are associated with elevated fetal hemoglobin (HbF) levels and alterations of other clinically important human erythroid traits. It is unclear how these noncoding sequence variants affect multiple erythrocyte characteristics. Here, we determined that several HBS1L-MYB intergenic variants affect regulatory elements that are occupied by key erythroid transcription factors within this region. These elements interact with MYB, a critical regulator of erythroid development and HbF levels. We found that several HBS1L-MYB intergenic variants reduce transcription factor binding, affecting long-range interactions with MYB and MYB expression levels. These data provide a functional explanation for the genetic association of HBS1L-MYB intergenic polymorphisms with human erythroid traits and HbF levels. Our results further designate MYB as a target for therapeutic induction of HbF to ameliorate sickle cell and β-thalassemia disease severity.
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50
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Gonzalez MV, Mousel MR, Herndon DR, Jiang Y, Dalrymple BP, Reynolds JO, Johnson WC, Herrmann-Hoesing LM, White SN. A divergent Artiodactyl MYADM-like repeat is associated with erythrocyte traits and weight of lamb weaned in domestic sheep. PLoS One 2013; 8:e74700. [PMID: 24023702 PMCID: PMC3758307 DOI: 10.1371/journal.pone.0074700] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 08/03/2013] [Indexed: 12/15/2022] Open
Abstract
A genome-wide association study (GWAS) was performed to investigate seven red blood cell (RBC) phenotypes in over 500 domestic sheep (Ovis aries) from three breeds (Columbia, Polypay, and Rambouillet). A single nucleotide polymorphism (SNP) showed genome-wide significant association with increased mean corpuscular hemoglobin concentration (MCHC, P = 6.2×10−14) and genome-wide suggestive association with decreased mean corpuscular volume (MCV, P = 2.5×10−6). The ovine HapMap project found the same genomic region and the same peak SNP has been under extreme historical selective pressure, demonstrating the importance of this region for survival, reproduction, and/or artificially selected traits. We observed a large (>50 kb) variant haplotype sequence containing a full-length divergent artiodactyl MYADM-like repeat in strong linkage disequilibrium with the associated SNP. MYADM gene family members play roles in membrane organization and formation in myeloid cells. However, to our knowledge, no member of the MYADM gene family has been identified in development of morphologically variant RBCs. The specific RBC differences may be indicative of alterations in morphology. Additionally, erythrocytes with altered morphological structure often exhibit increased structural fragility, leading to increased RBC turnover and energy expenditure. The divergent artiodactyl MYADM-like repeat was also associated with increased ewe lifetime kilograms of lamb weaned (P = 2×10−4). This suggests selection for normal RBCs might increase lamb weights, although further validation is required before implementation in marker-assisted selection. These results provide clues to explain the strong selection on the artiodactyl MYADM-like repeat locus in sheep, and suggest MYADM family members may be important for RBC morphology in other mammals.
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Affiliation(s)
- Michael V. Gonzalez
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Michelle R. Mousel
- U.S. Sheep Experiment Station, Agricultural Research Service, U.S. Department of Agriculture, Dubois, Idaho, United States of America
| | - David R. Herndon
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America
| | - Yu Jiang
- CSIRO Animal, Food and Health Sciences, St. Lucia, Australia
| | | | - James O. Reynolds
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America
| | - Wendell C. Johnson
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America
| | - Lynn M. Herrmann-Hoesing
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Stephen N. White
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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