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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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Tsukamoto M, Hishida A, Tamura T, Nagayoshi M, Okada R, Kubo Y, Kato Y, Hamajima N, Nishida Y, Shimanoe C, Ibusuki R, Shibuya K, Takashima N, Nakamura Y, Kusakabe M, Nakamura Y, Koyanagi YN, Oze I, Nishiyama T, Suzuki S, Watanabe I, Matsui D, Otonari J, Ikezaki H, Katsuura-Kamano S, Arisawa K, Kuriki K, Nakatochi M, Momozawa Y, Takeuchi K, Wakai K, Matsuo K. GWAS of Folate Metabolism With Gene-environment Interaction Analysis Revealed the Possible Role of Lifestyles in the Control of Blood Folate Metabolites in Japanese: The J-MICC Study. J Epidemiol 2024; 34:228-237. [PMID: 37517992 PMCID: PMC10999522 DOI: 10.2188/jea.je20220341] [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: 01/09/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023] Open
Abstract
BACKGROUND The present genome-wide association study (GWAS) aimed to reveal the genetic loci associated with folate metabolites, as well as to detect related gene-environment interactions in Japanese. METHODS We conducted the GWAS of plasma homocysteine (Hcy), folic acid (FA), and vitamin B12 (VB12) levels in the Japan Multi-Institutional Collaborative Cohort (J-MICC) Study participants who joined from 2005 to 2012, and also estimated gene-environment interactions. In the replication phase, we used data from the Yakumo Study conducted in 2009. In the discovery phase, data of 2,263 participants from four independent study sites of the J-MICC Study were analyzed. In the replication phase, data of 573 participants from the Yakumo Study were analyzed. RESULTS For Hcy, MTHFR locus on chr 1, NOX4 on chr 11, CHMP1A on chr 16, and DPEP1 on chr 16 reached genome-wide significance (P < 5 × 10-8). MTHFR also associated with FA, and FUT2 on chr 19 associated with VB12. We investigated gene-environment interactions in both studies and found significant interactions between MTHFR C677T and ever drinking, current drinking, and physical activity >33% on Hcy (β = 0.039, 0.038 and -0.054, P = 0.018, 0.021 and <0.001, respectively) and the interaction of MTHFR C677T with ever drinking on FA (β = 0.033, P = 0.048). CONCLUSION The present GWAS revealed the folate metabolism-associated genetic loci and gene-environment interactions with drinking and physical activity in Japanese, suggesting the possibility of future personalized cardiovascular disease prevention.
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Affiliation(s)
- Mineko Tsukamoto
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Tamura
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mako Nagayoshi
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Rieko Okada
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoko Kubo
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasufumi Kato
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuyuki Hamajima
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichiro Nishida
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | | | - Rie Ibusuki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kenichi Shibuya
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Naoyuki Takashima
- Department of Public Health, Shiga University of Medical Science, Otsu, Japan
| | - Yasuyuki Nakamura
- Department of Public Health, Shiga University of Medical Science, Otsu, Japan
| | - Miho Kusakabe
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Yohko Nakamura
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Yuriko N. Koyanagi
- Division of Cancer Information and Control, Department of Preventive Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Takeshi Nishiyama
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Sadao Suzuki
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Isao Watanabe
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Daisuke Matsui
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Jun Otonari
- Department of Psychosomatic Medicine, Kyushu University Graduate School of Medical Sciences, Faculty of Medical Sciences, Fukuoka, Japan
| | - Hiroaki Ikezaki
- Department of Comprehensive General Internal Medicine, Kyushu University Graduate School of Medical Sciences, Faculty of Medical Sciences, Fukuoka, Japan
| | - Sakurako Katsuura-Kamano
- Department of Preventive Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Kokichi Arisawa
- Laboratory of Public Health, Division of Nutritional Sciences, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kiyonori Kuriki
- Laboratory of Public Health, Division of Nutritional Sciences, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kenji Takeuchi
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of International and Community Oral Health, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Genetic Aspects of Micronutrients Important for Inflammatory Bowel Disease. Life (Basel) 2022; 12:life12101623. [PMID: 36295058 PMCID: PMC9604584 DOI: 10.3390/life12101623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Inflammatory bowel disease (IBD), Crohn’s disease (CD) and ulcerative colitis (UC) are complex diseases whose etiology is associated with genetic and environmental risk factors, among which are diet and gut microbiota. To date, IBD is an incurable disease and the main goal of its treatment is to reduce symptoms, prevent complications, and improve nutritional status and the quality of life. Patients with IBD usually suffer from nutritional deficiency with imbalances of specific micronutrient levels that contribute to the further deterioration of the disease. Therefore, along with medications usually used for IBD treatment, therapeutic strategies also include the supplementation of micronutrients such as vitamin D, folic acid, iron, and zinc. Micronutrient supplementation tailored according to individual needs could help patients to maintain overall health, avoid the triggering of symptoms, and support remission. The identification of individuals’ genotypes associated with the absorption, transport and metabolism of micronutrients can modify future clinical practice in IBD and enable individualized treatment. This review discusses the personalized approach with respect to genetics related to micronutrients commonly used in inflammatory bowel disease treatment.
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Zhang TP, Li R, Wang LJ, Tang F, Li HM. Clinical relevance of vitamin B12 level and vitamin B12 metabolic gene variation in pulmonary tuberculosis. Front Immunol 2022; 13:947897. [PMID: 36275653 PMCID: PMC9583150 DOI: 10.3389/fimmu.2022.947897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/09/2022] [Indexed: 11/14/2022] Open
Abstract
The aim of this study was to assess the association of vitamin B12 level and single nucleotide polymorphisms (SNPs) in vitamin B12 metabolic genes with pulmonary tuberculosis (PTB) in Chinese Han population. The plasma vitamin B12 expression level was detected using ELISA. Ten SNPs in six key genes (TCN1, TCN2, CUBN, MMACHC, FUT6, and MUT) of vitamin B12 metabolic pathway were included for genotyping by the SNPscan technique among 454 PTB patients and 467 controls. Our results found that vitamin B12 level was significantly reduced in PTB patients when compared with controls. There was no significant association between TCN1 rs526934, TCN2 rs1801198, CUBN rs7906242, rs10904861, rs1801222, MMACHC rs10789465, FUT6 rs3760776, rs3760775, MUT rs9473555, rs9381784 variants, and PTB susceptibility. TCN2 rs1801198 CC genotype, C allele was significantly associated with hypoproteinemia in PTB patients. In CUBN, rs7906242 GG genotype, G allele, rs10904861 TT genotype, and T allele were significantly related to the decreased frequency of sputum smear-positive, and rs10904861 variant affected the occurrence of drug resistance in PTB patients. In addition, the increased frequency of CUBN rs1801222 AA genotype was significantly associated with leukopenia. The decreased frequency of MUT rs9473555 CC genotype was found in the PTB patients with hypoproteinemia. However, vitamin B12 expression was not associated with the genotype distribution of above SNPs. In conclusion, vitamin B12 level was significantly decreased in PTB patients and genetic variants in vitamin B12 metabolic genes were not contributed to PTB susceptibility. Several SNPs in TCN2, CUBN, and MUT gene might associate with multiple clinical manifestations in PTB.
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Affiliation(s)
- Tian-Ping Zhang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Rui Li
- Department of Nosocomial Infection Management, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Li-Jun Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Fei Tang
- Department of Interventional Pulmonology and Endoscopic Diagnosis and Treatment Center, Anhui Chest Hospital, Hefei, China
- *Correspondence: Hong-Miao Li, ; Fei Tang,
| | - Hong-Miao Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- *Correspondence: Hong-Miao Li, ; Fei Tang,
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5
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Song Y, Wu Z, Zhao P. The effects of metformin in the treatment of osteoarthritis: Current perspectives. Front Pharmacol 2022; 13:952560. [PMID: 36081941 PMCID: PMC9445495 DOI: 10.3389/fphar.2022.952560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/27/2022] [Indexed: 02/04/2023] Open
Abstract
Osteoarthritis is a chronic and irreversible disease of the locomotor system which is closely associated with advancing age. Pain and limited mobility frequently affect the quality of life in middle-aged and older adults. With a global population of more than 350 million, osteoarthritis is becoming a health threat alongside cancer and cardiovascular disease. It is challenging to find effective treatments to promote cartilage repair and slow down disease progression. Metformin is the first-line drug for patients with type 2 diabetes, and current perspectives suggest that it cannot only lower glucose but also has anti-inflammatory and anti-aging properties. Experimental studies applying metformin for the treatment of osteoarthritis have received much attention in recent years. In our review, we first presented the history of metformin and the current status of osteoarthritis, followed by a brief review of the mechanism that metformin acts, involving AMPK-dependent and non-dependent pathways. Moreover, we concluded that metformin may be beneficial in the treatment of osteoarthritis by inhibiting inflammation, modulating autophagy, antagonizing oxidative stress, and reducing pain levels. Finally, we analyzed the relevant evidence from animal and human studies. The potential of metformin for the treatment of osteoarthritis deserves to be further explored.
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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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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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Li X, Thomsen H, Sundquist K, Sundquist J, Försti A, Hemminki K. Familial Risks between Pernicious Anemia and Other Autoimmune Diseases in the Population of Sweden. Autoimmune Dis 2021; 2021:8815297. [PMID: 33505716 PMCID: PMC7815416 DOI: 10.1155/2021/8815297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/21/2020] [Accepted: 12/30/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Pernicious anemia (PA) is an autoimmune disease (AID) which is caused by lack of vitamin B12 (cobalamin) due to its impaired uptake. PA is a multifactorial disease which is associated with a number of other AID comorbidities and which is manifested as part of autoimmune polyglandular syndrome. Due to the shortage of family studies on PA, we planned to address the problem by assessing familial risks for concordant PA between family members and for discordant PA in families of other AID patients. METHODS We collected data on patients diagnosed with AIDs from the Swedish hospitals and family data from a population register. We calculated standardized incidence ratios (SIRs) in families for concordant and discordant risks. RESULTS The number of PA patients in the offspring generation (for which the familial risk was calculated) was 7701; 278 (3.6%) patients had a family history of PA. The population prevalence of PA was 0.9/1000. The familial risk for PA was 3.88 when any first-degree relative was the proband, equal for men and women. The familial risk was two times higher between siblings than between offspring and parents which may be due to complex genetic background. Associations of PA with 14 discordant AIDs were significant; these included some AIDs that have previously been described as comorbidities in PA patients and several yet unreported associations, including rheumatoid arthritis and other AIDs. CONCLUSIONS The familial risks for PA were high suggesting multifactorial genetic etiology. The results call for further population-level studies to unravel mechanisms of familial PA which may help to understand the etiology of this disease.
