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Shen M, Luo X, Wu C, Wang J, Wang Z, Lei M. Pernicious anemia is a common cause of cobalamin deficiency-caused megaloblastic anemia in Hainan, China. Hematology 2024; 29:2399375. [PMID: 39248712 DOI: 10.1080/16078454.2024.2399375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 08/27/2024] [Indexed: 09/10/2024] Open
Abstract
BACKGROUND Pernicious anemia (PA) is believed to be highly prevalent in Western countries but has rarely been reported in China. The study explores whether PA, an autoimmune disease, is an uncommon cause of cobalamin (vitamin B12) deficiency anemia in China. METHODS Clinical and hematological data were collected from 90 cobalamin deficiency-caused megaloblastic anemia (MA) patients between July 2014 and December 2021. Through anti-intrinsic factor antibody (IFA) and anti-parietal cell antibody (PCA) testing, PA was distinguished from other causes of cobalamin deficiency leading to MA. Meanwhile, 30 healthy controls (HCs) were included to estimate the positive rates of IFA and PCA. RESULTS Of the 30 HCs, only one tested positive for IFA, and all 30 tested negative for PCA. Among the 90 patients with cobalamin deficiency-caused MA, 76.7% were positive for IFA, and 47.8% were positive for PCA; a total of 76 patients (84.4%) were diagnosed with PA. The mean follow-up time was 41.0 ± 16.3 months. During the follow-up period, no case relapsed among the continuous cobalamin-supply treatment patients, while 24.4% of patients relapsed due to the interruption of maintenance cobalamin-supplement therapy (the median recurrence time was 54.0 ± 17.7 months). CONCLUSIONS The proportion of PA in cobalamin deficiency-caused MA patients in Hainan province was higher than 80%, which was more common than expected. Therefore, screening for IFA, PCA, endoscopic biopsy, and thyroid-related parameters are recommended for all cobalamin deficiency-caused MA patients. Furthermore, maintenance cobalamin-supplement therapy is important for PA patients.
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Affiliation(s)
- Meixiao Shen
- Department of Hematology, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, People's Republic of China
| | - Xiansheng Luo
- Department of Hematology, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, People's Republic of China
| | - Cuiyun Wu
- Department of Laboratory Medicine, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, People's Republic of China
| | - Juan Wang
- Department of Hematology, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, People's Republic of China
| | - Zhiming Wang
- Department of Hematology, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, People's Republic of China
| | - Meiqing Lei
- Department of Hematology, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, People's Republic of China
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Kotowski MJ, Ostrowski P, Sieńko J, Czerny B, Tejchman K, Machaliński B, Górska A, Mrozikiewicz AE, Bogacz A. The Importance of the FUT2 rs602662 Polymorphism in the Risk of Cardiovascular Complications in Patients after Kidney Transplantation. Int J Mol Sci 2024; 25:6562. [PMID: 38928269 PMCID: PMC11203847 DOI: 10.3390/ijms25126562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/05/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The FUT2 gene encodes an enzyme called α-1,2-fucosyltransferase, which is involved in the formation of blood group antigens AB0(H) and is also involved in the processes of vitamin B12 absorption and its transport between cells. FUT2 gene polymorphisms are associated with vitamin B12 levels in the body. Vitamin B12 deficiency associated with hyperhomocysteinemia is a major risk factor for cardiovascular diseases (CVDs), which are one of the main causes of death in patients after kidney transplantation. The aim of our study was to determine the impact of the rs602662 (G>A) polymorphism of the FUT2 gene on the functionality of transplanted kidneys and the risk of CVD in patients after kidney transplantation. The study included 402 patients treated with immunosuppression (183 patients taking cyclosporine (CsA) and 219 patients taking tacrolimus (TAC)). The analysis of the FUT2 rs602662 (G>A) polymorphism was performed using real-time PCR. Patients with CsA were more likely to be underweight (1.64% vs. 0.91%) and obese (27.87% vs. 15.98%), while those taking TAC were more likely to be of normal weight (39.27%) or overweight (43.84%). No statistically significant differences were observed comparing the mean blood pressure, both systolic and diastolic. The renal profile showed a higher median urea nitrogen concentration in patients with CsA (26.45 mg/dL (20.60-35.40) vs. 22.95 mg/dL (17.60-33.30), p = 0.004). The observed frequency of rs602662 alleles of the FUT2 gene was similar in the analyzed groups. The A allele was present in 43.7% of patients with CsA and 41.1% of those taking TAC (OR = 0.898; 95% CI: 0.678-1.189; p = 0.453). In the group with CsA, the GG genotype was present in 32.2% of patients, the GA in 48.1% and the AA in 19.7%. A similar distribution was obtained in the TAC group: GG-33.8%, GA-50.2%, and AA-16.0%. An association of genotypes containing the G allele with a higher incidence of hypertension was observed. The G allele was present in 65% of people with hypertension and in 56% of patients with normal blood pressure (p = 0.036). Moreover, the evaluation of the renal parameters showed no effect of the FUT2 polymorphism on the risk of organ rejection because the levels of creatinine, eGFR, potassium, and urea nitrogen were prognostic of successful transplantation. Our results suggest that the rs6022662 FUT2 polymorphism may influence the risk of cardiovascular diseases.
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Affiliation(s)
- Maciej Józef Kotowski
- Department of General Surgery and Transplantology, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland; (M.J.K.); (P.O.); (K.T.)
| | - Piotr Ostrowski
- Department of General Surgery and Transplantology, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland; (M.J.K.); (P.O.); (K.T.)
| | - Jerzy Sieńko
- Institute of Physical Culture Sciences, University of Szczecin, 70-453 Szczecin, Poland;
| | - Bogusław Czerny
- Department of Stem Cells and Regenerative Medicine, Institute of Natural Fibres and Medicinal Plants, Kolejowa 2, 62-064 Plewiska, Poland; (B.C.); (A.G.)
- Department of Pharmacology and Pharmacoeconomics, Pomeranian Medical University in Szczecin, Żołnierska 48, 71-230 Szczecin, Poland
| | - Karol Tejchman
- Department of General Surgery and Transplantology, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland; (M.J.K.); (P.O.); (K.T.)
| | - Bogusław Machaliński
- Department of General Pathology, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland;
| | - Aleksandra Górska
- Department of Stem Cells and Regenerative Medicine, Institute of Natural Fibres and Medicinal Plants, Kolejowa 2, 62-064 Plewiska, Poland; (B.C.); (A.G.)
| | - Aleksandra E. Mrozikiewicz
- Department of Obstetrics and Women’s Diseases, Poznan University of Medical Sciences, Polna 33, 60-535 Poznan, Poland;
| | - Anna Bogacz
- Department of Personalized Medicine and Cell Therapy, Regional Blood Center, Marcelińska 44, 60-354 Poznan, Poland
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Moreno-Loro A, Giráldez Á, Jiménez F, López-Bueno I, Pérez-Ramírez A, Romero-Gómez M. Novel approaches in the medical management of compensated cirrhosis. Expert Rev Gastroenterol Hepatol 2024; 18:239-256. [PMID: 38785070 DOI: 10.1080/17474124.2024.2358149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
INTRODUCTION Classically, clinical practice guidelines and expert recommendations have focused on the management of decompensated cirrhotic patients, so we focused this review on improving care for compensated cirrhotic patients who are followed up in outpatient clinics. AREAS COVERED We reviewed the current methods for establishing liver function, the diagnosis and management of advanced chronic liver disease and clinically significant portal hypertension as well as the prevention of its complications, with special attention to covert hepatic encephalopathy, we also paid attention to the extrahepatic complications of cirrhosis and the palliative care. All this from the perspective of evidence-based medicine and trying to empower precision medicine. The literature search was undertaken by PubMed with 'cirrhosis,' 'advanced chronic liver disease,' 'liver function,' 'portal hypertension,' 'covert hepatic encephalopathy,' 'minimal hepatic encephalopathy,' 'palliative care' as MeSH terms. EXPERT OPINION We must offer compensated cirrhotic patients specific care and measures to prevent the progression of the disease and the appearance of its complications beyond the calculation of liver function and imaging screening for hepatocellular carcinoma that we perform every six months. Entities that have typically received little attention, such as covert hepatic encephalopathy, extrahepatic complications and symptoms of cirrhosis, and palliative care, must come to the spotlight.
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Affiliation(s)
- Antonio Moreno-Loro
- Digestive Diseases Department and ciberehd, Virgen del Rocío University Hospital, Institute of Biomedicine (HUVR/CSIC/US), University of Seville, Seville, Spain
| | - Álvaro Giráldez
- Digestive Diseases Department and ciberehd, Virgen del Rocío University Hospital, Institute of Biomedicine (HUVR/CSIC/US), University of Seville, Seville, Spain
| | - Fernando Jiménez
- Digestive Diseases Department and ciberehd, Virgen del Rocío University Hospital, Institute of Biomedicine (HUVR/CSIC/US), University of Seville, Seville, Spain
| | - Ignacio López-Bueno
- Digestive Diseases Department and ciberehd, Virgen del Rocío University Hospital, Institute of Biomedicine (HUVR/CSIC/US), University of Seville, Seville, Spain
| | - Alberto Pérez-Ramírez
- Digestive Diseases Department and ciberehd, Virgen del Rocío University Hospital, Institute of Biomedicine (HUVR/CSIC/US), University of Seville, Seville, Spain
| | - Manuel Romero-Gómez
- Digestive Diseases Department and ciberehd, Virgen del Rocío University Hospital, Institute of Biomedicine (HUVR/CSIC/US), University of Seville, Seville, Spain
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Soejima M, Koda Y. Detection of c.375A>G, c.385A>T, c.571C>T, and sedel2 of FUT2 via Real-Time PCR in a Single Tube. Diagnostics (Basel) 2023; 13:2022. [PMID: 37370917 DOI: 10.3390/diagnostics13122022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
α(1,2)fucosyltransferase (Se enzyme) encoded by FUT2 is involved in the secretor status of ABH(O) blood group antigens. The sedel2 allele is one of the non-functional FUT2 (se) alleles in which 9.3 kb, containing the entire coding region of FUT2, is deleted by Alu-mediated nonhomologous recombination. In addition to this allele, three SNPs of FUT2, c.375A>G, c.385A>T, and c.571C>T, appear to be prevalent in certain Oceanian populations such as Polynesians. Recently, we developed an endpoint genotyping assay to determine sedel2 zygosity, using a FAM-labeled probe for detection of the sedel2 allele and a VIC-labeled probe for the detection of FUT2. In this study, instead of the VIC probe, a HEX-labeled probe covering both c.375A>G and c.385A>T and a Cy5-labeled probe covering c.571C>T were added to the sedel2 allele assay mixture to allow for the simultaneous detection of these four variations via endpoint genotyping for sedel2 zygosity and fluorescence melting curve analysis for c.375A>G, c.385A>T, and c.571C>T genotyping. The results obtained from 24 Samoan subjects using this method were identical to those obtained using previous methods. Therefore, it appears that the present method can accurately determine these four variations simultaneously.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan
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5
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Packer RJ, Shrine N, Hall R, Melbourne CA, Thompson R, Williams AT, Paynton ML, Guyatt AL, Allen RJ, Lee PH, John C, Campbell A, Hayward C, de Vries M, Vonk JM, Davitte J, Hessel E, Michalovich D, Betts JC, Sayers I, Yeo A, Hall IP, Tobin MD, Wain LV. Genome-wide association study of chronic sputum production implicates loci involved in mucus production and infection. Eur Respir J 2023; 61:2201667. [PMID: 37263751 PMCID: PMC10284065 DOI: 10.1183/13993003.01667-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/17/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Chronic sputum production impacts on quality of life and is a feature of many respiratory diseases. Identification of the genetic variants associated with chronic sputum production in a disease agnostic sample could improve understanding of its causes and identify new molecular targets for treatment. METHODS We conducted a genome-wide association study (GWAS) of chronic sputum production in UK Biobank. Signals meeting genome-wide significance (p<5×10-8) were investigated in additional independent studies, were fine-mapped and putative causal genes identified by gene expression analysis. GWASs of respiratory traits were interrogated to identify whether the signals were driven by existing respiratory disease among the cases and variants were further investigated for wider pleiotropic effects using phenome-wide association studies (PheWASs). RESULTS From a GWAS of 9714 cases and 48 471 controls, we identified six novel genome-wide significant signals for chronic sputum production including signals in the human leukocyte antigen (HLA) locus, chromosome 11 mucin locus (containing MUC2, MUC5AC and MUC5B) and FUT2 locus. The four common variant associations were supported by independent studies with a combined sample size of up to 2203 cases and 17 627 controls. The mucin locus signal had previously been reported for association with moderate-to-severe asthma. The HLA signal was fine-mapped to an amino acid change of threonine to arginine (frequency 36.8%) in HLA-DRB1 (HLA-DRB1*03:147). The signal near FUT2 was associated with expression of several genes including FUT2, for which the direction of effect was tissue dependent. Our PheWAS identified a wide range of associations including blood cell traits, liver biomarkers, infections, gastrointestinal and thyroid-associated diseases, and respiratory disease. CONCLUSIONS Novel signals at the FUT2 and mucin loci suggest that mucin fucosylation may be a driver of chronic sputum production even in the absence of diagnosed respiratory disease and provide genetic support for this pathway as a target for therapeutic intervention.
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Affiliation(s)
- Richard J Packer
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Nick Shrine
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Robert Hall
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Carl A Melbourne
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Rebecca Thompson
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Alex T Williams
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Megan L Paynton
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Richard J Allen
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Paul H Lee
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Catherine John
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Maaike de Vries
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | | | | | | | | | - Ian Sayers
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | | | - Ian P Hall
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Martin D Tobin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Louise V Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Leicester, UK
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Singhal P, Veturi Y, Dudek SM, Lucas A, Frase A, van Steen K, Schrodi SJ, Fasel D, Weng C, Pendergrass R, Schaid DJ, Kullo IJ, Dikilitas O, Sleiman PMA, Hakonarson H, Moore JH, Williams SM, Ritchie MD, Verma SS. Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets. Am J Hum Genet 2023; 110:575-591. [PMID: 37028392 PMCID: PMC10119154 DOI: 10.1016/j.ajhg.2023.03.007] [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: 12/12/2022] [Accepted: 03/07/2023] [Indexed: 04/09/2023] Open
Abstract
Leveraging linkage disequilibrium (LD) patterns as representative of population substructure enables the discovery of additive association signals in genome-wide association studies (GWASs). Standard GWASs are well-powered to interrogate additive models; however, new approaches are required for invesigating other modes of inheritance such as dominance and epistasis. Epistasis, or non-additive interaction between genes, exists across the genome but often goes undetected because of a lack of statistical power. Furthermore, the adoption of LD pruning as customary in standard GWASs excludes detection of sites that are in LD but might underlie the genetic architecture of complex traits. We hypothesize that uncovering long-range interactions between loci with strong LD due to epistatic selection can elucidate genetic mechanisms underlying common diseases. To investigate this hypothesis, we tested for associations between 23 common diseases and 5,625,845 epistatic SNP-SNP pairs (determined by Ohta's D statistics) in long-range LD (>0.25 cM). Across five disease phenotypes, we identified one significant and four near-significant associations that replicated in two large genotype-phenotype datasets (UK Biobank and eMERGE). The genes that were most likely involved in the replicated associations were (1) members of highly conserved gene families with complex roles in multiple pathways, (2) essential genes, and/or (3) genes that were associated in the literature with complex traits that display variable expressivity. These results support the highly pleiotropic and conserved nature of variants in long-range LD under epistatic selection. Our work supports the hypothesis that epistatic interactions regulate diverse clinical mechanisms and might especially be driving factors in conditions with a wide range of phenotypic outcomes.
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Affiliation(s)
- Pankhuri Singhal
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yogasudha Veturi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott M Dudek
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anastasia Lucas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alex Frase
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristel van Steen
- Department of Human Genetics, Katholieke Universiteit Leuven, ON4 Herestraat 49, 3000 Leuven, Belgium
| | - Steven J Schrodi
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - David Fasel
- Columbia University, New York, NY 10027, USA
| | | | | | | | | | | | | | - Hakon Hakonarson
- Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jason H Moore
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Scott M Williams
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Shefali S Verma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Estimation of Lewis Blood Group Status by Fluorescence Melting Curve Analysis in Simultaneous Genotyping of c.385A>T and Fusion Gene in FUT2 and c.59T>G and c.314C>T in FUT3. Diagnostics (Basel) 2023; 13:diagnostics13050931. [PMID: 36900072 PMCID: PMC10000471 DOI: 10.3390/diagnostics13050931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Lewis blood group status is determined by two fucosyltransferase activities: those of FUT2-encoded fucosyltransferase (Se enzyme) and FUT3-encoded fucosyltransferase (Le enzyme). In Japanese populations, c.385A>T in FUT2 and a fusion gene between FUT2 and its pseudogene SEC1P are the cause of most Se enzyme-deficient alleles (Sew and sefus), and c.59T>G and c.314C>T in FUT3 are tag SNPs for almost all nonfunctional FUT3 alleles (le59, le59,508, le59,1067, and le202,314). In this study, we first conducted a single-probe fluorescence melting curve analysis (FMCA) to determine c.385A>T and sefus using a pair of primers that collectively amplify FUT2, sefus, and SEC1P. Then, to estimate Lewis blood group status, a triplex FMCA was performed with a c.385A>T and sefus assay system by adding primers and probes to detect c.59T>G and c.314C>T in FUT3. We also validated these methods by analyzing the genotypes of 96 selected Japanese people whose FUT2 and FUT3 genotypes were already determined. The single-probe FMCA was able to identify six genotype combinations: 385A/A, 385T/T, sefus/sefus, 385A/T, 385A/sefus, and 385T/sefus. In addition, the triplex FMCA successfully identified both FUT2 and FUT3 genotypes, although the resolutions of the analysis of c.385A>T and sefus were somewhat reduced compared to that of the analysis of FUT2 alone. The estimation of the secretor status and Lewis blood group status using the form of FMCA used in this study may be useful for large-scale association studies in Japanese populations.
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Jajosky RP, Wu SC, Zheng L, Jajosky AN, Jajosky PG, Josephson CD, Hollenhorst MA, Sackstein R, Cummings RD, Arthur CM, Stowell SR. ABO blood group antigens and differential glycan expression: Perspective on the evolution of common human enzyme deficiencies. iScience 2023; 26:105798. [PMID: 36691627 PMCID: PMC9860303 DOI: 10.1016/j.isci.2022.105798] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Enzymes catalyze biochemical reactions and play critical roles in human health and disease. Enzyme variants and deficiencies can lead to variable expression of glycans, which can affect physiology, influence predilection for disease, and/or directly contribute to disease pathogenesis. Although certain well-characterized enzyme deficiencies result in overt disease, some of the most common enzyme deficiencies in humans form the basis of blood groups. These carbohydrate blood groups impact fundamental areas of clinical medicine, including the risk of infection and severity of infectious disease, bleeding risk, transfusion medicine, and tissue/organ transplantation. In this review, we examine the enzymes responsible for carbohydrate-based blood group antigen biosynthesis and their expression within the human population. We also consider the evolutionary selective pressures, e.g. malaria, that may account for the variation in carbohydrate structures and the implications of this biology for human disease.
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Affiliation(s)
- Ryan Philip Jajosky
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Biconcavity Inc, Lilburn, GA, USA
| | - Shang-Chuen Wu
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Leon Zheng
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Audrey N. Jajosky
- University of Rochester Medical Center, Department of Pathology and Laboratory Medicine, West Henrietta, NY, USA
| | | | - Cassandra D. Josephson
- Cancer and Blood Disorders Institute and Blood Bank/Transfusion Medicine Division, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
- Departments of Oncology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marie A. Hollenhorst
- Department of Pathology and Department of Medicine, Stanford University, Stanford, CA, USA
| | - Robert Sackstein
- Translational Glycobiology Institute, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Richard D. Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Connie M. Arthur
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Sean R. Stowell
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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Guevara-Ramírez P, Cadena-Ullauri S, Ruiz-Pozo VA, Tamayo-Trujillo R, Paz-Cruz E, Simancas-Racines D, Zambrano AK. Genetics, genomics, and diet interactions in obesity in the Latin American environment. Front Nutr 2022; 9:1063286. [PMID: 36532520 PMCID: PMC9751379 DOI: 10.3389/fnut.2022.1063286] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 10/25/2022] [Indexed: 08/25/2023] Open
Abstract
Obesity is a chronic disease characterized by abnormal or excessive fat accumulation that could impact an individual's health; moreover, the World Health Organization (WHO) has declared obesity a global epidemic since 1997. In Latin America, in 2016, reports indicated that 24.2% of the adult population was obese. The environmental factor or specific behaviors like dietary intake or physical activity have a vital role in the development of a condition like obesity, but the interaction of genes could contribute to that predisposition. Hence, it is vital to understand the relationship between genes and disease. Indeed, genetics in nutrition studies the genetic variations and their effect on dietary response; while genomics in nutrition studies the role of nutrients in gene expression. The present review represents a compendium of the dietary behaviors in the Latin American environment and the interactions of genes with their single nucleotide polymorphisms (SNPs) associated with obesity, including the risk allele frequencies in the Latin American population. Additionally, a bibliographical selection of several studies has been included; these studies examined the impact that dietary patterns in Latin American environments have on the expression of numerous genes involved in obesity-associated metabolic pathways.
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Affiliation(s)
- Patricia Guevara-Ramírez
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Santiago Cadena-Ullauri
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Viviana A. Ruiz-Pozo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Rafael Tamayo-Trujillo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Elius Paz-Cruz
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Daniel Simancas-Racines
- Centro de Investigación en Salud Pública y Epidemiología Clínica (CISPEC), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Ana Karina Zambrano
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
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Li L, Chen J, Xiao C, Luo Y, Zhong N, Xie Q, Chang H, Zhong D, Xu Y, Zhao M, Liao Q. Recent advances in photoelectrochemical sensors for detection of ions in water. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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Brink LR, Bender TM, Davies R, Luo H, Miketinas D, Shah N, Loveridge N, Gross G, Fawkes N. Optimizing Maternal Nutrition: The Importance of a Tailored Approach. Curr Dev Nutr 2022; 6:nzac118. [PMID: 36157850 PMCID: PMC9492153 DOI: 10.1093/cdn/nzac118] [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: 02/11/2022] [Revised: 06/08/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Improving nutritional status during pregnancy is a global interest. Frequently, women either fail to meet or exceed nutrient recommendations. Current strategies to improve maternal nutrition focus on a "one-size-fits-all" approach and fail to consider individual factors that affect the mother's overall nutritional status. The objectives of this review were to determine the importance of key nutrients for optimal maternal and fetal health, to explore to what extent current recommendations consider individual factors, and to explore novel strategies to close the gap between current guidelines and real-world challenges through more personalized approaches. This review intercalated different nutritional guidelines and recent scientific publications and research initiatives related to maternal nutrition. Based on that, an overview of current recommendations, challenges related to present approaches, and perspectives for future directions are described. Current guidelines are not optimally supporting adequate nutrient intake and health of expectant mothers and their offspring. Existing recommendations are not consistent and do not sufficiently take into account how interindividual variation leads to differences in nutrient status. Personalized nutrition offers women the opportunity to improve their health by using strategies that are tailored to their unique nutritional needs. Such strategies can include personalized supplementation, holistic lifestyle interventions, digital and application-based technologies, and dietary assessment through blood biomarker and genetic analysis. However, these approaches warrant further investigation and optimization. More personalized approaches have the potential to optimize mothers' and their offspring's health outcomes more appropriately to their nutritional needs before, during, and after pregnancy. Moving away from a generalized "one-size-fits-all" approach can be achieved through a variety of means. Future aims should be to provide supporting evidence to create customized subpopulation-based or individualized recommendations, improve nutrition education, and develop novel approaches to improve adherence to dietary and lifestyle interventions.
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Affiliation(s)
- Lauren R Brink
- Medical and Scientific Affairs, Reckitt/Mead Johnson Nutrition Institute, Evansville, IN, USA
| | - Tonya M Bender
- Medical and Scientific Affairs, Reckitt/Mead Johnson Nutrition Institute, Evansville, IN, USA
| | - Rosalind Davies
- Medical and Scientific Affairs, Reckitt/Mead Johnson Nutrition Institute, Slough, UK
| | | | - Derek Miketinas
- Nutrition and Food Sciences, Texas Woman's University, Houston, TX, USA
| | - Neil Shah
- Medical and Scientific Affairs, Reckitt/Mead Johnson Nutrition Institute, Slough, UK
| | - Nik Loveridge
- Medical and Scientific Affairs, Reckitt/Mead Johnson Nutrition Institute, Slough, UK
| | - Gabriele Gross
- Medical and Scientific Affairs, Reckitt/Mead Johnson Nutrition Institute, Nijmegen, The Netherlands
| | - Neil Fawkes
- Medical and Scientific Affairs, Reckitt/Mead Johnson Nutrition Institute, Slough, UK
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12
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Le MK, Smith OS, Akbari A, Harpak A, Reich D, Narasimhan VM. 1,000 ancient genomes uncover 10,000 years of natural selection in Europe. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.24.505188. [PMID: 36052370 PMCID: PMC9435429 DOI: 10.1101/2022.08.24.505188] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Ancient DNA has revolutionized our understanding of human population history. However, its potential to examine how rapid cultural evolution to new lifestyles may have driven biological adaptation has not been met, largely due to limited sample sizes. We assembled genome-wide data from 1,291 individuals from Europe over 10,000 years, providing a dataset that is large enough to resolve the timing of selection into the Neolithic, Bronze Age, and Historical periods. We identified 25 genetic loci with rapid changes in frequency during these periods, a majority of which were previously undetected. Signals specific to the Neolithic transition are associated with body weight, diet, and lipid metabolism-related phenotypes. They also include immune phenotypes, most notably a locus that confers immunity to Salmonella infection at a time when ancient Salmonella genomes have been shown to adapt to human hosts, thus providing a possible example of human-pathogen co-evolution. In the Bronze Age, selection signals are enriched near genes involved in pigmentation and immune-related traits, including at a key human protein interactor of SARS-CoV-2. Only in the Historical period do the selection candidates we detect largely mirror previously-reported signals, highlighting how the statistical power of previous studies was limited to the last few millennia. The Historical period also has multiple signals associated with vitamin D binding, providing evidence that lactase persistence may have been part of an oligogenic adaptation for efficient calcium uptake and challenging the theory that its adaptive value lies only in facilitating caloric supplementation during times of scarcity. Finally, we detect selection on complex traits in all three periods, including selection favoring variants that reduce body weight in the Neolithic. In the Historical period, we detect selection favoring variants that increase risk for cardiovascular disease plausibly reflecting selection for a more active inflammatory response that would have been adaptive in the face of increased infectious disease exposure. Our results provide an evolutionary rationale for the high prevalence of these deadly diseases in modern societies today and highlight the unique power of ancient DNA in elucidating biological change that accompanied the profound cultural transformations of recent human history.