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Affiliation(s)
- Xinjun Li
- 1Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Hauke Thomsen
- 1Center for Primary Health Care Research, Lund University, Malmö, Sweden
- 2Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- 3Genewerk GmbH, Heidelberg, Germany
| | - Kristina Sundquist
- 1Center for Primary Health Care Research, Lund University, Malmö, Sweden
- 4Department of Family Medicine and Community Health, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, USA
- 5Center for Community-based Healthcare Research and Education (CoHRE), Department of Functional Pathology, School of Medicine, Shimane University, Matsue, Japan
| | - Jan Sundquist
- 1Center for Primary Health Care Research, Lund University, Malmö, Sweden
- 4Department of Family Medicine and Community Health, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, USA
- 5Center for Community-based Healthcare Research and Education (CoHRE), Department of Functional Pathology, School of Medicine, Shimane University, Matsue, Japan
| | - Asta Försti
- 1Center for Primary Health Care Research, Lund University, Malmö, Sweden
- 2Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- 6Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- 7Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kari Hemminki
- 1Center for Primary Health Care Research, Lund University, Malmö, Sweden
- 2Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- 8Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany
- 9Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
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9
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Cheng CF, Ku HC, Shen TC. The potential of using itaconate as treatment for inflammation-related heart diseases. Tzu Chi Med J 2021; 34:113-118. [PMID: 35465278 PMCID: PMC9020236 DOI: 10.4103/tcmj.tcmj_83_21] [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: 03/29/2021] [Revised: 05/03/2021] [Accepted: 06/07/2021] [Indexed: 11/04/2022] Open
Abstract
Intracellular metabolites can cause critical changes in biological functions. Itaconate is perhaps the most fascinating substance in macrophages. Lipopolysaccharide can activate aconitate decarboxylase 1 and induces the generation of itaconate from the tricarboxylic acid cycle by decarboxylation of cis-aconitate. It has been reported that itaconate has beneficial effects on inflammation and oxidation. The mechanisms involved in these effects include the suppression of succinate dehydrogenase, the activation of nuclear factor E2-related factor 2 by alkylation of Kelch-like ECH-associated protein 1, suppression of aerobic glycolysis through regulation of glyceraldehyde-3-phosphate dehydrogenase and fructose-bisphosphate aldolase A, and suppression of IκBζ translation through activating transcription factor 3 activation. All of these findings elucidated the possible therapeutic implications of itaconate in inflammation-related diseases. In this review, we highlight that itaconate is a crucial molecule of the immunomodulatory response in macrophages and can regulate between immune response and cardiovascular metabolism. Furthermore, these discoveries suggest that itaconate is a very novel therapeutic molecule for the treatment of inflammation-related heart diseases.
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Abstract
The paper presents the results of the literature review and the authors’ own studies of the association of several several single-nucleotide genetic polymorphisms (SNP), which affect one-carbon metabolism, with a risk of schizophrenia and the severity of some clusters of its symptoms. Directions for further study of the role of a number of SNP of enzymes in the folate metabolism cycle and related biochemical processes in schizophrenia (in particular, their influence on the effect of personalized correction of one-carbon metabolism disorders) are determined.
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11
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Gagliano Taliun SA. Genetic determinants of low vitamin B12 levels in Alzheimer's disease risk. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2019; 11:430-434. [PMID: 31206009 PMCID: PMC6558085 DOI: 10.1016/j.dadm.2019.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
INTRODUCTION There is observational evidence that low circulating levels of vitamin B12 are associated with an increased risk of Alzheimer's disease. METHODS We used a two-sample summary-statistics-based Mendelian randomization design to assess the relationship of genetic factors contributing to vitamin B12 with late-onset Alzheimer's disease risk. RESULTS Our results do not support a causal role of decreased vitamin B12 levels on Alzheimer's disease risk. DISCUSSION This work encourages research on other modifiable biomarkers for Alzheimer's disease risk.
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Affiliation(s)
- Sarah A. Gagliano Taliun
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
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12
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Li X, Li H, Dong Y, Gao B, Cheng H, Ni W, Gan S, Liu Z, Burgunder J, Wu Z. Haplotype analysis encompassing
HTT
gene in Chinese patients with Huntington's disease. Eur J Neurol 2019; 27:273-279. [DOI: 10.1111/ene.14072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/21/2019] [Indexed: 12/19/2022]
Affiliation(s)
- X.‐Y. Li
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang Province Zhejiang University School of Medicine HangzhouChina
| | - H.‐L. Li
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang Province Zhejiang University School of Medicine HangzhouChina
| | - Y. Dong
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang Province Zhejiang University School of Medicine HangzhouChina
| | - B. Gao
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang Province Zhejiang University School of Medicine HangzhouChina
| | - H.‐R. Cheng
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang Province Zhejiang University School of Medicine HangzhouChina
| | - W. Ni
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang Province Zhejiang University School of Medicine HangzhouChina
| | - S.‐R. Gan
- Department of Neurology and Institute of Neurology First Affiliated Hospital Fujian Medical University FuzhouChina
| | - Z.‐J. Liu
- Department of Neurology and Institute of Neurology Huashan Hospital Shanghai Medical College Fudan University Shanghai China
| | - J.‐M. Burgunder
- Swiss Huntington’s Disease Centre, Siloah, Gümligen and Department of Neurology, University of Bern Bern Switzerland
| | - Z.‐Y. Wu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang Province Zhejiang University School of Medicine HangzhouChina
- Joint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto Zhejiang University HangzhouChina
- CAS Center for Excellence in Brain Science and Intelligence Technology Shanghai China
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13
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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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14
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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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15
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Zhilyaeva TV, Sergeeva AV, Blagonravova AS, Mazo GE, Kibitov AO. One-Carbon Metabolism Disorders in Schizophrenia: Genetic and Therapeutic Aspects. NEUROCHEM J+ 2019. [DOI: 10.1134/s1819712419020156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Polfus LM, Raffield LM, Wheeler MM, Tracy RP, Lange LA, Lettre G, Miller A, Correa A, Bowler RP, Bis JC, Salimi S, Jenny NS, Pankratz N, Wang B, Preuss MH, Zhou L, Moscati A, Nadkarni GN, Loos RJF, Zhong X, Li B, Johnsen JM, Nickerson DA, Reiner AP, Auer PL. Whole genome sequence association with E-selectin levels reveals loss-of-function variant in African Americans. Hum Mol Genet 2019; 28:515-523. [PMID: 30307499 PMCID: PMC6337694 DOI: 10.1093/hmg/ddy360] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/01/2018] [Accepted: 10/07/2018] [Indexed: 12/13/2022] Open
Abstract
E-selectin mediates the rolling of circulating leukocytes during inflammatory processes. Previous genome-wide association studies in European and Asian individuals have identified the ABO locus associated with E-selectin levels. Using Trans-Omics for Precision Medicine whole genome sequencing data in 2249 African Americans (AAs) from the Jackson Heart Study, we examined genome-wide associations with soluble E-selectin levels. In addition to replicating known signals at ABO, we identified a novel association of a common loss-of-function, missense variant in Fucosyltransferase 6 (FUT6; rs17855739,p.Glu274Lys, P = 9.02 × 10-24) with higher soluble E-selectin levels. This variant is considerably more common in populations of African ancestry compared to non-African ancestry populations. We replicated the association of FUT6 p.Glu274Lys with higher soluble E-selectin in an independent population of 748 AAs from the Women's Health Initiative and identified an additional pleiotropic association with vitamin B12 levels. Despite the broad role of both selectins and fucosyltransferases in various inflammatory, immune and cancer-related processes, we were unable to identify any additional disease associations of the FUT6 p.Glu274Lys variant in an electronic medical record-based phenome-wide association scan of over 9000 AAs.
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Affiliation(s)
- Linda M Polfus
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Marsha M Wheeler
- Department of Genome Sciences, University of Washington Center for Mendelian Genomics, Seattle, WA, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Leslie A Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Guillaume Lettre
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
- Montreal Heart Institute, Montréal, QC, Canada
| | - Amanda Miller
- Zilber School of Public Health, University of Wisconsin–Milwaukee, Milwaukee, WI, USA
| | - Adolfo Correa
- Department of Pediatrics and Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Joshua C Bis
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Shabnam Salimi
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Nancy Swords Jenny
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Biqi Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Michael H Preuss
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisheng Zhou
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arden Moscati
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish N Nadkarni
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xue Zhong
- Vanderbilt Genetics Institute, Nashville, TN, USA
| | - Bingshan Li
- Vanderbilt Genetics Institute, Nashville, TN, USA
| | - Jill M Johnsen
- Bloodworks Northwest Research Institute, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington Center for Mendelian Genomics, Seattle, WA, USA
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin–Milwaukee, Milwaukee, WI, USA
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17
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Yu XH, Zhang DW, Zheng XL, Tang CK. Itaconate: an emerging determinant of inflammation in activated macrophages. Immunol Cell Biol 2018; 97:134-141. [PMID: 30428148 DOI: 10.1111/imcb.12218] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 12/26/2022]
Abstract
Macrophages play a central role in innate immunity as the first line of defense against pathogen infection. Upon exposure to inflammatory stimuli, macrophages rapidly respond and subsequently undergo metabolic reprogramming to substantially produce cellular metabolites such as itaconate. As a derivate of the tricarboxylic acid cycle, itaconate is derived from the decarboxylation of cis-aconitate mediated by immunoresponsive gene 1 in the mitochondrial matrix. It is well known that itaconate has a direct antimicrobial effect by inhibiting isocitrate lyase. Strikingly, two recent studies published in Nature showed that itaconate markedly decreases the production of proinflammatory mediators in lipopolysaccharide-treated macrophages and ameliorates sepsis and psoriasis in animal models, revealing a novel biological action of itaconate beyond its regular roles in antimicrobial defense. The mechanism for this anti-inflammatory effect has been proposed to involve the inhibition of succinate dehydrogenase, blockade of IκBζ translation and activation of Nrf2. These intriguing discoveries provide a new explanation for how macrophages are switched from a pro- to an anti-inflammatory state to limit the damage and facilitate tissue repair under proinflammatory conditions. Thus, the emerging effect of itaconate as a crucial determinant of macrophage inflammation has important implications in further understanding cellular immunometabolism and developing future therapeutics for the treatment of inflammatory diseases. In this review, we focus on the roles of itaconate in controlling the inflammatory response during macrophage activation, providing a rationale for future investigation and therapeutic intervention.