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Affiliation(s)
- Megan K Le
- Department of Computer Science, The University of Texas at Austin
| | - Olivia S Smith
- Department of Integrative Biology, The University of Texas at Austin
| | - Ali Akbari
- Department of Genetics, Harvard Medical School
- Department of Human Evolutionary Biology, Harvard University
- Broad Institute of MIT and Harvard
| | - Arbel Harpak
- Department of Integrative Biology, The University of Texas at Austin
- Department of Population Health, Dell Medical School
| | - David Reich
- Department of Genetics, Harvard Medical School
- Department of Human Evolutionary Biology, Harvard University
- Howard Hughes Medical Institute, Harvard Medical School
- Broad Institute of MIT and Harvard
| | - Vagheesh M Narasimhan
- Department of Integrative Biology, The University of Texas at Austin
- Department of Statistics and Data Science, The University of Texas at Austin
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13
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Chandwe K, Zyambo K, Mulenga C, Haritunians T, Amadi B, Kosek M, Heimburger DC, McGovern D, Kelly P. Histo-Blood Group Antigens, Enteropathogen Carriage and Environmental Enteropathy in Stunted Zambian Children. J Pediatr Gastroenterol Nutr 2022; 74:529-534. [PMID: 34724448 PMCID: PMC9046470 DOI: 10.1097/mpg.0000000000003343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVES Stunting, the most common form of childhood undernutrition, is associated with environmental enteropathy (EE). Enteric infections are believed to play a role in the pathophysiology of EE and stunting though the exact mechanism remains undetermined. The FUT2 (secretor) and FUT3 (Lewis) genes have been shown to be associated with some symptomatic enteric infections in both children and adults. These genes are responsible for the presence of histo-blood group antigens (HBGAs) in various secretions and epithelial surfaces.We evaluated whether the secretor and Lewis status influences asymptomatic enteric infections and thus EE severity on duodenal biopsies of stunted children. METHODS In this case-control study, we used saliva samples to determine the secretor and Lewis status of stunted children (cases, n = 113) enrolled in a nutritional rehabilitation program and from their well-nourished counterparts (controls, n = 42). Where available, saliva was also collected from the mothers. Baseline stool samples were used to detect asymptomatic enteropathogen carriage. Duodenal biopsies were collected from a subgroup of stunted children (n = 77) who had an upper gastrointestinal endoscopy done as part of the evaluation process for their non-response to nutritional therapy. RESULTS The proportion of secretors was similar between the cases and the controls (82% vs 81%, P = 0.81). The stunted children had significantly higher rates of carrying multiple enteropathogens, but this was not associated with their secretor status nor that of their mothers. The secretor status was also not associated with mucosal morphometry of duodenal biopsies. CONCLUSION This case-control analysis in Zambian children does not support the hypothesis that fucosylation status determines asymptomatic enteropathogen carriage in stunting.
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Affiliation(s)
- Kanta Chandwe
- University of Zambia School of Medicine, Lusaka, Zambia
- Tropical Gastroenterology & Nutrition group, Lusaka, Zambia
| | - Kanekwa Zyambo
- Tropical Gastroenterology & Nutrition group, Lusaka, Zambia
| | - Chola Mulenga
- Tropical Gastroenterology & Nutrition group, Lusaka, Zambia
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Beatrice Amadi
- University of Zambia School of Medicine, Lusaka, Zambia
- Tropical Gastroenterology & Nutrition group, Lusaka, Zambia
| | | | - Douglas C. Heimburger
- University of Zambia School of Medicine, Lusaka, Zambia
- Vanderbilt University Medical Center
| | - Dermot McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Paul Kelly
- Tropical Gastroenterology & Nutrition group, Lusaka, Zambia
- Queen Mary University of London, London, UK
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14
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Soejima M, Koda Y. Simultaneous genotyping of three major Se enzyme inactivating SNPs of FUT2 based on a triplex probe-based fluorescence melting-curve analysis. Clin Chim Acta 2022; 530:50-54. [PMID: 35271838 DOI: 10.1016/j.cca.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/04/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND The ABO(H) secretor status is controlled by FUT2-encoded α(1,2)fucosyltransferase (Se enzyme) activity. Three SNPs of FUT2, 302C>T (rs200157007), 385A>T (rs1047781), and 428G>A (rs601338), cause three major variants of nonsecretor (se) or weak-secretor (Sew) alleles. Evidence has been accumulating that suggests the secretor status is associated with various conditions including infectious diseases but a robust multiplex method for assaying relatively large-scale samples to determine the genotype of these three SNPs simultaneously has not been developed yet. METHODS By combined usage of two Eprobes and a dual-labeled fluorescence probe, we developed a real-time PCR, followed by triplex probe-based fluorescent melting-curve analysis (FMCA) for genotyping of 302C>T, 385A>T, and 428G>A of FUT2 in a single tube. RESULTS Three genotypes of each of three variants of FUT2 were accurately determined by the triplex probe-based FMCA. We then validated this method using genomic DNA samples of 47 Bangladeshis, and the results obtained by using this method were fully concordant with those by previous Sanger sequencing. CONCLUSIONS Since the present single triplex probe-based FMCA is robust, fast, and cost-effective, we are able to effectively estimate the secretor status of subjects on a large scale in many populations around the world.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan.
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15
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Battat R, Qatomah A, Kopylov U, Wyse J, Cohen A, Afif W, Lakatos PL, Seidman E, Bitton A, Bessissow T. Fucosyltransferase 2 Mutations Are Associated With a Favorable Clinical Course in Crohn's Disease. J Clin Gastroenterol 2022; 56:e166-e170. [PMID: 34739405 DOI: 10.1097/mcg.0000000000001626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/07/2021] [Indexed: 12/10/2022]
Abstract
BACKGROUND Fucosyltransferase 2 (FUT2) participates in intestinal antigen secretion and bacterial adherence. FUT2 homozygous nonsense mutations (FUT2M) and subsequent nonsecretor status is associated with Crohn's disease (CD). The common null allele is rs601338. We assessed the relationship between FUT2M and disease course. METHODS In consecutive adult CD outpatients, clinical, biochemical, and genetic data were collected at baseline visits. Patients were longitudinally followed over 5 years. The primary outcome analyzed the relationship between FUT2M and rates of CD patients in persistent steroid-free clinical remission requiring neither surgery, biologics, nor immunomodulators. RESULTS Sixty-two CD patients were recruited. FUT2M homozygotes (rs601338 or any mutation in linkage disequilibrium) were detected in 27% of CD (17/62). Patients with rs601338 mutations had higher rates of the primary outcome (homozygous: 46.6%, heterozygous: 28.0%, wild-type: 5.3%, P=0.02). Similar findings existed for CD patients with homozygous mutations in any single-nucleotide polymorphism for FUT2 (homozygous: 41.2%, heterozygous: 25.9%, wild-type: 5.6%, P=0.04). On multivariable analysis, rs601338 mutation was associated with the primary outcome (odds ratio=3.4, 95% confidence interval: 1.3-8.7, P=0.01), while other parameters were not. Mutation of rs601338 was associated with lower rates of penetrating disease (homozygous: 13.3%, heterozygous: 28.0%, wild-type: 52.6%, P=0.05) and particularly in high-risk patients (homozygous: 0%, heterozygous: 37.5%, wild-type: 83.3%, P=0.01). CONCLUSIONS FUT2 mutation status is associated with a favorable clinical course in CD. Further confirmatory studies are needed.
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Affiliation(s)
- Robert Battat
- Division of Gastroenterology and Hepatology, Department of Medicine, Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, New York, NY
- Division of Gastroenterology and Hepatology, McGill University Health Centre
| | - Abdulrahman Qatomah
- Division of Gastroenterology and Hepatology, McGill University Health Centre
| | - Uri Kopylov
- Department of Gastroenterology, Sheba Medical Center, Tel Hashomer
- Sackler Medical School, Tel Aviv, Israel
| | - Jonathan Wyse
- Division of Gastroenterology, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Albert Cohen
- Division of Gastroenterology, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Waqqas Afif
- Division of Gastroenterology and Hepatology, McGill University Health Centre
| | - Peter L Lakatos
- Division of Gastroenterology and Hepatology, McGill University Health Centre
- 1st Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Ernest Seidman
- Division of Gastroenterology and Hepatology, McGill University Health Centre
| | - Alain Bitton
- Division of Gastroenterology and Hepatology, McGill University Health Centre
| | - Talat Bessissow
- Division of Gastroenterology and Hepatology, McGill University Health Centre
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16
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Lee GY, Han SN. Direct-to-Consumer Genetic Testing in Korea: Current Status and Significance in Clinical Nutrition. Clin Nutr Res 2021; 10:279-291. [PMID: 34796133 PMCID: PMC8575646 DOI: 10.7762/cnr.2021.10.4.279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 12/26/2022] Open
Abstract
Direct-to-consumer genetic testing (DTC-GT) provides a means for consumers to gain insights into their genetic background and how it relates to their health without the involvement of medical institutions. In Korea, DTC-GT was introduced in 2016 in accordance with the legislation on Paragraph (3) 2 of Article 50 of the Bioethics and Safety Act. Only 12 genetic test items involving 46 genes were approved at first, but the approved items were expanded to 70 in November 2020. However, the genetic test items of DTC-GT services in Korea are still restricted to the wellness area, and access to disease risk related information is only permitted to medical institutions. Further, studies revealing the relationship between genotype differences and responses to nutrients, food components, or nutritional status are increasing, and this association appears to be robust for some genes. This strong association between genetic variations and nutrition suggests that DTC-GT can be used as an important tool by clinical nutritionists to gain insights into an individual's genetic susceptibilities and provide guidance on nutritional counseling and meal planning based on the patient's genetic information. This review summarized the history and current status of DTC-GT and investigated the relationship between genetic variations with associated phenotypic traits to clarify further the importance of DTC-GT in the field of clinical nutrition.
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Affiliation(s)
- Ga Young Lee
- Department of Food and Nutrition, College of Human Ecology, Seoul National University, Seoul 08826, Korea
| | - Sung Nim Han
- Department of Food and Nutrition, College of Human Ecology, Seoul National University, Seoul 08826, Korea.,Research Institute of Human Ecology, Seoul National University, Seoul 08826, Korea
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17
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Yuan S, Bruzelius M, Damrauer SM, Larsson SC. Cardiometabolic, Lifestyle, and Nutritional Factors in Relation to Varicose Veins: A Mendelian Randomization Study. J Am Heart Assoc 2021; 10:e022286. [PMID: 34666504 PMCID: PMC8751841 DOI: 10.1161/jaha.121.022286] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background We conducted a 2-sample Mendelian randomization study to assess the associations of cardiometabolic, lifestyle, and nutritional factors with varicose veins. Methods and Results Independent single-nucleotide polymorphisms associated with height (positive control), body mass index, type 2 diabetes, diastolic and systolic blood pressure, smoking, alcohol and coffee consumption, 7 circulating vitamins (A, B6, B9, B12, C, 25-hydroxyvitamin D, and E), and 5 circulating minerals (calcium, iron, magnesium, selenium, and zinc) at the genome-wide significance level were used as instrumental variables. Summary-level data for the genetic associations with varicose veins were obtained from the UK Biobank (8763 cases and 352 431 noncases) and the FinnGen consortium (13 928 cases and 153 951 noncases). Genetically predicted higher height, body mass index, smoking, and circulating iron levels were associated with an increased risk of varicose veins. The odds ratios (ORs) per 1-SD increase in the exposure were 1.34 (95% CI, 1.25-1.43) for height, 1.39 (95% CI, 1.27-1.52) for body mass index, 1.12 (95% CI, 1.04-1.22) for the prevalence of smoking initiation, and 1.24 (95% CI, 1.16-1.33) for iron. Higher genetically predicted systolic blood pressure and circulating calcium and zinc levels were associated with a reduced risk of varicose veins, whereas the association for systolic blood pressure did not persist after adjustment for genetically predicted height. The OR was 0.75 (95% CI, 0.62-0.92) per 1-SD increase in calcium levels and 0.97 (95% CI, 0.95-0.98) for zinc. Conclusions This study identified several modifiable risk factors for varicose veins.
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Affiliation(s)
- Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - Maria Bruzelius
- Coagulation Unit Department of Hematology Karolinska University Hospital Stockholm Sweden.,Department of Medicine Solna Karolinska Institutet Stockholm Sweden
| | - Scott M Damrauer
- Corporal Michael J. Crescenz VA Medical Center Philadelphia PA.,Department of Surgery University of Pennsylvania Perelman School of Medicine Philadelphia PA
| | - Susanna C Larsson
- Unit of Cardiovascular and Nutritional Epidemiology Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden.,Unit of Medical Epidemiology Department of Surgical Sciences Uppsala University Uppsala Sweden
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18
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Soejima M, Koda Y. Rapid detection of phenotypes Bombay se del and nonsecretor rs200157007 SNP (302C > T) by real-time PCR-based methods. Sci Rep 2021; 11:14996. [PMID: 34294843 PMCID: PMC8298435 DOI: 10.1038/s41598-021-94659-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/14/2021] [Indexed: 11/12/2022] Open
Abstract
The sedel allele is one of the nonsecretor alleles (se) of FUT2 generated by an Alu-mediated recombination event and was first found in Indian Bombay phenotype individuals who have anti-H, anti-A, and anti-B antibodies in their serum. As well as anti-A, and anti-B antibodies, anti-H is clinically significant because it causes sever hemolytic transfusion reactions. Like sedel, se302 having a missense single nucleotide polymorphism (SNP), 302C > T, is characteristic of South Asians with a frequency of 10-30%. We developed a real-time PCR melting curve analysis for detection of sedel using a 127-bp amplicon encompassing the breakpoint junction. In addition, by performing duplex PCR by amplifying a 65-bp amplicon of the FUT2 coding region at the same time, we could determine the zygosity of sedel in a single tube. We also developed an Eprobe-mediated PCR assay (Eprobe-PCR) for detection of 302C > T of FUT2. These methods were validated by analyzing 58 Tamils and 54 Sinhalese in Sri Lanka. Both the duplex PCR melting curve analysis for determination of sedel zygosity and the Eprobe-PCR assay for detection of 302C > T exactly determined three genotypes. In addition, the results of the present methods were in complete agreement with those obtained by previously established methods. The two present methods were reliable and seem to be advantageous for large-scale association studies of FUT2 polymorphisms in South Asian populations.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, 830-0011, Japan.
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19
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Fuzo CA, da Veiga Ued F, Moco S, Cominetti O, Métairon S, Pruvost S, Charpagne A, Carayol J, Torrieri R, Silva WA, Descombes P, Kaput J, Monteiro JP. Contribution of genetic ancestry and polygenic risk score in meeting vitamin B12 needs in healthy Brazilian children and adolescents. Sci Rep 2021; 11:11992. [PMID: 34099811 PMCID: PMC8184816 DOI: 10.1038/s41598-021-91530-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/25/2021] [Indexed: 02/08/2023] Open
Abstract
Polymorphisms in genes related to the metabolism of vitamin B12 haven’t been examined in a Brazilian population.
To (a) determine the correlation between the local genetic ancestry components and vitamin B12 levels using ninety B12-related genes; (b) determine associations between these genes and their SNPs with vitamin B12 levels; (c) determine a polygenic risk score (PRS) using significant variants. This cross-sectional study included 168 children and adolescents, aged 9–13 years old. Total cobalamin was measured in plasma. Genotyping arrays and whole exome data were combined to yield ~ 7000 SNPs in 90 genes related to vitamin B12. The Efficient Local Ancestry Inference was used to estimate local ancestry for African (AFR), Native American, and European (EUR). The association between the genotypes and vitamin B12 levels were determined with generalized estimating equation.
Vitamin B12 levels were driven by positive (EUR) and negative (AFR, AMR) correlations with genetic ancestry. A set of 36 variants were used to create a PRS that explained 42% of vitamin level variation.
Vitamin B12 levels are influenced by genetic ancestry and a PRS explained almost 50% of the variation in plasma cobalamin in Brazilian children and adolescents.
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Affiliation(s)
- Carlos Alessandro Fuzo
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutics Sciences, University of São Paulo, Ribeirão Preto, Brazil
| | - Fábio da Veiga Ued
- Department of Pediatrics and Department of Health Sciences, Ribeirão Preto Medical School, Nutrition and Metabolism Section, University of São Paulo, Avenida Bandeirantes, 3900, Bairro Monte Alegre, Ribeirão Preto, SP, 14040-900, Brazil
| | - Sofia Moco
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteite Amsterdam, Amsterdam, The Netherlands
| | - Ornella Cominetti
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Sylviane Métairon
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Solenn Pruvost
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Aline Charpagne
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland.,Sophia Genetics, Campus Biotech, 1202, Geneva, Switzerland
| | - Jerome Carayol
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Raul Torrieri
- Center for Medical Genomics, Ribeirão Preto Medical School Hospital, University of São Paulo, Ribeirão Preto, Brazil
| | - Wilson Araujo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Patrick Descombes
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Jim Kaput
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland.,, Vydiant, Folsom, CA, USA
| | - Jacqueline Pontes Monteiro
- Department of Pediatrics and Department of Health Sciences, Ribeirão Preto Medical School, Nutrition and Metabolism Section, University of São Paulo, Avenida Bandeirantes, 3900, Bairro Monte Alegre, Ribeirão Preto, SP, 14040-900, Brazil.
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20
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Development and Validation of a Clinical-Genetic Risk Score to Predict Hepatic Encephalopathy in Patients With Liver Cirrhosis. Am J Gastroenterol 2021; 116:1238-1247. [PMID: 33852451 DOI: 10.14309/ajg.0000000000001164] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022]
Abstract
INTRODUCTION We aimed to define the impact of the genetic background on overt hepatic encephalopathy (HE) in patients with liver cirrhosis by developing a combined clinical-genetic risk score. METHODS Patients suffering from liver cirrhosis from the outpatient clinics of 4 hospitals (n = 600) were included and followed up for at least 5 years until HE bouts, liver transplant, or death. Patients were genotyped for 60 candidate single nucleotide polymorphisms together with the microsatellite in the promoter region of the gene GLS. RESULTS Single nucleotide polymorphisms rs601338 (FUT2), rs5743836 (TRL9), rs2562582 (SLC1A3), rs313853 (SLC1A5), and GLS microsatellite did predict independently the incidence and severity of overt HE and were included as genetic score. Competing risk analysis revealed that bilirubin (subhazard ratio [sHR] 1.30 [1.15-1.48], P < 0.001), albumin (sHR 0.90 [0.86-0.93], P < 0.001), genetic score (sHR 1.90 [1.57-2.30], P < 0.001), and previous episodes of overt HE (sHR 2.60 [1.57-4.29], P < 0.001) were independently associated to HE bouts during the follow-up with an internal (C-index 0.83) and external validation (C-index 0.74). Patients in the low-risk group had 5% and 12% risk of HE at 1 (log-rank 92.1; P < 0.001) and 5 (log-rank 124.1; P < 0.001) years, respectively, whereas 36% and 48% in the high-risk group. DISCUSSION The genetic background influenced overt HE risk and severity. The clinical-genetic HE Risk score, which combined genetic background together with albumin, bilirubin, and previous episodes of overt HE, could be a useful tool to predict overt HE in patients with cirrhosis.
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O'Logbon J, Crook M, Steed D, Harrington DJ, Sobczyńska-Malefora A. Ethnicity influences total serum vitamin B 12 concentration: a study of Black, Asian and White patients in a primary care setting. J Clin Pathol 2021; 75:598-604. [PMID: 33952588 DOI: 10.1136/jclinpath-2021-207519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/21/2021] [Accepted: 04/06/2021] [Indexed: 11/03/2022]
Abstract
AIMS A growing body of evidence suggests that ethnicity and race influence vitamin B12 metabolism and status yet clinical awareness of this is poor, causing doubts regarding diagnosis and treatment. Moreover, deficiency and insufficiency cut-offs are universally applied for this test in most diagnostic settings. The objective of this study was to assess serum vitamin B12 concentrations in Black, Asian and White primary care patients in London, UK, particularly in patients of Black or Black British ethnic origin and establish if there is a need for specific reference ranges. METHODS Serum B12 results from 49 414 patients were processed between January 2018 and November 2019 using the Architect assay (Abbott Diagnostics) at St. Thomas' Hospital, London, UK. Age, sex and ethnicity data were collected from the laboratory Health Informatics Team. RESULTS Black patients (n=13 806) were found to have significantly higher serum vitamin B12 concentration across all age groups and both sexes, especially Nigerian patients (median B12 505 pmol/L,IQR: 362-727, n=891), compared with Asian and White ethnic groups (p<0.001). Binary logistic regression analysis revealed that the Black or Black British ethnic group had the strongest association with elevated serum B12 (>652 pmol/L) (adjusted OR 3.38, 95% CI 3.17 to 3.61, p<0.0001). CONCLUSIONS It is likely that a combination of genetic and acquired/environmental factors are responsible for the ethnic differences in serum B12. This suggests that there is a need for ethnic-specific reference ranges with indications for the incorporation of age and sex too.
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Affiliation(s)
- Jessica O'Logbon
- GKT School of Medicine, King's College London Faculty of Life Sciences and Medicine, London, UK jessica.o'
| | - Martin Crook
- Clinical Biochemistry and Metabolic Medicine, Guy's, St Thomas' Trust, London, UK.,Clinical Biochemistry and Metabolic Medicine, Lewisham and Greenwich Trust, London, UK.,Hon Professor in Biochemical Medicine, King's College London, London, UK
| | - David Steed
- Viapath Informatics, Viapath, Francis House, St Thomas' Hospital, London, UK
| | - Dominic Jon Harrington
- Faculty of Life Sciences and Medicine, King's College London, London, UK.,The Nutristasis Unit, Viapath, St. Thomas' Hospital, London, UK
| | - Agata Sobczyńska-Malefora
- Faculty of Life Sciences and Medicine, King's College London, London, UK.,The Nutristasis Unit, Viapath, St. Thomas' Hospital, London, UK
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Estimation of secretor status of ABO antigens by high-resolution melting analysis of rs601338 (428G > A). Clin Chim Acta 2021; 517:86-91. [PMID: 33667483 DOI: 10.1016/j.cca.2021.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/06/2021] [Accepted: 02/20/2021] [Indexed: 02/02/2023]
Abstract
BACKGROUND FUT2 determines the secretor status of ABH antigens. Many lines of evidence suggest an association between secretor status and susceptibility to various clinical conditions. For this kind of study, large-scale genotyping of FUT2 is necessary. Because FUT2 has a pseudogene (SEC1) with high DNA sequence similarity and is rich in population-specific SNPs, we need to pay attention in designing the primers for genotyping FUT2. The se428 allele having a 428G > A nonsense SNP (W143X, rs601338) is the predominant non-secretor allele in Europeans, Latin Americans and Africans. On the other hand, se357,480,778del having the 778C > del frameshift SNP (P260Lfs*16, rs1799761) is almost exclusively found in Africans with frequencies of 1-4%. STUDY DESIGN AND METHODS We developed high-resolution melting (HRM) analyses using short (69-bp for 428G > A, 65-bp for 778C > del) amplicons for genotyping two SNPs directly and validated the method by analyzing 95 Ghanaians whose FUT2 genotypes were previously determined. RESULTS Two sets of assays clearly discriminated three genotypes of 428G > A (G/G, G/A, A/A), and two genotypes of 778C > del (C/C, C/del). In addition, the results obtained for the 95 Ghanaians by HRM analysis were in full agreement with previous ones. CONCLUSION The present HRM analysis reliably genotyped 428G > A. Thus, estimation of secretor status based on se428 using the present HRM analysis may be useful for large scale association studies of FUT2. In addition to 428G > A, genotyping of other causal polymorphisms for non-secretors with high frequency, as is the case with 778C > del for Africans, is desirable for more accurate estimation of the secretor status of the target populations.
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Pharmacogenomics and COVID-19: clinical implications of human genome interactions with repurposed drugs. THE PHARMACOGENOMICS JOURNAL 2021; 21:275-284. [PMID: 33542445 PMCID: PMC7859465 DOI: 10.1038/s41397-021-00209-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 12/07/2020] [Accepted: 01/15/2021] [Indexed: 02/07/2023]
Abstract
The outbreak of Coronavirus disease 2019 (COVID-19) has evolved into an emergent global pandemic. Many drugs without established efficacy are being used to treat COVID-19 patients either as an offlabel/compassionate use or as a clinical trial. Although drug repurposing is an attractive approach with reduced time and cost, there is a need to make predictions on success before the start of therapy. For the optimum use of these repurposed drugs, many factors should be considered such as drug–gene or dug–drug interactions, drug toxicity, and patient co-morbidity. There is limited data on the pharmacogenomics of these agents and this may constitute an obstacle for successful COVID-19 therapy. This article reviewed the available human genome interactions with some promising repurposed drugs for COVID-19 management. These drugs include chloroquine (CQ), hydroxychloroquine (HCQ), azithromycin, lopinavir/ritonavir (LPV/r), atazanavir (ATV), favipiravir (FVP), nevirapine (NVP), efavirenz (EFV), oseltamivir, remdesivir, anakinra, tocilizumab (TCZ), eculizumab, heme oxygenase 1 (HO-1) regulators, renin–angiotensin–aldosterone system (RAAS) inhibitors, ivermectin, and nitazoxanide. Drug-gene variant pairs that may alter the therapeutic outcomes in COVID-19 patients are presented. The major drug variant pairs that associated with variations in clinical efficacy include CQ/HCQ (CYP2C8, CYP2D6, ACE2, and HO-1); azithromycin (ABCB1); LPV/r (SLCO1B1, ABCB1, ABCC2 and CYP3A); NVP (ABCC10); oseltamivir (CES1 and ABCB1); remdesivir (CYP2C8, CYP2D6, CYP3A4, and OATP1B1); anakinra (IL-1a); and TCZ (IL6R and FCGR3A). The major drug variant pairs that associated with variations in adverse effects include CQ/HCQ (G6PD; hemolysis and ABCA4; retinopathy), ATV (MDR1 and UGT1A1*28; hyperbilirubinemia; and APOA5; dyslipidemia), NVP (HLA-DRB1*01, HLA-B*3505 and CYP2B6; skin rash and MDR1; hepatotoxicity), and EFV (CYP2B6; depression and suicidal tendencies).
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Kachuri L, Francis SS, Morrison ML, Wendt GA, Bossé Y, Cavazos TB, Rashkin SR, Ziv E, Witte JS. The landscape of host genetic factors involved in immune response to common viral infections. Genome Med 2020; 12:93. [PMID: 33109261 PMCID: PMC7590248 DOI: 10.1186/s13073-020-00790-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/07/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the genetic mechanisms of immune response to viral infection provides insight into disease etiology and therapeutic opportunities. METHODS We conducted a comprehensive study including genome-wide and transcriptome-wide association analyses to identify genetic loci associated with immunoglobulin G antibody response to 28 antigens for 16 viruses using serological data from 7924 European ancestry participants in the UK Biobank cohort. RESULTS Signals in human leukocyte antigen (HLA) class II region dominated the landscape of viral antibody response, with 40 independent loci and 14 independent classical alleles, 7 of which exhibited pleiotropic effects across viral families. We identified specific amino acid (AA) residues that are associated with seroreactivity, the strongest associations presented in a range of AA positions within DRβ1 at positions 11, 13, 71, and 74 for Epstein-Barr virus (EBV), Varicella zoster virus (VZV), human herpesvirus 7, (HHV7), and Merkel cell polyomavirus (MCV). Genome-wide association analyses discovered 7 novel genetic loci outside the HLA associated with viral antibody response (P < 5.0 × 10-8), including FUT2 (19q13.33) for human polyomavirus BK (BKV), STING1 (5q31.2) for MCV, and CXCR5 (11q23.3) and TBKBP1 (17q21.32) for HHV7. Transcriptome-wide association analyses identified 114 genes associated with response to viral infection, 12 outside of the HLA region, including ECSCR: P = 5.0 × 10-15 (MCV), NTN5: P = 1.1 × 10-9 (BKV), and P2RY13: P = 1.1 × 10-8 EBV nuclear antigen. We also demonstrated pleiotropy between viral response genes and complex diseases, from autoimmune disorders to cancer to neurodegenerative and psychiatric conditions. CONCLUSIONS Our study confirms the importance of the HLA region in host response to viral infection and elucidates novel genetic determinants beyond the HLA that contribute to host-virus interaction.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Stephen S Francis
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
| | - Maike L Morrison
- Department of Biology, Stanford University, Stanford, CA, USA
- Summer Research Training Program, Graduate Division, University of California San Francisco, San Francisco, CA, USA
- Department of Mathematics, The University of Texas, Austin, TX, USA
| | - George A Wendt
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Université Laval, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
| | - Taylor B Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California San Francisco, San Francisco, CA, USA.