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Affiliation(s)
- Xiao-Hua Yu
- Key Laboratory for Arteriosclerology of Hunan Province, Medical Research Experiment Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Cardiovascular Disease, University of South China, Hengyang, Hunan, 421001, China
| | - Da-Wei Zhang
- Department of Pediatrics and Group on the Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, AB T6G 2S2, Canada
| | - Xi-Long Zheng
- Department of Biochemistry and Molecular Biology, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Health Sciences Center, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | - Chao-Ke Tang
- Key Laboratory for Arteriosclerology of Hunan Province, Medical Research Experiment Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Cardiovascular Disease, University of South China, Hengyang, Hunan, 421001, China
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18
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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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19
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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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20
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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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21
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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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22
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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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23
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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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24
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Shen H, Campanello GC, Flicker D, Grabarek Z, Hu J, Luo C, Banerjee R, Mootha VK. The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B 12. Cell 2017; 171:771-782.e11. [PMID: 29056341 PMCID: PMC5827971 DOI: 10.1016/j.cell.2017.09.051] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/17/2017] [Accepted: 09/28/2017] [Indexed: 11/27/2022]
Abstract
CLYBL encodes a ubiquitously expressed mitochondrial enzyme, conserved across all vertebrates, whose cellular activity and pathway assignment are unknown. Its homozygous loss is tolerated in seemingly healthy individuals, with reduced circulating B12 levels being the only and consistent phenotype reported to date. Here, by combining enzymology, structural biology, and activity-based metabolomics, we report that CLYBL operates as a citramalyl-CoA lyase in mammalian cells. Cells lacking CLYBL accumulate citramalyl-CoA, an intermediate in the C5-dicarboxylate metabolic pathway that includes itaconate, a recently identified human anti-microbial metabolite and immunomodulator. We report that CLYBL loss leads to a cell-autonomous defect in the mitochondrial B12 metabolism and that itaconyl-CoA is a cofactor-inactivating, substrate-analog inhibitor of the mitochondrial B12-dependent methylmalonyl-CoA mutase (MUT). Our work de-orphans the function of human CLYBL and reveals that a consequence of exposure to the immunomodulatory metabolite itaconate is B12 inactivation.
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Affiliation(s)
- Hongying Shen
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02141, USA
| | - Gregory C Campanello
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Daniel Flicker
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02141, USA
| | - Zenon Grabarek
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02141, USA
| | - Junchi Hu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02141, USA.
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25
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Nongmaithem SS, Joglekar CV, Krishnaveni GV, Sahariah SA, Ahmad M, Ramachandran S, Gandhi M, Chopra H, Pandit A, Potdar RD, H D Fall C, Yajnik CS, Chandak GR. GWAS identifies population-specific new regulatory variants in FUT6 associated with plasma B12 concentrations in Indians. Hum Mol Genet 2017; 26:2551-2564. [PMID: 28334792 PMCID: PMC5886186 DOI: 10.1093/hmg/ddx071] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/20/2017] [Indexed: 01/26/2023] Open
Abstract
Vitamin B12 is an important cofactor in one-carbon metabolism whose dysregulation is associated with various clinical conditions. Indians have a high prevalence of B12 deficiency but little is known about the genetic determinants of circulating B12 concentrations in Indians. We performed a genome-wide association study in 1001 healthy participants in the Pune Maternal Nutrition Study (PMNS), replication studies in 3418 individuals from other Indian cohorts and by meta-analysis identified new variants, rs3760775 (P = 1.2 × 10−23) and rs78060698 (P = 8.3 × 10−17) in FUT6 to be associated with circulating B12 concentrations. Although in-silico analysis replicated both variants in Europeans, differences in the effect allele frequency, effect size and the linkage disequilibrium structure of credible set variants with the reported variants suggest population-specific characteristics in this region. We replicated previously reported variants rs602662, rs601338 in FUT2, rs3760776, rs708686 in FUT6, rs34324219 in TCN1 (all P < 5 × 10−8), rs1131603 in TCN2 (P = 3.4 × 10−5), rs12780845 in CUBN (P = 3.0 × 10−3) and rs2270655 in MMAA (P = 2.0 × 10−3). Circulating B12 concentrations in the PMNS and Parthenon study showed a significant decline with increasing age (P < 0.001), however, the genetic contribution to B12 concentrations remained constant. Luciferase reporter and electrophoretic-mobility shift assay for the FUT6 variant rs78060698 using HepG2 cell line demonstrated strong allele-specific promoter and enhancer activity and differential binding of HNF4α, a key regulator of expression of various fucosyltransferases. Hence, the rs78060698 variant, through regulation of fucosylation may control intestinal host-microbial interaction which could influence B12 concentrations. Our results suggest that in addition to established genetic variants, population-specific variants are important in determining plasma B12 concentrations.
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Affiliation(s)
- Suraj S Nongmaithem
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500 007, India
| | - Charudatta V Joglekar
- Diabetes Unit, King Edward Memorial Hospital and Research Centre, Rasta Peth, Pune, Maharashtra 411 011, India
| | - Ghattu V Krishnaveni
- Epidemiology Research Unit, CSI Holdsworth Memorial Hospital, Mysore, Karnataka 570 021, India
| | - Sirazul A Sahariah
- Research Department, Centre for the Study of Social Change, Mumbai, Maharashtra 400 051, India
| | - Meraj Ahmad
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500 007, India
| | - Swetha Ramachandran
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500 007, India
| | - Meera Gandhi
- Research Department, Centre for the Study of Social Change, Mumbai, Maharashtra 400 051, India
| | - Harsha Chopra
- Research Department, Centre for the Study of Social Change, Mumbai, Maharashtra 400 051, India
| | - Anand Pandit
- Department of Pediatrics, King Edward Memorial Hospital and Research Centre, Rasta Peth, Pune, Maharashtra 411 011, India
| | - Ramesh D Potdar
- Research Department, Centre for the Study of Social Change, Mumbai, Maharashtra 400 051, India
| | - Caroline H D Fall
- Research Department, Centre for the Study of Social Change, Mumbai, Maharashtra 400 051, India.,MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Chittaranjan S Yajnik
- Diabetes Unit, King Edward Memorial Hospital and Research Centre, Rasta Peth, Pune, Maharashtra 411 011, India
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500 007, India.,Human Genetics Unit, Genome Institute of Singapore, Biopolis, 138 672, Singapore
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26
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Chen CT, Liao WY, Hsu CC, Hsueh KC, Yang SF, Teng YH, Yu YL. FUT2 genetic variants as predictors of tumor development with hepatocellular carcinoma. Int J Med Sci 2017; 14:885-890. [PMID: 28824326 PMCID: PMC5562196 DOI: 10.7150/ijms.19734] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/20/2017] [Indexed: 01/10/2023] Open
Abstract
Lewis antigens related to the ABO blood group are fucosylated oligosaccharides and are synthesized by specific glycosyltransferases (FUTs). FUTs are involved in various biological processes including cell adhesion and tumor progression. The fucosyltransferase-2 gene (FUT2) encodes alpha (1,2) fucosyltransferase, which is responsible for the addition of the alpha (1,2)-linkage of fucose to glycans. Aberrant fucosylation occurs frequently during the development and progression of hepatocellular carcinoma (HCC). However, the association of FUT2 polymorphisms with HCC development has not been studied. Therefore, we aimed to investigate the association of FUT2 polymorphisms with demographic, etiological, and clinical characteristics and with susceptibility to HCC. In this study, a total of 339 patients and 720 controls were recruited. The genotypes of FUT2 at four single-nucleotide polymorphisms (SNPs; rs281377, rs1047781, rs601338, and rs602662) were detected by real-time polymerase chain reaction from these samples. Compared with the wild-type genotype at SNP rs1047781, which is homozygous for nucleotides AA, at least one polymorphic T allele (AT or TT) displayed significant association with clinical stage (p = 0.048) and tumor size (p = 0.022). Our study strongly implicates the polymorphic locus rs1047781 of FUT2 as being associated with HCC development.
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Affiliation(s)
- Chih Tien Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Wen Ying Liao
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chia Chun Hsu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan
- Institute of Biotechnology, National Tsing-Hua University, Hsinchu, Taiwan
| | - Kuan Chun Hsueh
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of General Surgery, Department of Surgery, Tungs' Taichung MetroHarbour Hospital, Taichung, Taiwan
| | - Shun Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Ying Hock Teng
- Department of Emergency Medicine, School of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Emergency Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yung Luen Yu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Biotechnology, Asia University, Taichung, Taiwan
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27
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Allin KH, Friedrich N, Pietzner M, Grarup N, Thuesen BH, Linneberg A, Pisinger C, Hansen T, Pedersen O, Sandholt CH. Genetic determinants of serum vitamin B12 and their relation to body mass index. Eur J Epidemiol 2017; 32:125-134. [PMID: 27995393 PMCID: PMC5374184 DOI: 10.1007/s10654-016-0215-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 11/28/2016] [Indexed: 12/03/2022]
Abstract
Lower serum vitamin B12 levels have been related to adverse metabolic health profiles, including adiposity. We used a Mendelian randomization design to test whether this relation might be causal. We included two Danish population-based studies (ntotal = 9311). Linear regression was used to test for associations between (1) serum vitamin B12 levels and body mass index (BMI), (2) genetic variants and serum vitamin B12 levels, and (3) genetic variants and BMI. The effect of a genetically determined decrease in serum vitamin B12 on BMI was estimated by instrumental variable regression. Decreased serum vitamin B12 associated with increased BMI (P < 1 × 10-4). A genetic risk score based on eight vitamin B12 associated variants associated strongly with serum vitamin B12 (P < 2 × 10-43), but not with BMI (P = 0.91). Instrumental variable regression showed that a 20% decrease in serum vitamin B12 was associated with a 0.09 kg/m2 (95% CI 0.05; 0.13) increase in BMI (P = 3 × 10-5), whereas a genetically induced 20% decrease in serum vitamin B12 had no effect on BMI [-0.03 (95% CI -0.22; 0.16) kg/m2] (P = 0.74). Nevertheless, the strongest serum vitamin B12 variant, FUT2 rs602662, which was excluded from the B12 genetic risk score due to potential pleiotropic effects, showed a per allele effect of 0.15 kg/m2 (95% CI 0.01; 0.32) on BMI (P = 0.03). This association was accentuated including two German cohorts (ntotal = 5050), with a combined effect of 0.19 kg/m2 (95% CI 0.08; 0.30) (P = 4 × 10-4). We found no support for a causal role of decreased serum vitamin B12 levels in obesity. However, our study suggests that FUT2, through its regulation of the cross-talk between gut microbes and the human host, might explain a part of the observational association between serum vitamin B12 and BMI.
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Affiliation(s)
- Kristine H Allin
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen, Denmark.
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
- Research Centre for Prevention and Health, The Capital Region of Denmark, Copenhagen, Denmark
| | - Maik Pietzner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen, Denmark
| | - Betina H Thuesen
- Research Centre for Prevention and Health, The Capital Region of Denmark, Copenhagen, Denmark
| | - Allan Linneberg
- Research Centre for Prevention and Health, The Capital Region of Denmark, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, Glostrup, Denmark
| | - Charlotta Pisinger
- Research Centre for Prevention and Health, The Capital Region of Denmark, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen, Denmark
- Faculty of Health Sciences, University of Aarhus, Aarhus, Denmark
| | - Camilla H Sandholt
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen, Denmark
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28
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Cavalcoli F, Zilli A, Conte D, Massironi S. Micronutrient deficiencies in patients with chronic atrophic autoimmune gastritis: A review. World J Gastroenterol 2017; 23:563-572. [PMID: 28216963 PMCID: PMC5292330 DOI: 10.3748/wjg.v23.i4.563] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 10/08/2016] [Accepted: 11/13/2016] [Indexed: 02/06/2023] Open
Abstract
Chronic atrophic autoimmune gastritis (CAAG) is an organ-specific autoimmune disease characterized by an immune response, which is directed towards the parietal cells and intrinsic factor of the gastric body and fundus and leads to hypochlorhydria, hypergastrinemia and inadequate production of the intrinsic factor. As a result, the stomach’s secretion of essential substances, such as hydrochloric acid and intrinsic factor, is reduced, leading to digestive impairments. The most common is vitamin B12 deficiency, which results in a megaloblastic anemia and iron malabsorption, leading to iron deficiency anemia. However, in the last years the deficiency of several other vitamins and micronutrients, such as vitamin C, vitamin D, folic acid and calcium, has been increasingly described in patients with CAAG. In addition the occurrence of multiple vitamin deficiencies may lead to severe hematological, neurological and skeletal manifestations in CAAG patients and highlights the importance of an integrated evaluation of these patients. Nevertheless, the nutritional deficiencies in CAAG are largely understudied. We have investigated the frequency and associated features of nutritional deficiencies in CAAG in order to focus on any deficit that may be clinically significant, but relatively easy to correct. This descriptive review updates and summarizes the literature on different nutrient deficiencies in CAAG in order to optimize the treatment and the follow-up of patients affected with CAAG.
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29
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Molloy A, Pangilinan F, Mills J, Shane B, O’Neill M, McGaughey D, Velkova A, Abaan H, Ueland P, McNulty H, Ward M, Strain J, Cunningham C, Casey M, Cropp C, Kim Y, Bailey-Wilson J, Wilson A, Brody L. A Common Polymorphism in HIBCH Influences Methylmalonic Acid Concentrations in Blood Independently of Cobalamin. Am J Hum Genet 2016; 98:869-882. [PMID: 27132595 DOI: 10.1016/j.ajhg.2016.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 03/08/2016] [Indexed: 12/20/2022] Open
Abstract
Methylmalonic acid (MMA) is a by-product of propionic acid metabolism through the vitamin B12 (cobalamin)-dependent enzyme methylmalonyl CoA mutase. Elevated MMA concentrations are a hallmark of several inborn errors of metabolism and indicators of cobalamin deficiency in older persons. In a genome-wide analysis of 2,210 healthy young Irish adults (median age 22 years) we identified a strong association of plasma MMA with SNPs in 3-hydroxyisobutyryl-CoA hydrolase (HIBCH, p = 8.42 × 10(-89)) and acyl-CoA synthetase family member 3 (ACSF3, p = 3.48 × 10(-19)). These loci accounted for 12% of the variance in MMA concentration. The most strongly associated SNP (HIBCH rs291466; c:2T>C) causes a missense change of the initiator methionine codon (minor-allele frequency = 0.43) to threonine. Surprisingly, the resulting variant, p.Met1?, is associated with increased expression of HIBCH mRNA and encoded protein. These homozygotes had, on average, 46% higher MMA concentrations than methionine-encoding homozygotes in young adults with generally low MMA concentrations (0.17 [0.14-0.21] μmol/L; median [25(th)-75(th) quartile]). The association between MMA levels and HIBCH rs291466 was highly significant in a replication cohort of 1,481 older individuals (median age 79 years) with elevated plasma MMA concentrations (0.34 [0.24-0.51] μmol/L; p = 4.0 × 10(-26)). In a longitudinal study of 185 pregnant women and their newborns, the association of this SNP remained significant across the gestational trimesters and in newborns. HIBCH is unique to valine catabolism. Studies evaluating flux through the valine catabolic pathway in humans should account for these variants. Furthermore, this SNP could help resolve equivocal clinical tests where plasma MMA values have been used to diagnose cobalamin deficiency.
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30
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Zhao L, Wei Y, Song A, Li Y. Association study between genome-wide significant variants of vitamin B12 metabolism and gastric cancer in a han Chinese population. IUBMB Life 2016; 68:303-10. [PMID: 26959381 DOI: 10.1002/iub.1485] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 01/21/2016] [Accepted: 01/24/2016] [Indexed: 11/06/2022]
Abstract
Gastric cancer is one of the leading causes of cancer mortality worldwide. Accumulating evidence suggests that vitamin B12 plays an important role in the development of gastric cancer. Genome-wide association studies on metabolites in the one-carbon metabolism pathway identified several vitamin B12-related polymorphisms. Therefore, we investigated the association between variants within vitamin B12-related genes and gastric cancer in a Han Chinese population. Eight variants within the genome were significant vitamin B12-related genes, and they were selected for analysis in this case-control study. This study used a total of 492 gastric cancer patients and 550 noncancer controls. The variant rs526934 from the TCN1 gene was associated with an increased risk of developing gastric cancer. Increased risks of gastric cancer occurrence were observed in the minor G allele (OR = 1.25, 95% CI = 1.03-1.52, P = 0.031) and GG genotype (OR = 2.06, 95% CI = 1.24-3.42, P = 0.0043) compared with the wild-type A allele and AA-GA genotype, respectively. In the haplotypic analysis, we found that the CUBN haplotypes were associated with an altered gastric cancer risk. The rs1801222T/rs11254363A (OR = 1.40, 95% CI = 1.05-1.86, P = 0.021) and rs1801222C/rs11254363G (OR = 4.39, 95% CI = 2.32-8.30, P < 0.0001) haplotypes exhibited an increased gastric cancer risk, while rs1801222T/rs11254363G showed protective effects against gastric cancer (OR = 0.43, 95% CI = 0.25-0.73, P = 0.002) compared with the wild-type rs1801222C/rs11254363A haplotype. The circulating vitamin B12 concentration-related variants were associated with the occurrence of gastric cancer. This finding shed light on the unexpected role of vitamin B12 metabolism genes in gastric carcinogenesis and highlighted the interplay of diet, genetics, and human cancers.