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Kachuri L, Francis SS, Morrison M, Wendt GA, Bossé Y, Cavazos TB, Rashkin SR, Ziv E, Witte JS. The landscape of host genetic factors involved in immune response to common viral infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.05.01.20088054. [PMID: 32511533 PMCID: PMC7273301 DOI: 10.1101/2020.05.01.20088054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the genetic mechanisms of immune response to viral infection provides insight into disease etiology and therapeutic opportunities. METHODS We conducted a comprehensive study including genome-wide and transcriptome-wide association analyses to identify genetic loci associated with immunoglobulin G antibody response to 28 antigens for 16 viruses using serological data from 7924 European ancestry participants in the UK Biobank cohort. RESULTS Signals in human leukocyte antigen (HLA) class II region dominated the landscape of viral antibody response, with 40 independent loci and 14 independent classical alleles, 7 of which exhibited pleiotropic effects across viral families. We identified specific amino acid (AA) residues that are associated with seroreactivity, the strongest associations presented in a range of AA positions within DRβ1 at positions 11, 13, 71, and 74 for Epstein-Barr Virus (EBV), Varicella Zoster Virus (VZV), Human Herpes virus 7, (HHV7) and Merkel cell polyomavirus (MCV). Genome-wide association analyses discovered 7 novel genetic loci outside the HLA associated with viral antibody response (P<5.×10-8), including FUT2 (19q13.33) for human polyomavirus BK (BKV), STING1 (5q31.2) for MCV, as well as CXCR5 (11q23.3) and TBKBP1 (17q21.32) for HHV7. Transcriptome-wide association analyses identified 114 genes associated with response to viral infection, 12 outside of the HLA region, including ECSCR: P=5.0×10-15 (MCV), NTN5: P=1.1×10-9 (BKV), and P2RY13: P=1.1×10-8 EBV nuclear antigen. We also demonstrated pleiotropy between viral response genes and complex diseases; from autoimmune disorders to cancer to neurodegenerative and psychiatric conditions. CONCLUSIONS Our study confirms the importance of the HLA region in host response to viral infection and elucidates novel genetic determinants beyond the HLA that contribute to host-virus interaction.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
| | - Stephen S. Francis
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, USA
| | - Maike Morrison
- Summer Research Training Program, Graduate Division, University of California San Francisco, San Francisco, USA
- Department of Mathematics, The University of Texas at Austin, Austin, USA
| | - George A. Wendt
- Department of Neurological Surgery, University of California San Francisco, San Francisco, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Université Laval, Quebec City, Canada
| | - Taylor B. Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, USA
| | - Sara R. Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, USA
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
- Department of Medicine, University of California, San Francisco, San Francisco, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, USA
| | - John S. Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, USA
- Department of Urology, University of California San Francisco, San Francisco, USA
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Personalized Nutrition for Management of Micronutrient Deficiency-Literature Review in Non-bariatric Populations and Possible Utility in Bariatric Cohort. Obes Surg 2020; 30:3570-3582. [PMID: 32564308 PMCID: PMC7378102 DOI: 10.1007/s11695-020-04762-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023]
Abstract
Background Bariatric surgery can effectively treat morbid obesity; however, micronutrient deficiencies are common despite recommendations for high-dose supplements. Genetic predisposition to deficiencies underscores necessary identification of high-risk candidates. Personalized nutrition (PN) can be a tool to manage these deficiencies. Methods Medline, PubMed, and Google Scholar were searched. Articles involving genetic testing, micronutrient metabolism, and bariatric surgery were included. Results Studies show associations between genetic variants and micronutrient metabolism. Research demonstrates genetic testing to be a predictor for outcomes among obesity and bariatric surgery populations. There is limited research in bariatric surgery and micronutrient genetic variants. Conclusion Genotype-based PN is becoming feasible to provide an effective treatment of micronutrient deficiencies associated with bariatric surgery. The role of genomic technology in micronutrient recommendations needs further investigation.
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Vesnina A, Prosekov A, Kozlova O, Atuchin V. Genes and Eating Preferences, Their Roles in Personalized Nutrition. Genes (Basel) 2020; 11:genes11040357. [PMID: 32230794 PMCID: PMC7230842 DOI: 10.3390/genes11040357] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/20/2020] [Accepted: 03/26/2020] [Indexed: 12/20/2022] Open
Abstract
At present, personalized diets, which take into account consumer genetic characteristics, are growing popular. Nutrigenetics studies the effect of gene variations on metabolism and nutrigenomics, which branches off further and investigates how nutrients and food compounds affect genes. This work deals with the mutations affecting the assimilation of metabolites, contributing to nutrigenetic studies. We searched for the genes responsible for eating preferences which allow for the tailoring of personalized diets. Presently, genetic nutrition is growing in demand, as it contributes to the prevention and/or rehabilitation of non-communicable diseases, both monogenic and polygenic. In this work, we showed single-nucleotide polymorphisms in genes-missense mutations that change the functions of coded proteins, resulting in a particular eating preferences or a disease. We studied the genes influencing food preferences-particularly those responsible for fats and carbohydrates absorption, food intolerance, metabolism of vitamins, taste sensations, oxidation of xenobiotics, eating preferences and food addiction. As a result, 34 genes were identified that affect eating preferences. Significant shortcomings were found in the methods/programs for developing personalized diets that are used today, and the weaknesses were revealed in the development of nutrigenetics (inconsistency of data on SNP genes, ignoring population genetics data, difficult information to understand consumer, etc.). Taking into account all the shortcomings, an approximate model was proposed in the review for selecting an appropriate personalized diet. In the future, it is planned to develop the proposed model for the compilation of individual diets.
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Affiliation(s)
- Anna Vesnina
- Department of Bionanotechnology, Kemerovo State University, 650043 Kemerovo, Russia; (A.V.); (O.K.)
| | - Alexander Prosekov
- Laboratory of Biocatalysis, Kemerovo State University, 650043 Kemerovo, Russia;
| | - Oksana Kozlova
- Department of Bionanotechnology, Kemerovo State University, 650043 Kemerovo, Russia; (A.V.); (O.K.)
| | - Victor Atuchin
- Laboratory of Optical Materials and Structures, Institute of Semiconductor Physics, 630090 Novosibirsk, Russia
- Laboratory of Semiconductor and Dielectric Materials, Novosibirsk State University, 630090 Novosibirsk, Russia
- Research and Development Department, Kemerovo State University, 650000 Kemerovo, Russia
- Correspondence: ; Tel.: +7-(383)-3308889
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Santos-Cortez RLP, Bhutta MF, Earl JP, Hafrén L, Jennings M, Mell JC, Pichichero ME, Ryan AF, Tateossian H, Ehrlich GD. Panel 3: Genomics, precision medicine and targeted therapies. Int J Pediatr Otorhinolaryngol 2020; 130 Suppl 1:109835. [PMID: 32007292 PMCID: PMC7155947 DOI: 10.1016/j.ijporl.2019.109835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVE To review the most recent advances in human and bacterial genomics as applied to pathogenesis and clinical management of otitis media. DATA SOURCES PubMed articles published since the last meeting in June 2015 up to June 2019. REVIEW METHODS A panel of experts in human and bacterial genomics of otitis media was formed. Each panel member reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019, discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members. CONCLUSION Trans-disciplinary approaches applying pan-omic technologies to identify human susceptibility to otitis media and to understand microbial population dynamics, patho-adaptation and virulence mechanisms are crucial to the development of novel, personalized therapeutics and prevention strategies for otitis media. IMPLICATIONS FOR PRACTICE In the future otitis media prevention strategies may be augmented by mucosal immunization, combination vaccines targeting multiple pathogens, and modulation of the middle ear microbiome. Both treatment and vaccination may be tailored to an individual's otitis media phenotype as defined by molecular profiles obtained by using rapidly developing techniques in microbial and host genomics.
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Affiliation(s)
- Regie Lyn P. Santos-Cortez
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, 12700 E. 19 Ave., Aurora, CO 80045, USA
| | - Mahmood F. Bhutta
- Department of ENT, Royal Sussex County Hospital, Eastern Road, Brighton BN2 5BE, UK
| | - Joshua P. Earl
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
| | - Lena Hafrén
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Tukholmankatu 8A, 00290 Helsinki, Finland
| | - Michael Jennings
- Institute for Glycomics, Gold Coast campus, Griffith University, QLD 4222, Australia
| | - Joshua C. Mell
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
| | - Michael E. Pichichero
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, 1425 Portland Ave., Rochester, NY 14621, USA
| | - Allen F. Ryan
- Department of Surgery/Otolaryngology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Hilda Tateossian
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell, Oxford, Didcot OX11 0RD, UK
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
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Williams AM, Ladva CN, Leon JS, Lopman BA, Tangpricha V, Whitehead RD, Armitage AE, Wray K, Morovat A, Pasricha SR, Thurnham D, Tanumihardjo SA, Shahab-Ferdows S, Allen L, Flores-Ayala RC, Suchdev PS. Changes in micronutrient and inflammation serum biomarker concentrations after a norovirus human challenge. Am J Clin Nutr 2019; 110:1456-1464. [PMID: 31504095 PMCID: PMC6885472 DOI: 10.1093/ajcn/nqz201] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/25/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND To accurately assess micronutrient status, it is necessary to characterize the effects of inflammation and the acute-phase response on nutrient biomarkers. OBJECTIVE Within a norovirus human challenge study, we aimed to model the inflammatory response of C-reactive protein (CRP) and α-1-acid glycoprotein (AGP) by infection status, model kinetics of micronutrient biomarkers by inflammation status, and evaluate associations between inflammation and micronutrient biomarkers from 0 to 35 d post-norovirus exposure. METHODS Fifty-two healthy adults were enrolled into challenge studies in a hospital setting and followed longitudinally; all were exposed to norovirus, half were infected. Post hoc analysis of inflammatory and nutritional biomarkers was performed. Subjects were stratified by inflammation resulting from norovirus exposure. Smoothed regression models analyzed the kinetics of CRP and AGP by infection status, and nutritional biomarkers by inflammation. Linear mixed-effects models were used to analyze the independent relations between CRP, AGP, and biomarkers for iron, vitamin A, vitamin D, vitamin B-12, and folate from 0 to 35 d post-norovirus exposure. RESULTS Norovirus-infected subjects had median (IQR) peak concentrations for CRP [16.0 (7.9-29.5) mg/L] and AGP [0.9 (0.8-1.2) g/L] on day 3 and day 4 postexposure, respectively. Nutritional biomarkers that differed (P < 0.05) from baseline within the inflamed group were ferritin (elevated day 3), hepcidin (elevated days 2, 3), serum iron (depressed days 2-4), transferrin saturation (depressed days 2-4), and retinol (depressed days 3, 4, and 7). Nutritional biomarker concentrations did not differ over time within the uninflamed group. In mixed models, CRP was associated with ferritin (positive) and serum iron and retinol (negative, P < 0.05). CONCLUSION Using an experimental infectious challenge model in healthy adults, norovirus infection elicited a time-limited inflammatory response associated with altered serum concentrations of certain iron and vitamin A biomarkers, confirming the need to consider adjustments of these biomarkers to account for inflammation when assessing nutritional status. These trials were registered at clinicaltrials.gov as NCT00313404 and NCT00674336.