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Affiliation(s)
- Lei Zhao
- The Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, People's Republic of China
| | - Yucai Wei
- The Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, People's Republic of China
| | - Ailing Song
- The Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, People's Republic of China
| | - Yumin Li
- The Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, People's Republic of China
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31
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Nagasaki M, Yasuda J, Katsuoka F, Nariai N, Kojima K, Kawai Y, Yamaguchi-Kabata Y, Yokozawa J, Danjoh I, Saito S, Sato Y, Mimori T, Tsuda K, Saito R, Pan X, Nishikawa S, Ito S, Kuroki Y, Tanabe O, Fuse N, Kuriyama S, Kiyomoto H, Hozawa A, Minegishi N, Douglas Engel J, Kinoshita K, Kure S, Yaegashi N, Yamamoto M. Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. Nat Commun 2015; 6:8018. [PMID: 26292667 PMCID: PMC4560751 DOI: 10.1038/ncomms9018] [Citation(s) in RCA: 297] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 07/07/2015] [Indexed: 12/19/2022] Open
Abstract
The Tohoku Medical Megabank Organization reports the whole-genome sequences of 1,070 healthy Japanese individuals and construction of a Japanese population reference panel (1KJPN). Here we identify through this high-coverage sequencing (32.4 × on average), 21.2 million, including 12 million novel, single-nucleotide variants (SNVs) at an estimated false discovery rate of <1.0%. This detailed analysis detected signatures for purifying selection on regulatory elements as well as coding regions. We also catalogue structural variants, including 3.4 million insertions and deletions, and 25,923 genic copy-number variants. The 1KJPN was effective for imputing genotypes of the Japanese population genome wide. These data demonstrate the value of high-coverage sequencing for constructing population-specific variant panels, which covers 99.0% SNVs of minor allele frequency ≥0.1%, and its value for identifying causal rare variants of complex human disease phenotypes in genetic association studies. The Tohoku Medical Megabank Organization establishes a biobank with detailed patient health care and genome information. Here the authors analyse whole-genome sequences of 1,070 Japanese individuals, allowing them to catalogue 21 million single-nucleotide variants including 12 million novel ones.
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Affiliation(s)
- Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Naoki Nariai
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Kaname Kojima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Yosuke Kawai
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Yumi Yamaguchi-Kabata
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Junji Yokozawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Sakae Saito
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Yukuto Sato
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Takahiro Mimori
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Kaoru Tsuda
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Rumiko Saito
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Xiaoqing Pan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Satoshi Nishikawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Shin Ito
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Yoko Kuroki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.,International Research Institute of Disaster Science, Tohoku University, 468-1, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Hideyasu Kiyomoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109-2200, USA
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan.,Institute of Development, Aging and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | | | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
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32
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Maroni L, van de Graaf SFJ, Hohenester SD, Oude Elferink RPJ, Beuers U. Fucosyltransferase 2: a genetic risk factor for primary sclerosing cholangitis and Crohn's disease--a comprehensive review. Clin Rev Allergy Immunol 2015; 48:182-91. [PMID: 24828903 DOI: 10.1007/s12016-014-8423-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fucosyltransferase 2 (FUT2) mediates the inclusion of fucose in sugar moieties of glycoproteins and glycolipids. ABO blood group antigens and host-microbe interactions are influenced by FUT2 activity. About 20 % of the population has a "non-secretor" status caused by inactivating variants of FUT2 on both alleles. The non-sense mutation G428A and the missense mutation A385T are responsible for the vast majority of the non-secretor status in Caucasians, Africans, and Asians, respectively. Non-secretor individuals do not secrete fucose-positive antigens and lack fucosylation in epithelia. They also appear to be protected against a number of infectious diseases, such as Norovirus and Rotavirus infections. In recent years, genome-wide association studies (GWAS) identified inactivating variants at the FUT2 locus to be associated with primary sclerosing cholangitis (PSC), Crohn's disease (CD), and biochemical markers of biliary damage. These associations are intriguing given the important roles of fucosylated glycans in host-microbe interactions and membrane stability. Non-secretors have a reduced fecal content of Bifidobacteria. The intestinal bacterial composition of CD patients resembles the one of non-secretors, with an increase in Firmicutes and decreases in Proteobacteria and Actinobacteria. Non-secretor individuals lack fucosylated glycans at the surface of biliary epithelium and display a different bacterial composition of bile compared to secretors. Notably, an intact biliary epithelial glycocalix is relevant for a stable 'biliary HCO3 (-) umbrella' to protect against toxic effects of hydrophobic bile salt monomers. Here, the biology of FUT2 will be discussed as well as hypotheses to explain the role of FUT2 in the pathophysiology of PSC and Crohn's disease.
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Affiliation(s)
- Luca Maroni
- Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1100 DD, Amsterdam, The Netherlands
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33
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Goodlin GT, Roos AK, Roos TR, Hawkins C, Beache S, Baur S, Kim SK. Applying personal genetic data to injury risk assessment in athletes. PLoS One 2015; 10:e0122676. [PMID: 25919592 PMCID: PMC4412532 DOI: 10.1371/journal.pone.0122676] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 02/24/2015] [Indexed: 01/08/2023] Open
Abstract
Recent studies have identified genetic markers associated with risk for certain sports-related injuries and performance-related conditions, with the hope that these markers could be used by individual athletes to personalize their training and diet regimens. We found that we could greatly expand the knowledge base of sports genetic information by using published data originally found in health and disease studies. For example, the results from large genome-wide association studies for low bone mineral density in elderly women can be re-purposed for low bone mineral density in young endurance athletes. In total, we found 124 single-nucleotide polymorphisms associated with: anterior cruciate ligament tear, Achilles tendon injury, low bone mineral density and stress fracture, osteoarthritis, vitamin/mineral deficiencies, and sickle cell trait. Of these single nucleotide polymorphisms, 91% have not previously been used in sports genetics. We conducted a pilot program on fourteen triathletes using this expanded knowledge base of genetic variants associated with sports injury. These athletes were genotyped and educated about how their individual genetic make-up affected their personal risk profile during an hour-long personal consultation. Overall, participants were favorable of the program, found it informative, and most acted upon their genetic results. This pilot program shows that recent genetic research provides valuable information to help reduce sports injuries and to optimize nutrition. There are many genetic studies for health and disease that can be mined to provide useful information to athletes about their individual risk for relevant injuries.
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Affiliation(s)
- Gabrielle T Goodlin
- Departments of Developmental Biology and Genetics, Stanford University Medical Center, Stanford, CA, 94305, United States of America
| | - Andrew K Roos
- Division of Epidemiology, Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, 94305, United States of America
| | - Thomas R Roos
- Division of Epidemiology, Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, 94305, United States of America
| | - Claire Hawkins
- Department of Human Biology, Stanford University, Stanford, CA, 94305, United States of America
| | - Sydney Beache
- Department of Human Biology, Stanford University, Stanford, CA, 94305, United States of America
| | - Stephen Baur
- Departments of Developmental Biology and Genetics, Stanford University Medical Center, Stanford, CA, 94305, United States of America
| | - Stuart K Kim
- Departments of Developmental Biology and Genetics, Stanford University Medical Center, Stanford, CA, 94305, United States of America
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34
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Lahner E, Gentile G, Purchiaroni F, Mora B, Simmaco M, Annibale B. Single nucleotide polymorphisms related to vitamin B12 serum levels in autoimmune gastritis patients with or without pernicious anaemia. Dig Liver Dis 2015; 47:285-90. [PMID: 25681243 DOI: 10.1016/j.dld.2015.01.147] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 01/10/2015] [Accepted: 01/15/2015] [Indexed: 02/05/2023]
Abstract
BACKGROUND Autoimmune gastritis may present as pernicious anaemia arising from vitamin B12 malabsorption, but also with iron deficiency anaemia due to iron malabsorption. These different clinical presentations might have a genetic basis. Single nucleotide polymorphisms associated with vitamin B12 levels have not been investigated in autoimmune gastritis. AIMS To determine the frequency of single nucleotide polymorphisms related to vitamin B12 levels in autoimmune gastritis patients, with or without pernicious anaemia, compared to healthy controls. METHODS 14 single nucleotide polymorphisms associated with vitamin B12 levels were selected from literature. 83 autoimmune gastritis patients (43 with and 40 without pernicious anaemia) and 173 controls were enrolled. Genomic DNA was extracted from peripheral blood leukocytes. Genotyping was performed using Sequenom MALDI-TOF mass spectrometry iPLEX platform. RESULTS TCN2 (rs9606756) GG genotype, related with lower vitamin B12 levels, was found in 3 (3.6%) autoimmune gastritis patients (2 with pernicious anaemia), but in none of controls (p = 0.02). FUT6 (rs3760776) AA genotype was present in four (4.8%) autoimmune gastritis patients (all pernicious anaemia) and three (1.7%) controls (p = 0.007). CONCLUSION A genetic variant of TCN2 (rs9606756) related to lower vitamin B12 levels was more frequent in pernicious anaemia patients compared to controls, showing the plausibility of genetic factors determining the possible clinical manifestation of autoimmune gastritis.
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Affiliation(s)
- Edith Lahner
- Digestive and Liver Disease Unit, Department of Medical and Surgery Sciences and Translational Medicine, Sant'Andrea Hospital, Sapienza University Rome, Rome, Italy
| | - Giovanna Gentile
- Advanced Molecular Diagnostics Unit, Sant'Andrea Hospital, Rome, Italy
| | - Flaminia Purchiaroni
- Digestive and Liver Disease Unit, Department of Medical and Surgery Sciences and Translational Medicine, Sant'Andrea Hospital, Sapienza University Rome, Rome, Italy
| | - Barbara Mora
- Department of Pathology, Policlinico Umberto I, Medical School, Sapienza University Rome, Rome, Italy
| | - Maurizio Simmaco
- Advanced Molecular Diagnostics Unit, Sant'Andrea Hospital, Rome, Italy; Department of Neuroscience, Mental Health and Sense Organs, Faculty of Medicine and Psychology, Sapienza University Rome, Rome, Italy
| | - Bruno Annibale
- Digestive and Liver Disease Unit, Department of Medical and Surgery Sciences and Translational Medicine, Sant'Andrea Hospital, Sapienza University Rome, Rome, Italy.
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35
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Keene KL, Chen WM, Chen F, Williams SR, Elkhatib SD, Hsu FC, Mychaleckyj JC, Doheny KF, Pugh EW, Ling H, Laurie CC, Gogarten SM, Madden EB, Worrall BB, Sale MM. Genetic Associations with Plasma B12, B6, and Folate Levels in an Ischemic Stroke Population from the Vitamin Intervention for Stroke Prevention (VISP) Trial. Front Public Health 2014; 2:112. [PMID: 25147783 PMCID: PMC4123605 DOI: 10.3389/fpubh.2014.00112] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 07/21/2014] [Indexed: 11/13/2022] Open
Abstract
Background: B vitamins play an important role in homocysteine metabolism, with vitamin deficiencies resulting in increased levels of homocysteine and increased risk for stroke. We performed a genome-wide association study (GWAS) in 2,100 stroke patients from the Vitamin Intervention for Stroke Prevention (VISP) trial, a clinical trial designed to determine whether the daily intake of high-dose folic acid, vitamins B6, and B12 reduce recurrent cerebral infarction. Methods: Extensive quality control (QC) measures resulted in a total of 737,081 SNPs for analysis. Genome-wide association analyses for baseline quantitative measures of folate, Vitamins B12, and B6 were completed using linear regression approaches, implemented in PLINK. Results: Six associations met or exceeded genome-wide significance (P ≤ 5 × 10−08). For baseline Vitamin B12, the strongest association was observed with a non-synonymous SNP (nsSNP) located in the CUBN gene (P = 1.76 × 10−13). Two additional CUBN intronic SNPs demonstrated strong associations with B12 (P = 2.92 × 10−10 and 4.11 × 10−10), while a second nsSNP, located in the TCN1 gene, also reached genome-wide significance (P = 5.14 × 10−11). For baseline measures of Vitamin B6, we identified genome-wide significant associations for SNPs at the ALPL locus (rs1697421; P = 7.06 × 10−10 and rs1780316; P = 2.25 × 10−08). In addition to the six genome-wide significant associations, nine SNPs (two for Vitamin B6, six for Vitamin B12, and one for folate measures) provided suggestive evidence for association (P ≤ 10−07). Conclusion: Our GWAS study has identified six genome-wide significant associations, nine suggestive associations, and successfully replicated 5 of 16 SNPs previously reported to be associated with measures of B vitamins. The six genome-wide significant associations are located in gene regions that have shown previous associations with measures of B vitamins; however, four of the nine suggestive associations represent novel finding and warrant further investigation in additional populations.
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Affiliation(s)
- Keith L Keene
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA ; Department of Biology, Center for Health Disparities, East Carolina University , Greenville, NC , USA
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA ; Department of Public Health Sciences, University of Virginia , Charlottesville, VA , USA
| | - Fang Chen
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA
| | - Stephen R Williams
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA
| | - Stacey D Elkhatib
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA
| | - Fang-Chi Hsu
- Department of Biostatistical Sciences, Wake Forest School of Medicine , Winston Salem, NC , USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA ; Department of Public Health Sciences, University of Virginia , Charlottesville, VA , USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine , Baltimore, MD , USA
| | - Elizabeth W Pugh
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine , Baltimore, MD , USA
| | - Hua Ling
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine , Baltimore, MD , USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington , Seattle, WA , USA
| | | | - Ebony B Madden
- National Human Genome Research Institute, National Institutes of Health , Bethesda, MD , USA
| | - Bradford B Worrall
- Department of Public Health Sciences, University of Virginia , Charlottesville, VA , USA ; Department of Neurology, University of Virginia , Charlottesville, VA , USA
| | - Michele M Sale
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA ; Department of Public Health Sciences, University of Virginia , Charlottesville, VA , USA ; Department of Biochemistry & Molecular Genetics, University of Virginia , Charlottesville, VA , USA
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36
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Lim ET, Würtz P, Havulinna AS, Palta P, Tukiainen T, Rehnström K, Esko T, Mägi R, Inouye M, Lappalainen T, Chan Y, Salem RM, Lek M, Flannick J, Sim X, Manning A, Ladenvall C, Bumpstead S, Hämäläinen E, Aalto K, Maksimow M, Salmi M, Blankenberg S, Ardissino D, Shah S, Horne B, McPherson R, Hovingh GK, Reilly MP, Watkins H, Goel A, Farrall M, Girelli D, Reiner AP, Stitziel NO, Kathiresan S, Gabriel S, Barrett JC, Lehtimäki T, Laakso M, Groop L, Kaprio J, Perola M, McCarthy MI, Boehnke M, Altshuler DM, Lindgren CM, Hirschhorn JN, Metspalu A, Freimer NB, Zeller T, Jalkanen S, Koskinen S, Raitakari O, Durbin R, MacArthur DG, Salomaa V, Ripatti S, Daly MJ, Palotie A. Distribution and medical impact of loss-of-function variants in the Finnish founder population. PLoS Genet 2014; 10:e1004494. [PMID: 25078778 PMCID: PMC4117444 DOI: 10.1371/journal.pgen.1004494] [Citation(s) in RCA: 277] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/14/2014] [Indexed: 01/19/2023] Open
Abstract
Exome sequencing studies in complex diseases are challenged by the allelic heterogeneity, large number and modest effect sizes of associated variants on disease risk and the presence of large numbers of neutral variants, even in phenotypically relevant genes. Isolated populations with recent bottlenecks offer advantages for studying rare variants in complex diseases as they have deleterious variants that are present at higher frequencies as well as a substantial reduction in rare neutral variation. To explore the potential of the Finnish founder population for studying low-frequency (0.5-5%) variants in complex diseases, we compared exome sequence data on 3,000 Finns to the same number of non-Finnish Europeans and discovered that, despite having fewer variable sites overall, the average Finn has more low-frequency loss-of-function variants and complete gene knockouts. We then used several well-characterized Finnish population cohorts to study the phenotypic effects of 83 enriched loss-of-function variants across 60 phenotypes in 36,262 Finns. Using a deep set of quantitative traits collected on these cohorts, we show 5 associations (p<5×10⁻⁸) including splice variants in LPA that lowered plasma lipoprotein(a) levels (P = 1.5×10⁻¹¹⁷). Through accessing the national medical records of these participants, we evaluate the LPA finding via Mendelian randomization and confirm that these splice variants confer protection from cardiovascular disease (OR = 0.84, P = 3×10⁻⁴), demonstrating for the first time the correlation between very low levels of LPA in humans with potential therapeutic implications for cardiovascular diseases. More generally, this study articulates substantial advantages for studying the role of rare variation in complex phenotypes in founder populations like the Finns and by combining a unique population genetic history with data from large population cohorts and centralized research access to National Health Registers.
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Affiliation(s)
- Elaine T. Lim
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter Würtz
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Computational Medicine, Institute of Health Sciences, University of Oulu, Oulu, Finland
| | - Aki S. Havulinna
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Priit Palta
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Taru Tukiainen
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Karola Rehnström
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Tõnu Esko
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Michael Inouye
- Medical Systems Biology, Department of Pathology and Department of Microbiology & Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Tuuli Lappalainen
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Stanford Center for Computational, Evolutionary and Human Genomics, Stanford, California, United States of America
| | - Yingleong Chan
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | - Rany M. Salem
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jason Flannick
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xueling Sim
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alisa Manning
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Claes Ladenvall
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Lund University Diabetes Center, Department of Clinical Sciences, Diabetes & Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | | | - Eija Hämäläinen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | | | - Marko Salmi
- Department of Medical Microbiology and Immunology, University of Turku and National Institute for Health and Welfare, Turku, Finland
| | - Stefan Blankenberg
- University Heart Centre Hamburg, Clinic for General and Interventional Cardiology, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Diego Ardissino
- Division of Cardiology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Svati Shah
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Benjamin Horne
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, Utah, United States of America
| | - Ruth McPherson
- Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Gerald K. Hovingh
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Muredach P. Reilly
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Anuj Goel
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Martin Farrall
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Domenico Girelli
- University of Verona School of Medicine, Department of Medicine, Verona, Italy
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Nathan O. Stitziel
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sekar Kathiresan
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Stacey Gabriel
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere School of Medicine, Tampere, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Leif Groop
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Lund University Diabetes Center, Department of Clinical Sciences, Diabetes & Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- University of Helsinki, Hjelt Institute, Dept of Public Health, Helsinki, Finland
- National Institute for Health and Welfare, Dept of Mental Health and Substance Abuse Services, Helsinki, Finland
| | - Markus Perola
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Mark I. McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Headington, Oxford, United Kingdom
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David M. Altshuler
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Cecilia M. Lindgren
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Joel N. Hirschhorn
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | | | - Nelson B. Freimer
- University of California Los Angeles Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tanja Zeller
- University Heart Centre Hamburg, Clinic for General and Interventional Cardiology, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Sirpa Jalkanen
- Department of Medical Microbiology and Immunology, University of Turku and National Institute for Health and Welfare, Turku, Finland
| | - Seppo Koskinen
- Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, Helsinki, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Daniel G. MacArthur
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Veikko Salomaa
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- University of Helsinki, Hjelt Institute, Dept of Public Health, Helsinki, Finland
- Department of Biometry, Hjelt Institute, University of Helsinki, Helsinki, Finland
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (MJD); (AP)
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail: (MJD); (AP)
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Liang Y, Tang W, Huang T, Gao Y, Tan A, Yang X, Zhang H, Hu Y, Qin X, Li S, Zhang S, Mo L, Liang Z, Shi D, Huang Z, Guan Y, Zhou J, Winkler C, O'Brien SJ, Xu J, Mo Z, Peng T. Genetic variations affecting serum carcinoembryonic antigen levels and status of regional lymph nodes in patients with sporadic colorectal cancer from Southern China. PLoS One 2014; 9:e97923. [PMID: 24941225 PMCID: PMC4062418 DOI: 10.1371/journal.pone.0097923] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 04/27/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Serum carcinoembryonic antigen (sCEA) level might be an indicator of disease. Indeed, an elevated sCEA level is a prognostic factor in colorectal cancer (CRC) patients. However, the genetic determinants of sCEA level in healthy and CRC population remains unclear. Thus we investigated the genetic markers associated with elevated serum sCEA level in these two populations and its clinical implications. METHODS AND FINDINGS Genome-wide association study (GWAS) was conducted in a cohort study with 4,346 healthy male adults using the Illumina Omni 1 M chip. Candidate SNPs associated with elevated sCEA levels were validated in 194 CRC patients on ABI Taqman platform. Eight candidate SNPs were validated in CRC patients. The rs1047781 (chr19- FUT2) (A/T) was associated with elevated sCEA levels, and rs8176746 (chr9- ABO) was associated with the regional lymph metastasis in the CRC patients. The preoperative sCEA level was a risk factor for tumor recurrence in 5 years after operation (OR = 1.427, 95% CI: 1.005∼1.843, P = 0.006). It was also one of the risk factors for regional lymph node metastasis (OR = 2.266, 95% CI: 1.196∼4.293, P = 0.012). The sCEA level in rs1047781-T carriers was higher than that in the A carriers in CRC patients without lymph node metastasis (P = 0.006). The regional lymph node metastasis in patients with homozygote AA of rs8176746 was more common than that in the heterozygote AG carriers (P = 0.022). In addition, rs1047781-AT and TT CRC patients exhibited a worse disease-free survival than AA genotype carriers (P = 0.023). CONCLUSIONS We found candidate SNPs associated with elevated sCEA levels in both healthy males and CRC population. Rs1047781 (chr19- FUT2) may be the susceptible locus for recurrence of CRC in a population from Southern China.