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Affiliation(s)
- Anne M Williams
- Hubert Department of Global Health, Emory University, Atlanta, GA, USA,McKing Consulting Corporation, Atlanta, GA, USA,Address correspondence to AMW (e-mail: )
| | | | - Juan S Leon
- Hubert Department of Global Health, Emory University, Atlanta, GA, USA
| | - Ben A Lopman
- Department of Epidemiology, Emory University, Atlanta, GA, USA
| | - Vin Tangpricha
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA,Atlanta VA Medical Center, Decatur, GA, USA
| | | | - Andrew E Armitage
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Katherine Wray
- Department of Clinical Biochemistry, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - Alireza Morovat
- Department of Clinical Biochemistry, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - Sant-Rayn Pasricha
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia,Departments of Medical Biology and Medicine and Radiology, University of Melbourne, Parkville, Victoria, Australia
| | - David Thurnham
- School of Biomedical Sciences, Ulster University, Coleraine, United Kingdom
| | - Sherry A Tanumihardjo
- Interdepartmental Graduate Program in Nutritional Sciences, Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Setti Shahab-Ferdows
- USDA, Agricultural Research Service Western Human Nutrition Research Center, Davis, CA, USA
| | - Lindsay Allen
- USDA, Agricultural Research Service Western Human Nutrition Research Center, Davis, CA, USA
| | | | - Parminder S Suchdev
- Hubert Department of Global Health, Emory University, Atlanta, GA, USA,Nutrition Branch, CDC, Atlanta, GA, USA,Emory Global Health Institute, Atlanta, GA, USA
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30
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Wang J, Asante I, Baron JA, Figueiredo JC, Haile R, Joan Levine A, Newcomb PA, Templeton AS, Schumacher FR, Louie SG, Casey G, Conti DV. Genome-wide association study of circulating folate one-carbon metabolites. Genet Epidemiol 2019; 43:1030-1045. [PMID: 31502714 DOI: 10.1002/gepi.22249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/16/2019] [Accepted: 07/11/2019] [Indexed: 12/31/2022]
Abstract
Experimental, observational, and clinical trials support a critical role of folate one-carbon metabolism (FOCM) in colorectal cancer (CRC) development. In this report, we focus on understanding the relationship between common genetic variants and metabolites of FOCM. We conducted a genome-wide association study of FOCM biomarkers among 1,788 unaffected (without CRC) individuals of European ancestry from the Colon Cancer Family Registry. Twelve metabolites, including 5-methyltetrahydrofolate, vitamin B2 (flavin mononucleotide and riboflavin), vitamin B6 (4-pyridoxic acid, pyridoxal, and pyridoxamine), total homocysteine, methionine, S-adenosylmethionine, S-adenosylhomocysteine, cystathionine, and creatinine were measured from plasma using liquid chromatography-mass spectrometry (LC-MS) or LC-MS/MS. For each individual biomarker, we estimated genotype array-specific associations followed by a fixed-effect meta-analysis. We identified the variant rs35976024 (at 2p11.2 and intronic of ATOH8) associated with total homocysteine (p = 4.9 × 10-8 ). We found a group of six highly correlated variants on chromosome 15q14 associated with cystathionine (all p < 5 × 10-8 ), with the most significant variant rs28391580 (p = 2.8 × 10-8 ). Two variants (rs139435405 and rs149119426) on chromosome 14q13 showed significant (p < 5 × 10-8 ) associations with S-adenosylhomocysteine. These three biomarkers with significant associations are closely involved in homocysteine metabolism. Furthermore, when assessing the principal components (PCs) derived from seven individual biomarkers, we identified the variant rs12665366 (at 6p25.3 and intronic of EXOC2) associated with the first PC (p = 2.3 × 10-8 ). Our data suggest that common genetic variants may play an important role in FOCM, particularly in homocysteine metabolism.
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Affiliation(s)
- Jun Wang
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Isaac Asante
- Department of Clinical Pharmacy and Pharmaceutical Economics and Policy, School of Pharmacy, University of Southern California, Los Angeles, California
| | - John A Baron
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Jane C Figueiredo
- Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California
| | - Robert Haile
- Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - A Joan Levine
- Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Allyson S Templeton
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Stan G Louie
- Department of Clinical Pharmacy and Pharmaceutical Economics and Policy, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - David V Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
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31
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A genetic epidemiological study in British adults and older adults shows a high heritability of the combined indicator of vitamin B12 status (cB12) and connects B12 status with utilization of mitochondrial substrates and energy metabolism. J Nutr Biochem 2019; 70:156-163. [DOI: 10.1016/j.jnutbio.2019.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 03/25/2019] [Accepted: 04/25/2019] [Indexed: 01/03/2023]
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32
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A critical evaluation of results from genome-wide association studies of micronutrient status and their utility in the practice of precision nutrition. Br J Nutr 2019; 122:121-130. [DOI: 10.1017/s0007114519001119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AbstractRapid advances in ‘omics’ technologies have paved the way forward to an era where more ‘precise’ approaches – ‘precision’ nutrition – which leverage data on genetic variability alongside the traditional indices, have been put forth as the state-of-the-art solution to redress the effects of malnutrition across the life course. We purport that this inference is premature and that it is imperative to first review and critique the existing evidence from large-scale epidemiological findings. We set out to provide a critical evaluation of findings from genome-wide association studies (GWAS) in the roadmap to precision nutrition, focusing on GWAS of micronutrient disposition. We found that a large number of loci associated with biomarkers of micronutrient status have been identified. Mean estimates of heritability of micronutrient status ranged between 20 and 35 % for minerals, 56–59 % for water-soluble and 30–70 % for fat-soluble vitamins. With some exceptions, the majority of the identified genetic variants explained little of the overall variance in status for each micronutrient, ranging between 1·3 and 8 % (minerals), <0·1–12 % (water-soluble) and 1·7–2·3 % for (fat-soluble) vitamins. However, GWAS have provided some novel insight into mechanisms that underpin variability in micronutrient status. Our findings highlight obvious gaps that need to be addressed if the full scope of precision nutrition is ever to be realised, including research aimed at (i) dissecting the genetic basis of micronutrient deficiencies or ‘response’ to intake/supplementation (ii) identifying trans-ethnic and ethnic-specific effects (iii) identifying gene–nutrient interactions for the purpose of unravelling molecular ‘behaviour’ in a range of environmental contexts.
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Guest NS, Horne J, Vanderhout SM, El-Sohemy A. Sport Nutrigenomics: Personalized Nutrition for Athletic Performance. Front Nutr 2019; 6:8. [PMID: 30838211 PMCID: PMC6389634 DOI: 10.3389/fnut.2019.00008] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/18/2019] [Indexed: 12/14/2022] Open
Abstract
An individual's dietary and supplement strategies can influence markedly their physical performance. Personalized nutrition in athletic populations aims to optimize health, body composition, and exercise performance by targeting dietary recommendations to an individual's genetic profile. Sport dietitians and nutritionists have long been adept at placing additional scrutiny on the one-size-fits-all general population dietary guidelines to accommodate various sporting populations. However, generic "one-size-fits-all" recommendations still remain. Genetic differences are known to impact absorption, metabolism, uptake, utilization and excretion of nutrients and food bioactives, which ultimately affects a number of metabolic pathways. Nutrigenomics and nutrigenetics are experimental approaches that use genomic information and genetic testing technologies to examine the role of individual genetic differences in modifying an athlete's response to nutrients and other food components. Although there have been few randomized, controlled trials examining the effects of genetic variation on performance in response to an ergogenic aid, there is a growing foundation of research linking gene-diet interactions on biomarkers of nutritional status, which impact exercise and sport performance. This foundation forms the basis from which the field of sport nutrigenomics continues to develop. We review the science of genetic modifiers of various dietary factors that impact an athlete's nutritional status, body composition and, ultimately athletic performance.
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Affiliation(s)
- Nanci S Guest
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada.,Nutrigenomix Inc., Toronto, ON, Canada
| | - Justine Horne
- Department of Health and Rehabilitation Sciences, University of Western Ontario, London, ON, Canada
| | - Shelley M Vanderhout
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada.,Nutrigenomix Inc., Toronto, ON, Canada
| | - Ahmed El-Sohemy
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada.,Nutrigenomix Inc., Toronto, ON, Canada
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Houghton SC, Eliassen AH, Zhang SM, Selhub J, Rosner BA, Willett WC, Hankinson SE. Plasma B-vitamin and one-carbon metabolites and risk of breast cancer before and after folic acid fortification in the United States. Int J Cancer 2019; 144:1929-1940. [PMID: 30346061 DOI: 10.1002/ijc.31934] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/26/2018] [Indexed: 01/01/2023]
Abstract
Prior epidemiologic findings for plasma folate and B-vitamins and breast cancer risk are inconsistent and have not assessed the influence of folic acid fortification. Therefore, we examined the associations of plasma folate, B12 , pyridoxal 5'-phosphate (PLP), homocysteine, cysteine and cysteinylglycine with breast cancer risk, before and after fortification. We conducted a nested case-control study within the prospective Nurses' Health Study. In 1989-1990 (pre-fortification), 32,826 women donated a blood sample and 18,743 donated an additional blood sample in 2000-2001 (post-fortification). Between the first blood collection and 2006, 1874 incident breast cancer cases with at least one blood sample and 367 with two were 1:1 matched to controls. Conditional logistic regression was used to estimate relative risks (RR) and 95% confidence intervals (CI) adjusting for breast cancer risk factors. Overall, higher plasma folate, B12 , PLP, homocysteine, cysteine and cysteinylglycine levels were not associated with breast cancer risk. Associations did not vary by in situ/invasive, hormone receptor status, or tumor molecular subtype. Additionally, associations were null before and after fortification. For example, the RR (95% CI) for the highest versus lowest tertile of 1990 (pre-fortification) plasma folate with 1990-2000 follow-up was 0.93 (0.75-1.16) and for the 2000 plasma folate (post-fortification) with 2000-2006 follow-up the RR (95% CI) was 1.17 (0.79-1.74). Plasma folate, B12 , PLP, homocysteine, cysteine and cysteinylglycine were not significantly associated with breast cancer overall, before and after fortification, or with specific tumor molecular subtypes. However, long term associations (>8 years) after the implementation of fortification could not be examined.
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Affiliation(s)
- Serena C Houghton
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA
| | - A Heather Eliassen
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Shumin M Zhang
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Jacob Selhub
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA
| | - Bernard A Rosner
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Walter C Willett
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Susan E Hankinson
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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Wallace TC, Bultman S, D'Adamo C, Daniel CR, Debelius J, Ho E, Eliassen H, Lemanne D, Mukherjee P, Seyfried TN, Tian Q, Vahdat LT. Personalized Nutrition in Disrupting Cancer - Proceedings From the 2017 American College of Nutrition Annual Meeting. J Am Coll Nutr 2018; 38:1-14. [PMID: 30511901 DOI: 10.1080/07315724.2018.1500499] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cancer is a major public health problem and is the second leading cause of death in the United States and worldwide; nearly one in six deaths are attributable to cancer. Approximately 20% of all cancers diagnosed in the United States are attributable to unhealthy diet, excessive alcohol consumption, physical inactivity, and body fatness. Individual cancers are distinct disease states that are multifactorial in their causation, making them exceedingly cumbersome to study from a nutrition standpoint. Genetic influences are a major piece of the puzzle and personalized nutrition is likely to be most effective in disrupting cancer during all stages. Increasing evidence shows that after a cancer diagnosis, continuing standard dietary recommendations may not be appropriate. This is because powerful dietary interventions such as short-term fasting and carbohydrate restriction can disrupt tumor metabolism, synergizing with standard therapies such as radiation and drug therapy to improve efficacy and ultimately, cancer survival. The importance of identifying dietary interventions cannot be overstated, and the American College of Nutrition's commitment to advancing knowledge and research is evidenced by dedication of the 2017 ACN Annual Meeting to "Disrupting Cancer: The Role of Personalized Nutrition" and this resulting proceedings manuscript, which summarizes the meeting's findings.
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Affiliation(s)
- Taylor C Wallace
- a Department of Nutrition and Food Studies , George Mason University , Fairfax, VA , USA.,b Think Healthy Group, Inc , Washington, DC , USA
| | - Scott Bultman
- c Department of Genetics, University of North Carolina School of Medicine
| | - Chris D'Adamo
- d Departments of Family and Community Medicine and Epidemiology and Public Health , Center for Integrative Medicine, University of Maryland School of Medicine
| | - Carrie R Daniel
- e Department of Epidemiology, Division of Cancer Prevention and Population Sciences , The University of Texas MD Anderson Cancer Center
| | - Justine Debelius
- f Department of Medical Epidemiology and Biostatistics , Karolinska Institute , Stockholm , Sweden
| | - Emily Ho
- g Moore Family Center for Whole Grain Foods, Nutrition and Preventive Health, School of Biological and Population Health Sciences, Linus Pauling Institute, Oregon State University
| | - Heather Eliassen
- h Channing Division of Network Medicine , Brigham and Women's Hospital and Harvard Medical School.,i Harvard T.H. Chan School of Public Health
| | - Dawn Lemanne
- j Department of Medicine , University of Arizona , Tucson.,k National Institute of Integrative Medicine , Melbourne , Australia.,l Oregon Integrative Oncology , Ashland , Oregon
| | | | | | - Qiang Tian
- n Institute for Systems Biology, P4 Medicine Institute
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36
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Ferkingstad E, Oddsson A, Gretarsdottir S, Benonisdottir S, Thorleifsson G, Deaton AM, Jonsson S, Stefansson OA, Norddahl GL, Zink F, Arnadottir GA, Gunnarsson B, Halldorsson GH, Helgadottir A, Jensson BO, Kristjansson RP, Sveinbjornsson G, Sverrisson DA, Masson G, Olafsson I, Eyjolfsson GI, Sigurdardottir O, Holm H, Jonsdottir I, Olafsson S, Steingrimsdottir T, Rafnar T, Bjornsson ES, Thorsteinsdottir U, Gudbjartsson DF, Sulem P, Stefansson K. Genome-wide association meta-analysis yields 20 loci associated with gallstone disease. Nat Commun 2018; 9:5101. [PMID: 30504769 PMCID: PMC6269469 DOI: 10.1038/s41467-018-07460-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 11/01/2018] [Indexed: 01/07/2023] Open
Abstract
Gallstones are responsible for one of the most common diseases in the Western world and are commonly treated with cholecystectomy. We perform a meta-analysis of two genome-wide association studies of gallstone disease in Iceland and the UK, totaling 27,174 cases and 736,838 controls, uncovering 21 novel gallstone-associated variants at 20 loci. Two distinct low frequency missense variants in SLC10A2, encoding the apical sodium-dependent bile acid transporter (ASBT), associate with an increased risk of gallstone disease (Pro290Ser: OR = 1.36 [1.25-1.49], P = 2.1 × 10-12, MAF = 1%; Val98Ile: OR = 1.15 [1.10-1.20], P = 1.8 × 10-10, MAF = 4%). We demonstrate that lower bile acid transport by ASBT is accompanied by greater risk of gallstone disease and highlight the role of the intestinal compartment of the enterohepatic circulation of bile acids in gallstone disease susceptibility. Additionally, two low frequency missense variants in SERPINA1 and HNF4A and 17 common variants represent novel associations with gallstone disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Florian Zink
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
| | | | | | | | | | | | | | | | | | - Gisli Masson
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspítali University Hospital, Reykjavik, 101, Iceland
| | | | - Olof Sigurdardottir
- Department of Clinical Biochemistry, Akureyri Hospital, Akureyri, 600, Iceland
| | - Hilma Holm
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
| | - Ingileif Jonsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Immunology, Landspitali University Hospital, Reykjavik, 101, Iceland
| | - Sigurdur Olafsson
- Department of Internal Medicine, Landspitali University Hospital, Reykjavik, 101, Iceland
| | - Thora Steingrimsdottir
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, 101, Iceland
| | | | - Einar S Bjornsson
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Internal Medicine, Landspitali University Hospital, Reykjavik, 101, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Patrick Sulem
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland.
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland.
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland.
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37
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Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome. Nat Genet 2018; 50:1524-1532. [PMID: 30250126 PMCID: PMC6241851 DOI: 10.1038/s41588-018-0224-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 08/02/2018] [Indexed: 02/05/2023]
Abstract
Despite a growing body of evidence, the role of the gut microbiome in cardiovascular diseases (CVDs) is still unclear. Here we present a systems-genome-wide and metagenome-wide association study on plasma concentrations of 92 CVD-related proteins in the population cohort Lifelines-DEEP. We identified genetic components for 73 proteins and microbial associations for 41 proteins, of which 31 were associated to both. The genetic and microbial factors identified mostly exert additive effects and collectively explain up to 76.6% of inter-individual variation (17.5% on average). Genetics contributes most to concentrations of immune-related proteins, while the gut microbiome contributes most to proteins involved in metabolism and intestinal health. We found several host-microbe interactions that impact proteins involved in epithelial function, lipid metabolism and central nervous system function. This study reveals important evidence for a joint genetic and microbial effect in cardiovascular disease and provides directions for future applications in personalized medicine.
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38
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Moen GH, Qvigstad E, Birkeland KI, Evans DM, Sommer C. Are serum concentrations of vitamin B-12 causally related to cardiometabolic risk factors and disease? A Mendelian randomization study. Am J Clin Nutr 2018; 108:398-404. [PMID: 29982347 DOI: 10.1093/ajcn/nqy101] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/24/2018] [Indexed: 12/15/2022] Open
Abstract
Background Several observational studies have shown that low serum vitamin B-12 is associated with increased body mass index (BMI) and adverse cardiometabolic outcomes. However, it is unclear if these associations reflect a causal effect of vitamin B-12 on cardiometabolic risk factors and diseases, latent confounding, or reverse causality. Objectives The aims of this study were to investigate 1) the possible causal relation between vitamin B-12 and indicators of body fat, lipid, and glucose variables; type 2 diabetes (T2D); and cardiovascular disease by using a 2-sample Mendelian randomization (MR) method and 2) the possible pleiotropic role of fucosyltransferase 2 (FUT2). Design We selected 11 single nucleotide polymorphisms (SNPs) robustly associated with serum concentrations of vitamin B-12 in a previous genomewide association study (GWAS) in 45,576 individuals. We performed 2-sample MR analyses of the relation between vitamin B-12 and cardiometabolic risk factors and diseases with the use of publicly available GWAS summary statistics for 15 outcomes in ≤339,224 individuals. The robustness of results was tested with sensitivity analyses by using MR Egger regression and weighted-median estimation, and by performing additional analyses excluding a variant in the FUT2 gene, which may be pleiotropic. Results We found a suggestive causal relation between vitamin B-12 and fasting glucose and β cell function [homeostatic model assessment (HOMA) of β cell function (HOMA-B)]. However, we found no evidence that serum concentrations of vitamin B-12 were causally related to BMI, waist-to-hip ratio, plasma leptin, body fat, fasting insulin, insulin resistance (from HOMA of insulin resistance), glycated hemoglobin, triglycerides, T2D, coronary artery disease, or HDL, LDL, or total cholesterol. Conclusions We found no evidence that serum concentrations of vitamin B-12 are causally related to body weight or the majority of cardiometabolic outcomes investigated. However, vitamin B-12 may have a causal effect on fasting glucose and HOMA-B, although these results will require replication in large independent data sets. This trialwas registered at http://www.isrctn.com/ISRCTN47414943 as ISRCTN47414943.
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Affiliation(s)
- Gunn-Helen Moen
- Department of Endocrinology, Morbid Obesity, and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Institute of Clinical Medicine, Oslo, Norway
| | - Elisabeth Qvigstad
- Department of Endocrinology, Morbid Obesity, and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| | - Kåre I Birkeland
- Department of Endocrinology, Morbid Obesity, and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Institute of Clinical Medicine, Oslo, Norway
- Department of Transplantation Medicine, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - David M Evans
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Christine Sommer
- Department of Endocrinology, Morbid Obesity, and Preventive Medicine, Oslo University Hospital, Oslo, Norway
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39
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K RP, T S, B S, T MK, A J. LRP2 gene variants and their haplotypes strongly influence the risk of developing neural tube defects in the fetus: a family-triad study from South India. Metab Brain Dis 2018; 33:1343-1352. [PMID: 29728895 DOI: 10.1007/s11011-018-0242-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/16/2018] [Indexed: 10/17/2022]
Abstract
Neural tube defects (NTDs) are the leading cause of infant deaths worldwide. Lipoprotein related receptor 2 (LRP2) has been shown to play a crucial role in neural tube development in mouse models. However, the role of LRP2 gene in the development of human NTDs is not yet known. In view of this, family-based triad approach has been followed considering 924 subjects comprising 124 NTD case-parent trios and 184 control-parent trios diagnosed at Institute of Genetics and Hospital for Genetic Diseases, Hyderabad. Blood and tissue samples were genotyped for rs3755166 (-G759A) and rs2544390 (C835T) variants of LRP2 gene for their association with NTDs. Assessment of maternal-paternal genotype incompatibility risk for NTD revealed 3.77-folds risk with a combination of maternal GA and paternal GG genotypes (GAxGG = GA,p < 0.001), while CT genotypes of both the parents showed 4.19-folds risk for NTDs (CTxCT = CT,p = 0.009). Haplotype analysis revealed significant risk of maternal A-T (OR = 4.48,p < 0.001) and paternal G-T haplotypes (OR = 5.22,p < 0.001) for NTD development. Further, linkage analysis for parent-of-origin effects (POE) also revealed significant transmission of maternal 'A' allele (OR = 2.33,p = 0.028) and paternal 'T' allele (OR = 6.00,p = 0.016) to NTDs. Analysis of serum folate and active-B12 levels revealed significant association with LRP2 gene variants in the causation of NTDs. In conclusion, the present family-based triad study provides the first report on association of LRP2 gene variants with human NTDs.
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Affiliation(s)
- Rebekah Prasoona K
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Begumpet, Hyderabad, Telangana State, 500016, India
| | - Sunitha T
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Begumpet, Hyderabad, Telangana State, 500016, India
| | - Srinadh B
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Begumpet, Hyderabad, Telangana State, 500016, India
| | - Muni Kumari T
- Modern Government Maternity Hospital, Hyderabad, Telangana, 500012, India
| | - Jyothy A
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Begumpet, Hyderabad, Telangana State, 500016, India.
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40
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Hu Y, Raffield LM, Polfus LM, Moscati A, Nadkarni G, Preuss MH, Zhong X, Wei Q, Rich SS, Li Y, Wilson JG, Correa A, Loos RJF, Li B, Auer PL, Reiner AP. A common TCN1 loss-of-function variant is associated with lower vitamin B 12 concentration in African Americans. Blood 2018; 131:2859-2863. [PMID: 29764838 PMCID: PMC6014360 DOI: 10.1182/blood-2018-03-841023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Yao Hu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Linda M Polfus
- Center for Genetic Epidemiology, Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Arden Moscati
- Charles Bronfman Institute for Personalized Medicine and
| | - Girish Nadkarni
- Department of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Xue Zhong
- Vanderbilt Genetics Institute, Nashville, TN
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Qiang Wei
- Vanderbilt Genetics Institute, Nashville, TN
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Yun Li
- Department of Genetics
- Department of Biostatistics, and
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Adolfo Correa
- Department of Pediatrics and Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine and
- Genetics of Obesity and Related Metabolic Traits Program and
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bingshan Li
- Vanderbilt Genetics Institute, Nashville, TN
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI; and
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
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41
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Abstract
Malnutrition is a complex disorder, defined by an imbalance, excess, or deficiency of nutrient intake. The visible signs of malnutrition are stunted growth and wasting, but malnourished children are also more likely to have delays in neurocognitive development, vaccine failure, and susceptibility to infection. Despite malnutrition being a major global health problem, we do not yet understand the pathogenesis of this complex disorder. Although lack of food is a major contributor to childhood malnutrition, it is not the sole cause. The mother's prenatal nutritional status, enteric infections, and intestinal inflammation also contribute to the risk of childhood malnutrition and recovery. Here, we discuss another potential risk factor, host and maternal genetics, that may play a role in the risk of malnutrition via several biological pathways. Understanding the genetic risks of malnutrition may help to identify ideal targets for intervention and treatment of malnutrition.
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Affiliation(s)
- Priya Duggal
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 20215, USA;
| | - William A Petri
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA;
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42
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DeBoever C, Tanigawa Y, Lindholm ME, McInnes G, Lavertu A, Ingelsson E, Chang C, Ashley EA, Bustamante CD, Daly MJ, Rivas MA. Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study. Nat Commun 2018; 9:1612. [PMID: 29691392 PMCID: PMC5915386 DOI: 10.1038/s41467-018-03910-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/21/2018] [Indexed: 02/08/2023] Open
Abstract
Protein-truncating variants can have profound effects on gene function and are critical for clinical genome interpretation and generating therapeutic hypotheses, but their relevance to medical phenotypes has not been systematically assessed. Here, we characterize the effect of 18,228 protein-truncating variants across 135 phenotypes from the UK Biobank and find 27 associations between medical phenotypes and protein-truncating variants in genes outside the major histocompatibility complex. We perform phenome-wide analyses and directly measure the effect in homozygous carriers, commonly referred to as “human knockouts,” across medical phenotypes for genes implicated as being protective against disease or associated with at least one phenotype in our study. We find several genes with strong pleiotropic or non-additive effects. Our results illustrate the importance of protein-truncating variants in a variety of diseases. Protein-truncating variants (PTVs) are predicted to significantly affect a gene’s function and, thus, human traits. Here, DeBoever et al. systematically analyze PTVs in more than 300,000 individuals across 135 phenotypes and identify 27 associations between PTVs and medical conditions.
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Affiliation(s)
- Christopher DeBoever
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Yosuke Tanigawa
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | | | - Greg McInnes
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Adam Lavertu
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Erik Ingelsson
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chris Chang
- Grail, Inc., 1525 O'Brien Drive, Menlo Park, CA, 94025, USA
| | - Euan A Ashley
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Carlos D Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Mark J Daly
- Analytical and Translational Genetics Unit, Boston, MA, 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.
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43
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Frayling TM, Beaumont RN, Jones SE, Yaghootkar H, Tuke MA, Ruth KS, Casanova F, West B, Locke J, Sharp S, Ji Y, Thompson W, Harrison J, Etheridge AS, Gallins PJ, Jima D, Wright F, Zhou Y, Innocenti F, Lindgren CM, Grarup N, Murray A, Freathy RM, Weedon MN, Tyrrell J, Wood AR. A Common Allele in FGF21 Associated with Sugar Intake Is Associated with Body Shape, Lower Total Body-Fat Percentage, and Higher Blood Pressure. Cell Rep 2018; 23:327-336. [PMID: 29641994 PMCID: PMC5912948 DOI: 10.1016/j.celrep.2018.03.070] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/19/2017] [Accepted: 03/15/2018] [Indexed: 01/09/2023] Open
Abstract
Fibroblast growth factor 21 (FGF21) is a hormone that has insulin-sensitizing properties. Some trials of FGF21 analogs show weight loss and lipid-lowering effects. Recent studies have shown that a common allele in the FGF21 gene alters the balance of macronutrients consumed, but there was little evidence of an effect on metabolic traits. We studied a common FGF21 allele (A:rs838133) in 451,099 people from the UK Biobank study, aiming to use the human allele to inform potential adverse and beneficial effects of targeting FGF21. We replicated the association between the A allele and higher percentage carbohydrate intake. We then showed that this allele is more strongly associated with higher blood pressure and waist-hip ratio, despite an association with lower total body-fat percentage, than it is with BMI or type 2 diabetes. These human phenotypes of variation in the FGF21 gene will inform research into FGF21's mechanisms and therapeutic potential.