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Affiliation(s)
- Yu Liang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Weizhong Tang
- Department of Anal and colorectal Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Tiqiang Huang
- Department of Anal and colorectal Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Yong Gao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Aihua Tan
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Xiaobo Yang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Haiying Zhang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Yanling Hu
- Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Xue Qin
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Shan Li
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Shijun Zhang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Linjian Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
- Institute of Urology and Nephrology, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Zhenjia Liang
- Medical Examination Center, Fangchenggang First People's Hospital, Fangchenggang, Guangxi, People's Republic of China
| | - Deyi Shi
- Medical Examination Center, Fangchenggang First People's Hospital, Fangchenggang, Guangxi, People's Republic of China
| | - Zhang Huang
- Medical Examination Center, Guigang First People's Hospital, Guigang, Guangxi, People's Republic of China
| | - Yingyong Guan
- Medical Examination Center, Yulin First People's Hospital, Yulin, Guangxi, People's Republic of China
| | - Jicheng Zhou
- Department of Hematology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Cheryl Winkler
- Molecular Genetics Epidemiology Sec., Frederick Nat. Lab for Cancer Research, National Cancer Institute, NIH, Frederick, Maryland, United States of America
| | - Stephen J. O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, NIH, Frederick, Maryland, United States of America
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
- Oceanographic Center, Nova Southeastern University, Ft. Lauderdale, Florida, United States of America
| | - Jianfeng Xu
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
- Institute of Urology and Nephrology, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
- * E-mail: (TP); (ZM)
| | - Tao Peng
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
- Laboratory of Genomic Diversity, National Cancer Institute, NIH, Frederick, Maryland, United States of America
- * E-mail: (TP); (ZM)
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Irizar H, Muñoz-Culla M, Sepúlveda L, Sáenz-Cuesta M, Prada Á, Castillo-Triviño T, Zamora-López G, de Munain AL, Olascoaga J, Otaegui D. Transcriptomic profile reveals gender-specific molecular mechanisms driving multiple sclerosis progression. PLoS One 2014; 9:e90482. [PMID: 24587374 PMCID: PMC3938749 DOI: 10.1371/journal.pone.0090482] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 01/31/2014] [Indexed: 12/21/2022] Open
Abstract
Background Although the most common clinical presentation of multiple sclerosis (MS) is the so called Relapsing-Remitting MS (RRMS), the molecular mechanisms responsible for its progression are currently unknown. To tackle this problem, a whole-genome gene expression analysis has been performed on RRMS patients. Results The comparative analysis of the Affymetrix Human Gene 1.0 ST microarray data from peripheral blood leucocytes obtained from 25 patients in remission and relapse and 25 healthy subjects has revealed 174 genes altered in both remission and relapse, a high proportion of them showing what we have called “mirror pattern”: they are upregulated in remission and downregulated in relapse or vice versa. The coexpression analysis of these genes has shown that they are organized in three female-specific and one male-specific modules. Conclusions The interpretation of the modules of the coexpression network suggests that Epstein-Barr virus (EBV) reactivation of B cells happens in MS relapses; however, qPCR expression data of the viral genes supports that hypothesis only in female patients, reinforcing the notion that different molecular processes drive disease progression in females and males. Besides, we propose that the “primed” state showed by neutrophils in women is an endogenous control mechanism triggered to keep EBV reactivation under control through vitamin B12 physiology. Finally, our results also point towards an important sex-specific role of non-coding RNA in MS.
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Affiliation(s)
- Haritz Irizar
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
| | - Maider Muñoz-Culla
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
| | - Lucia Sepúlveda
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
| | - Matías Sáenz-Cuesta
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
| | - Álvaro Prada
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
- Hospital Universitario Donostia, Immunology Department, Donostia-San Sebastian, Spain
| | - Tamara Castillo-Triviño
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
| | - Gorka Zamora-López
- Bernstein Center for Computational Neuroscience, Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Brain and Cognition, Universistat Pompeu Fabra, Barcelona, Spain
| | - Adolfo López de Munain
- Hospital Universitario Donostia, Neurology Department, Donostia-San Sebastian, Spain
- Centro de Investigaciones Biomédicas en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, Ministerio de Ciencia e Innovación, Madrid, Spain
| | - Javier Olascoaga
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
- Hospital Universitario Donostia, Neurology Department, Donostia-San Sebastian, Spain
| | - David Otaegui
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
- * E-mail:
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Opportunism: a panacea for implementation of whole-genome sequencing studies in nutrigenomics research? GENES AND NUTRITION 2014; 9:387. [PMID: 24535715 DOI: 10.1007/s12263-014-0387-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 02/03/2014] [Indexed: 10/25/2022]
Abstract
Observational studies have consistently shown associations between mild deficiencies in folate and vitamin B12 with increased risk of a myriad of common diseases. These findings have invariably translated into null outcomes in intervention trials due in part to our ignorance of the specific genomic and environmental factors that underpin population variability in requirements to these B-vitamins. Although genome-wide association studies have shed initial light on the genetic architecture of variability in status of these vitamins, particularly vitamin B12, the causal mechanisms remain uncharacterised. A recent study by Grarup et al. (PLoS Genet 9(6):e1003530, 2013) used next-generation whole-genome sequencing to gain further insight into the genetic architecture of vitamin B12 and folate status in the general population. Their study represents the analysis of approximately ten times greater number of genetic variants and nearly four times the number of individuals compared to the largest previous GWAS study of these B-vitamins. In light of this, we purport that although the study may be viewed as the state of the art in the roadmap to personalised or precision nutrition, the lack of insight provided by the study serves as a cautionary reminder of the importance of study design, particularly when leveraging large-scale data, such as those from whole-genome sequences. We believe that the precedent set by such large-scale "proof of principle" type projects will wrongly enforce a negative outlook for nutrigenomics research and present alternative study designs, which although less opportunistic are far more likely to be informative and yield novel results.
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Bossini-Castillo L, de Kovel C, Kallberg H, van ‘t Slot R, Italiaander A, Coenen M, Tak PP, Posthumus MD, Wijmenga C, Huizinga T, van der Helm-van Mil AHM, Stoeken-Rijsbergen G, Rodriguez-Rodriguez L, Balsa A, González-Álvaro I, González-Gay MÁ, Gómez-Vaquero C, Franke B, Vermeulen S, van der Horst-Bruinsma IE, Dijkmans BAC, Wolbink GJ, Ophoff RA, Maehlen MT, van Riel P, Merriman M, Klareskog L, Lie BA, Merriman T, Crusius JBA, Brouwer E, Martin J, de Vries N, Toes R, Padyukov L, Koeleman BPC. A genome-wide association study of rheumatoid arthritis without antibodies against citrullinated peptides. Ann Rheum Dis 2014; 74:e15. [DOI: 10.1136/annrheumdis-2013-204591] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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41
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Wang J, Zhao JY, Wang F, Peng QQ, Hou J, Sun SN, Gui YH, Duan WY, Qiao B, Wang HY. A genetic variant in vitamin B12 metabolic genes that reduces the risk of congenital heart disease in Han Chinese populations. PLoS One 2014; 9:e88332. [PMID: 24533076 PMCID: PMC3922769 DOI: 10.1371/journal.pone.0088332] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/06/2014] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Genome-wide association studies on components of the one-carbon metabolic pathway revealed that human vitamin B12 levels could be significantly influenced by variations in the fucosyltransferase 2 (FUT2), cubilin (CUBN), and transcobalamin-I (TCN1) genes. An altered vitamin B12 level is an important factor that disturbs the homeostasis of the folate metabolism pathway, which in turn can potentially lead to the development of congenital heart disease (CHD). Therefore, we investigated the association between the variants of vitamin B12-related genes and CHD in Han Chinese populations. METHODS AND RESULTS Six variants of the vitamin B12-related genes were selected for analysis in two independent case-control studies, with a total of 868 CHD patients and 931 controls. The variant rs11254363 of the CUBN gene was associated with a decreased risk of developing CHD in both the separate and combined case-control studies. Combined samples from the two cohorts had a significant decrease in CHD risk for the G allele (OR = 0.48, P = 1.7×10⁻⁵) and AG+GG genotypes (OR = 0.49, P = 4×10⁻⁵), compared with the wild-type A allele and AA genotype, respectively. CONCLUSIONS Considering the G allele of variant rs11254363 of the CUBN gene was associated with an increased level of circulating vitamin B12. This result suggested that the carriers of the G allele would benefit from the protection offered by the high vitamin B12 concentration during critical heart development stages. This finding shed light on the unexpected role of CUBN in CHD development and highlighted the interplay of diet, genetics, and human birth defects.