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Affiliation(s)
- Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK.
| | - Robin N Beaumont
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Samuel E Jones
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Marcus A Tuke
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Katherine S Ruth
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Francesco Casanova
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK; Diabetes and Vascular Research Centre, University of Exeter Medical School, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Ben West
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Jonathan Locke
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Seth Sharp
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Yingjie Ji
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - William Thompson
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Jamie Harrison
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Amy S Etheridge
- The University of North Carolina, Eshelman School of Pharmacy and Center for Pharmacogenomics and Individualized Therapy, Chapel Hill, NC, USA
| | - Paul J Gallins
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Dereje Jima
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Fred Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Yihui Zhou
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Federico Innocenti
- The University of North Carolina, Eshelman School of Pharmacy and Center for Pharmacogenomics and Individualized Therapy, Chapel Hill, NC, USA
| | - Cecilia M Lindgren
- Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anna Murray
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Rachel M Freathy
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Michael N Weedon
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Jessica Tyrrell
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK; European Centre for Environment and Human Health, University of Exeter Medical School, The Knowledge Spa, Royal Cornwall Hospital, Truro TR1 3HD, UK
| | - Andrew R Wood
- Genetics of Complex Traits, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
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44
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Surendran S, Adaikalakoteswari A, Saravanan P, Shatwaan IA, Lovegrove JA, Vimaleswaran KS. An update on vitamin B12-related gene polymorphisms and B12 status. GENES AND NUTRITION 2018; 13:2. [PMID: 29445423 PMCID: PMC5801754 DOI: 10.1186/s12263-018-0591-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/23/2018] [Indexed: 12/12/2022]
Abstract
Background Vitamin B12 is an essential micronutrient in humans needed for health maintenance. Deficiency of vitamin B12 has been linked to dietary, environmental and genetic factors. Evidence for the genetic basis of vitamin B12 status is poorly understood. However, advancements in genomic techniques have increased the knowledge-base of the genetics of vitamin B12 status. Based on the candidate gene and genome-wide association (GWA) studies, associations between genetic loci in several genes involved in vitamin B12 metabolism have been identified. Objective The objective of this literature review was to identify and discuss reports of associations between single-nucleotide polymorphisms (SNPs) in vitamin B12 pathway genes and their influence on the circulating levels of vitamin B12. Methods Relevant articles were obtained through a literature search on PubMed through to May 2017. An article was included if it examined an association of a SNP with serum or plasma vitamin B12 concentration. Beta coefficients and odds ratios were used to describe the strength of an association, and a P < 0.05 was considered as statistically significant. Two reviewers independently evaluated the eligibility for the inclusion criteria and extracted the data. Results From 23 studies which fulfilled the selection criteria, 16 studies identified SNPs that showed statistically significant associations with vitamin B12 concentrations. Fifty-nine vitamin B12-related gene polymorphisms associated with vitamin B12 status were identified in total, from the following populations: African American, Brazilian, Canadian, Chinese, Danish, English, European ancestry, Icelandic, Indian, Italian, Latino, Northern Irish, Portuguese and residents of the USA. Conclusion Overall, the data analyzed suggests that ethnic-specific associations are involved in the genetic determination of vitamin B12 concentrations. However, despite recent success in genetic studies, the majority of identified genes that could explain variation in vitamin B12 concentrations were from Caucasian populations. Further research utilizing larger sample sizes of non-Caucasian populations is necessary in order to better understand these ethnic-specific associations.
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Affiliation(s)
- S Surendran
- 1Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, PO Box 226, Whiteknights, Reading, RG6 6AP UK
| | - A Adaikalakoteswari
- 2Warwick Medical School - Population Evidence and Technologies, University of Warwick, Coventry, CV4 7AL UK.,3UK Academic Department of Diabetes and Metabolism, George Eliot Hospital, Nuneaton, UK
| | - P Saravanan
- 2Warwick Medical School - Population Evidence and Technologies, University of Warwick, Coventry, CV4 7AL UK.,3UK Academic Department of Diabetes and Metabolism, George Eliot Hospital, Nuneaton, UK
| | - I A Shatwaan
- 1Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, PO Box 226, Whiteknights, Reading, RG6 6AP UK
| | - J A Lovegrove
- 1Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, PO Box 226, Whiteknights, Reading, RG6 6AP UK
| | - K S Vimaleswaran
- 1Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, PO Box 226, Whiteknights, Reading, RG6 6AP UK
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45
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Taylor SL, McGuckin MA, Wesselingh S, Rogers GB. Infection's Sweet Tooth: How Glycans Mediate Infection and Disease Susceptibility. Trends Microbiol 2018; 26:92-101. [PMID: 29079498 PMCID: PMC7125966 DOI: 10.1016/j.tim.2017.09.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 09/10/2017] [Accepted: 09/29/2017] [Indexed: 12/21/2022]
Abstract
Glycans form a highly variable constituent of our mucosal surfaces and profoundly affect our susceptibility to infection and disease. The diversity and importance of these surface glycans can be seen in individuals who lack a functional copy of the fucosyltransferase gene, FUT2. Representing around one-fifth of the population, these individuals have an altered susceptibility to many bacterial and viral infections and diseases. The mediation of host-pathogen interactions by mucosal glycans, such as those added by FUT2, is poorly understood. We highlight, with specific examples, important mechanisms by which host glycans influence infection dynamics, including by: acting as pathogen receptors (or receptor-decoys), promoting microbial stability, altering the physical characteristics of mucus, and acting as immunological markers. We argue that the effect glycans have on infection dynamics has profound implications for many aspects of healthcare and policy, including clinical management, outbreak control, and vaccination policy.
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Affiliation(s)
- Steven L Taylor
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Michael A McGuckin
- Inflammatory Diseases Biology and Therapeutics, Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Steve Wesselingh
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Geraint B Rogers
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia.
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46
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Molloy AM. Should vitamin B 12 status be considered in assessing risk of neural tube defects? Ann N Y Acad Sci 2018; 1414:109-125. [PMID: 29377209 PMCID: PMC5887889 DOI: 10.1111/nyas.13574] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/07/2017] [Accepted: 11/11/2017] [Indexed: 02/06/2023]
Abstract
There is a strong biological premise for including vitamin B12 with folic acid in strategies to prevent neural tube defects (NTDs), due to the closely interlinked metabolism of these two vitamins. For example, reduction of B12 deficiency among women of reproductive age could enhance the capacity of folic acid to prevent NTDs by optimizing the cellular uptake and utilization of natural folate cofactors. Vitamin B12 might also have an independent role in NTD prevention, such that adding it in fortification programs might be more effective than fortifying with folic acid alone. Globally, there is ample evidence of widespread vitamin B12 deficiency in low‐ and middle‐income countries, but there is also considerable divergence of vitamin B12 status across regions, likely due to genetic as well as nutritional factors. Here, I consider the evidence that low vitamin B12 status may be an independent factor associated with risk of NTDs, and whether a fortification strategy to improve B12 status would help reduce the prevalence of NTDs. I seek to identify knowledge gaps in this respect and specify research goals that would address these gaps.
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Affiliation(s)
- Anne M Molloy
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Ireland
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47
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Caramaschi D, Sharp GC, Nohr EA, Berryman K, Lewis SJ, Davey Smith G, Relton CL. Exploring a causal role of DNA methylation in the relationship between maternal vitamin B12 during pregnancy and child's IQ at age 8, cognitive performance and educational attainment: a two-step Mendelian randomization study. Hum Mol Genet 2018; 26:3001-3013. [PMID: 28453778 PMCID: PMC5703349 DOI: 10.1093/hmg/ddx164] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/24/2017] [Indexed: 12/15/2022] Open
Abstract
An adequate intake of vitamin B12 during pregnancy plays an important role in
offspring neurodevelopment, potentially via epigenetic processes. We used a two-step
Mendelian randomization approach to assess whether DNA methylation plays a mediating and
causal role in associations between maternal vitamin B12 status and offspring’s
cognition. Firstly, we estimated the causal effect of maternal vitamin B12
levels on cord blood DNA methylation using the maternal FUT2 genotypes
rs492602:A > G and rs1047781:A > T as proxies for circulating vitamin B12
levels in the Avon Longitudinal Study of Parents and Children (ALSPAC) and we tested the
observed associations in a replication cohort. Secondly, we estimated the causal effect of
DNA methylation on IQ using the offspring genotype at sites close to the methylated CpG
site as a proxy for DNA methylation in ALSPAC and in a replication sample. The first step
Mendelian randomization estimated that maternal vitamin B12 had a small causal
effect on DNA methylation in offspring at three CpG sites, which was replicated for one of
the sites. The second step Mendelian randomization found weak evidence of a causal effect
of DNA methylation at two of these sites on childhood performance IQ which was replicated
for one of the sites. The findings support a causal effect of maternal vitamin
B12 levels on cord blood DNA methylation, and a causal effect of vitamin
B12-responsive DNA methylation changes on children’s cognition. Some
limitations were identified and future studies using a similar approach should aim to
overcome such issues.
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Affiliation(s)
- Doretta Caramaschi
- Medical Research Council Integrative Epidemiology Unit, School of Social and Community Medicine
| | - Gemma C Sharp
- Medical Research Council Integrative Epidemiology Unit, School of Social and Community Medicine.,School of Oral and Dental Sciences, The Cleft Collective, University of Bristol, Bristol BS8 2BN, UK
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense 5000C, Denmark
| | - Katie Berryman
- School of Social and Community Medicine, University of Bristol, Bristol BS8?2BN, UK
| | - Sarah J Lewis
- School of Social and Community Medicine, University of Bristol, Bristol BS8?2BN, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, School of Social and Community Medicine
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, School of Social and Community Medicine
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48
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Guéant-Rodriguez RM, Chery C, Caillierez-Fofou BM, Voirin J, Foliguet B, Josse T, Tramoy D, Feillet F, Guéant JL. Association of combined GIF290T>C heterozygous mutation/FUT2 secretor variant with neural tube defects. Clin Genet 2018; 93:191-193. [PMID: 28742214 DOI: 10.1111/cge.13104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 01/22/2023]
Abstract
Folate and vitamin B12 are needed for the proper embryo-fetal development possibly through their interacting role in the 1-carbon metabolism. Folate fortification reduces the prevalence of complex birth defects, and more specifically neural tube defects (NTDs). GIF and FUT2 are 2 genes associated with the uptake and blood level of vitamin B12. We evaluated GIF and FUT2 as predictors of severe birth defects, in 183 aborted fetuses compared with 375 healthy newborns. The GIF290C allele frequency was estimated to 0.4% in healthy newborns and to 8.1% in NTD fetuses (odds ratio 17.8 [95% confidence interval CI: 4.0-77.6]). The frequency of FUT2 rs601338 secretor variant was not different among groups. The GIF 290C heterozygous/FUT2 rs601338 secretor variant combined genotype was reported in 6 of the 37 NTD fetuses, but not in other fetuses and healthy newborns (P < .0001). This GIF/FUT2 combined genotype has been previously reported in children with congenital gastric intrinsic factor (GIF) deficiency, with respective consequences on B12 binding activity and GIF secretion. In conclusion, a genotype reported in congenital GIF deficiency produces also severe forms of NTD. This suggests that vitamin B12 delivery to neural tissue by the CUBN/GIF pathway could play a role in the neural tube closure mechanisms.
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Affiliation(s)
- R M Guéant-Rodriguez
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - C Chery
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - B-M Caillierez-Fofou
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - J Voirin
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - B Foliguet
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - T Josse
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - D Tramoy
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - F Feillet
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
| | - J-L Guéant
- Inserm-UMRS 954 (Nutrition-Genetics-Environmental Risks) and National Reference Centre for Inherited Metabolic Diseases, University of Lorraine and University Regional Hospital Center, Vandoeuvre lès Nancy, France
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49
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Velkova A, Diaz JEL, Pangilinan F, Molloy AM, Mills JL, Shane B, Sanchez E, Cunningham C, McNulty H, Cropp CD, Bailey-Wilson JE, Wilson AF, Brody LC. The FUT2 secretor variant p.Trp154Ter influences serum vitamin B12 concentration via holo-haptocorrin, but not holo-transcobalamin, and is associated with haptocorrin glycosylation. Hum Mol Genet 2017; 26:4975-4988. [PMID: 29040465 PMCID: PMC5886113 DOI: 10.1093/hmg/ddx369] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 11/14/2022] Open
Abstract
Vitamin B12 deficiency is common in older individuals. Circulating vitamin B12 concentration can be used to diagnose deficiency, but this test has substantial false positive and false negative rates. We conducted genome-wide association studies (GWAS) in which we resolved total serum vitamin B12 into the fractions bound to transcobalamin and haptocorrin: two carrier proteins with very different biological properties. We replicated reported associations between total circulating vitamin B12 concentrations and a common null variant in FUT2. This allele determines the secretor phenotype in which blood group antigens are found in non-blood body fluids. Vitamin B12 bound to haptocorrin (holoHC) remained highly associated with FUT2 rs601338 (p.Trp154Ter). Transcobalamin bound vitamin B12 (holoTC) was not influenced by this variant. HoloTC is the bioactive the form of the vitamin and is taken up by all tissues. In contrast, holoHC is only taken up by the liver. Using holoHC from individuals with known FUT2 genotypes, we demonstrated that FUT2 rs601338 genotype influences the glycosylation of haptocorrin. We then developed an experimental model demonstrating that holoHC is transported into cultured hepatic cells (HepG2) via the asialoglycoprotein receptor (ASGR). Our data challenge current published hypotheses on the influence of genetic variation on this clinically important measure and are consistent with a model in which FUT2 rs601338 influences holoHC by altering haptocorrin glycosylation, whereas B12 bound to non-glycosylated transcobalamin (i.e. holoTC) is not affected. Our findings explain some of the observed disparity between use of total B12 or holoTC as first-line clinical tests of vitamin B12 status.
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Affiliation(s)
- Aneliya Velkova
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Jennifer E L Diaz
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Faith Pangilinan
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Anne M Molloy
- Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - James L Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver NICHD, Bethesda, MD 20852, USA
| | - Barry Shane
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Erica Sanchez
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | | | - Helene McNulty
- Northern Ireland Centre for Food and Health, University of Ulster, Coleraine BT52 1SA, Northern Ireland
| | - Cheryl D Cropp
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 21224, USA
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 21224, USA
| | - Alexander F Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 21224, USA
| | - Lawrence C Brody
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
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Comments on “Vitamin Pharmacogenomics: New Insight into Individual Differences in Diseases and Drug Responses”. GENOMICS, PROTEOMICS & BIOINFORMATICS 2017; 15:405-406. [PMID: 29017966 PMCID: PMC5828657 DOI: 10.1016/j.gpb.2017.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/22/2017] [Indexed: 11/22/2022]
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