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Affiliation(s)
- Jue Wang
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jian-Yuan Zhao
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Feng Wang
- Children’s Hospital Shanghai, Fudan University, Shanghai, China
| | - Qian-Qian Peng
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jia Hou
- Children’s Hospital Shanghai, Fudan University, Shanghai, China
| | - Shu-Na Sun
- Children’s Hospital Shanghai, Fudan University, Shanghai, China
| | - Yong-Hao Gui
- Children’s Hospital Shanghai, Fudan University, Shanghai, China
| | - Wen-Yuan Duan
- Institute of Cardiovascular Disease General Hospital of Jinan Military Region, Jinan, China
| | - Bin Qiao
- Institute of Cardiovascular Disease General Hospital of Jinan Military Region, Jinan, China
| | - Hong-Yan Wang
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- Children’s Hospital Shanghai, Fudan University, Shanghai, China
- The Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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Strittmatter L, Li Y, Nakatsuka NJ, Calvo SE, Grabarek Z, Mootha VK. CLYBL is a polymorphic human enzyme with malate synthase and β-methylmalate synthase activity. Hum Mol Genet 2013; 23:2313-23. [PMID: 24334609 DOI: 10.1093/hmg/ddt624] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CLYBL is a human mitochondrial enzyme of unknown function that is found in multiple eukaryotic taxa and conserved to bacteria. The protein is expressed in the mitochondria of all mammalian organs, with highest expression in brown fat and kidney. Approximately 5% of all humans harbor a premature stop polymorphism in CLYBL that has been associated with reduced levels of circulating vitamin B12. Using comparative genomics, we now show that CLYBL is strongly co-expressed with and co-evolved specifically with other components of the mitochondrial B12 pathway. We confirm that the premature stop polymorphism in CLYBL leads to a loss of protein expression. To elucidate the molecular function of CLYBL, we used comparative operon analysis, structural modeling and enzyme kinetics. We report that CLYBL encodes a malate/β-methylmalate synthase, converting glyoxylate and acetyl-CoA to malate, or glyoxylate and propionyl-CoA to β-methylmalate. Malate synthases are best known for their established role in the glyoxylate shunt of plants and lower organisms and are traditionally described as not occurring in humans. The broader role of a malate/β-methylmalate synthase in human physiology and its mechanistic link to vitamin B12 metabolism remain unknown.
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Affiliation(s)
- Laura Strittmatter
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
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Cornelis MC, Hu FB. Systems Epidemiology: A New Direction in Nutrition and Metabolic Disease Research. Curr Nutr Rep 2013; 2. [PMID: 24278790 DOI: 10.1007/s13668-013-0052-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Systems epidemiology applied to the field of nutrition has potential to provide new insight into underlying mechanisms and ways to study the health effects of specific foods more comprehensively. Human intervention and population-based studies have identified i) common genetic factors associated with several nutrition-related traits and ii) dietary factors altering the expression of genes and levels of proteins and metabolites related to inflammation, lipid metabolism and/or gut microbial metabolism, results of high relevance to metabolic disease. System-level tools applied type 2 diabetes and related conditions have revealed new pathways that are potentially modified by diet and thus offer additional opportunities for nutritional investigations. Moving forward, harnessing the resources of existing large prospective studies within which biological samples have been archived and diet and lifestyle have been measured repeatedly within individual will enable systems-level data to be integrated, the outcome of which will be improved personalized optimal nutrition for prevention and treatment of disease.
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Affiliation(s)
- Marilyn C Cornelis
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
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Grarup N, Sulem P, Sandholt CH, Thorleifsson G, Ahluwalia TS, Steinthorsdottir V, Bjarnason H, Gudbjartsson DF, Magnusson OT, Sparsø T, Albrechtsen A, Kong A, Masson G, Tian G, Cao H, Nie C, Kristiansen K, Husemoen LL, Thuesen B, Li Y, Nielsen R, Linneberg A, Olafsson I, Eyjolfsson GI, Jørgensen T, Wang J, Hansen T, Thorsteinsdottir U, Stefánsson K, Pedersen O. Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets. PLoS Genet 2013; 9:e1003530. [PMID: 23754956 PMCID: PMC3674994 DOI: 10.1371/journal.pgen.1003530] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 04/11/2013] [Indexed: 11/26/2022] Open
Abstract
Genome-wide association studies have mainly relied on common HapMap sequence variations. Recently, sequencing approaches have allowed analysis of low frequency and rare variants in conjunction with common variants, thereby improving the search for functional variants and thus the understanding of the underlying biology of human traits and diseases. Here, we used a large Icelandic whole genome sequence dataset combined with Danish exome sequence data to gain insight into the genetic architecture of serum levels of vitamin B12 (B12) and folate. Up to 22.9 million sequence variants were analyzed in combined samples of 45,576 and 37,341 individuals with serum B12 and folate measurements, respectively. We found six novel loci associating with serum B12 (CD320, TCN2, ABCD4, MMAA, MMACHC) or folate levels (FOLR3) and confirmed seven loci for these traits (TCN1, FUT6, FUT2, CUBN, CLYBL, MUT, MTHFR). Conditional analyses established that four loci contain additional independent signals. Interestingly, 13 of the 18 identified variants were coding and 11 of the 13 target genes have known functions related to B12 and folate pathways. Contrary to epidemiological studies we did not find consistent association of the variants with cardiovascular diseases, cancers or Alzheimer's disease although some variants demonstrated pleiotropic effects. Although to some degree impeded by low statistical power for some of these conditions, these data suggest that sequence variants that contribute to the population diversity in serum B12 or folate levels do not modify the risk of developing these conditions. Yet, the study demonstrates the value of combining whole genome and exome sequencing approaches to ascertain the genetic and molecular architectures underlying quantitative trait associations. Genome-wide association studies have in recent years revealed a wealth of common variants associated with common diseases and phenotypes. We took advantage of the advances in sequencing technologies to study the association of low frequency and rare variants in conjunction with common variants with serum levels of vitamin B12 (B12) and folate in Icelanders and Danes. We found 18 independent signals in 13 loci associated with serum B12 or folate levels. Interestingly, 13 of the 18 identified variants are coding and 11 of the 13 target genes have known functions related to B12 and folate pathways. These data indicate that the target genes at all of the loci have been identified. Epidemiological studies have shown a relationship between serum B12 and folate levels and the risk of cardiovascular diseases, cancers, and Alzheimer's disease. We investigated association between the identified variants and these diseases but did not find consistent association.
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Affiliation(s)
- Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Camilla H. Sandholt
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Tarunveer S. Ahluwalia
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Thomas Sparsø
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Albrechtsen
- Centre of Bioinformatics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | - Karsten Kristiansen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Lise Lotte Husemoen
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark
| | - Betina Thuesen
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark
| | | | - Rasmus Nielsen
- Centre of Bioinformatics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
- Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Allan Linneberg
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark
| | - Isleifur Olafsson
- Landspitali, The National University Hospital of Iceland, Department of Clinical Biochemistry, Reykjavik, Iceland
| | | | - Torben Jørgensen
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Medicine, University of Aalborg, Aalborg, Denmark
| | - Jun Wang
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen, China
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Reykjavik, Iceland
- University of Iceland Faculty of Medicine, Reykjavik, Iceland
| | - Kari Stefánsson
- deCODE Genetics, Reykjavik, Iceland
- University of Iceland Faculty of Medicine, Reykjavik, Iceland
- * E-mail: (K. Stefánsson); (O. Pedersen)
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
- Hagedorn Research Institute, Gentofte, Denmark
- Institute of Biomedical Science, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (K. Stefánsson); (O. Pedersen)
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Chery C, Hehn A, Mrabet N, Oussalah A, Jeannesson E, Besseau C, Alberto JM, Gross I, Josse T, Gérard P, Guéant-Rodriguez RM, Freund JN, Devignes J, Bourgaud F, Peyrin-Biroulet L, Feillet F, Guéant JL. Gastric intrinsic factor deficiency with combined GIF heterozygous mutations and FUT2 secretor variant. Biochimie 2013; 95:995-1001. [PMID: 23402911 DOI: 10.1016/j.biochi.2013.01.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 01/30/2013] [Indexed: 11/27/2022]
Abstract
Several genome-wide association studies (GWAS) have identified a strong association between serum vitamin B12 and fucosyltransferase 2 (FUT2), a gene associated with susceptibility to Helicobacter pylori infection. Hazra et al. conducted a meta-analysis of three GWAS and found three additional loci in MUT, CUBN and TCN1. Other GWAS conducted in Italy and China confirmed the association for FUT2 gene. Alpha-2-fucosyltransferase (FUT2) catalyzes fucose addition to form H-type antigens in exocrine secretions. FUT2 non-secretor variant produces no secretion of H-type antigens and is associated with high-plasma vitamin B12 levels. This association was explained by the influence of FUT2 on H. pylori, which is a risk factor of gastritis, a main cause of vitamin B12 impaired absorption. However, we recently showed that H. pylori serology had no influence on FUT2 association with vitamin B12, in a large sample population, suggesting the involvement of an alternative mechanism. GIF is another gene associated with plasma levels of vitamin B12 and gastric intrinsic factor (GIF) is a fucosylated protein needed for B12 absorption. Inherited GIF deficiency produces B12 deficiency unrelated with gastritis. We report 2 families with heterozygous GIF mutation, 290T>C, M97T, with decreased binding affinity of GIF for vitamin B12 and one family with heterozygous GIF mutation 435_437delGAA, K145_N146delinsN and no B12 binding activity of mutated GIF. All cases with vitamin B12 deficit carried the FUT2 rs601338 secretor variant. Ulex europeus binding to GIF was influenced by FUT2 genotypes and GIF concentration was lower, in gastric juice from control subjects with the secretor genotype. GIF290C allele was reported in 5 European cases and no Africans among 1282 ambulatory subjects and was associated with low plasma vitamin B12 and anaemia in the single case bearing the FUT2 secretor variant. We concluded that FUT2 secretor variant worsens B12 status in cases with heterozygous GIF mutations by impairing GIF secretion, independently from H. pylori-related gastritis.
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Affiliation(s)
- Celine Chery
- Inserm-U954, National reference centre for inherited metabolic diseases, University Hospital Center, Nancy-Université, 54500 Vandoeuvre lès Nancy, France
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