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Huang M, Lyu C, Liu N, Nembhard WN, Witte JS, Hobbs CA, Li M. A gene-based association test of interactions for maternal-fetal genotypes identifies genes associated with nonsyndromic congenital heart defects. Genet Epidemiol 2023; 47:475-495. [PMID: 37341229 DOI: 10.1002/gepi.22533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/13/2023] [Accepted: 06/02/2023] [Indexed: 06/22/2023]
Abstract
The risk of congenital heart defects (CHDs) may be influenced by maternal genes, fetal genes, and their interactions. Existing methods commonly test the effects of maternal and fetal variants one-at-a-time and may have reduced statistical power to detect genetic variants with low minor allele frequencies. In this article, we propose a gene-based association test of interactions for maternal-fetal genotypes (GATI-MFG) using a case-mother and control-mother design. GATI-MFG can integrate the effects of multiple variants within a gene or genomic region and evaluate the joint effect of maternal and fetal genotypes while allowing for their interactions. In simulation studies, GATI-MFG had improved statistical power over alternative methods, such as the single-variant test and functional data analysis (FDA) under various disease scenarios. We further applied GATI-MFG to a two-phase genome-wide association study of CHDs for the testing of both common variants and rare variants using 947 CHD case mother-infant pairs and 1306 control mother-infant pairs from the National Birth Defects Prevention Study (NBDPS). After Bonferroni adjustment for 23,035 genes, two genes on chromosome 17, TMEM107 (p = 1.64e-06) and CTC1 (p = 2.0e-06), were identified for significant association with CHD in common variants analysis. Gene TMEM107 regulates ciliogenesis and ciliary protein composition and was found to be associated with heterotaxy. Gene CTC1 plays an essential role in protecting telomeres from degradation, which was suggested to be associated with cardiogenesis. Overall, GATI-MFG outperformed the single-variant test and FDA in the simulations, and the results of application to NBDPS samples are consistent with existing literature supporting the association of TMEM107 and CTC1 with CHDs.
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Affiliation(s)
- Manyan Huang
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Chen Lyu
- Department of Population Health, New York University Grossman School of Medicine, New York City, New York, USA
| | - Nianjun Liu
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Wendy N Nembhard
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, California, USA
- Department of Biomedical Data Sciences, Stanford University, Stanford, California, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Ming Li
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, Bloomington, Indiana, USA
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Dewelle WK, Melka DS, Aklilu AT, Gebremariam MY, Alemayehu MA, Alemayehu DH, Woldemichael TS, Gebre SG. Polymorphisms in Maternal Selected Folate Metabolism-Related Genes in Neural Tube Defect-Affected Pregnancy. Adv Biomed Res 2023; 12:160. [PMID: 37564453 PMCID: PMC10410419 DOI: 10.4103/abr.abr_103_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 10/26/2022] [Accepted: 03/03/2023] [Indexed: 08/12/2023] Open
Abstract
Background Neural tube defects (NTDs) are abnormalities of the brain and spinal cord, which occur as a result of failure in neural tube closure during embryogenesis. Causes of NTDs are complex and multiple, with hereditary, lifestyle, and environmental factors appearing to play a role. In spite of their impact on public health, the role genetics play on NTDs in Ethiopia is lacking. In this study, the role of polymorphisms in MTHFR 677C > T (rs1801133), MTHFR 1298A > C (rs1801131), MTRR 66A > G (rs1801394), RFC1 80A > G (rs1051266), and TCN2 776C > G (rs1801198) on the risk of having NTD-affected pregnancy was investigated. Materials and Methods One hundred women with NTD-affected pregnancy and 100 women with normal pregnancy were included in the study. DNA was extracted from saliva and genotyping for five polymorphisms in four genes was analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The departure of the genotype's distribution from Hardy-Weinberg equilibrium (HWE) was evaluated using the x2 goodness-of-fit test. Frequencies of genotypes and alleles in case and control mothers were determined and differences between relative frequencies were evaluated by the x2 or the Fisher's exact test. Results The statistically significant difference was absent in the genotype and allele frequencies for all the analyzed polymorphisms between cases and controls (P > 0.05). Conclusion MTHFR 677C > T, MTHFR 1298A > C, MTRR 66A > G, RFC1 80A > G, and TCN2 776C > G polymorphisms lack association with the risk of having a pregnancy affected by NTD. The role of other genes or environmental factors in NTD etiology needs to be investigated.
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Affiliation(s)
- Winner K. Dewelle
- Department of Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, Ethiopia, East Africa
| | - Daniel S. Melka
- Biochemistry Division of Basic Sciences, University of Global Health Equity, Kigali, Rwanda, East Africa
| | - Abenezer T. Aklilu
- Department of Neurosurgery, School of Medicine, College of Health Sciences, Addis Ababa University, Ethiopia, East Africa
| | - Mahlet Y. Gebremariam
- Department of Obstetrics and Gynecology, School of Medicine, College of Health Sciences, Addis Ababa University, Ethiopia, East Africa
| | - Markos A. Alemayehu
- Department of Biotechnology and Bioinformatics, Armauer Hansen Research Institute, Addis Ababa, Ethiopia, East Africa
| | - Dawit H. Alemayehu
- Department of Biotechnology and Bioinformatics, Armauer Hansen Research Institute, Addis Ababa, Ethiopia, East Africa
| | - Tamrayehu S. Woldemichael
- Department of Biotechnology and Bioinformatics, Armauer Hansen Research Institute, Addis Ababa, Ethiopia, East Africa
| | - Solomon G. Gebre
- Department of Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, Ethiopia, East Africa
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Eph and Ephrin Variants in Malaysian Neural Tube Defect Families. Genes (Basel) 2022; 13:genes13060952. [PMID: 35741713 PMCID: PMC9222557 DOI: 10.3390/genes13060952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
Neural tube defects (NTDs) are common birth defects with a complex genetic etiology. Mouse genetic models have indicated a number of candidate genes, of which functional mutations in some have been found in human NTDs, usually in a heterozygous state. This study focuses on Ephs-ephrins as candidate genes of interest owing to growing evidence of the role of this gene family during neural tube closure in mouse models. Eph-ephrin genes were analyzed in 31 Malaysian individuals comprising seven individuals with sporadic spina bifida, 13 parents, one twin-sibling and 10 unrelated controls. Whole exome sequencing analysis and bioinformatic analysis were performed to identify variants in 22 known Eph-ephrin genes. We reported that three out of seven spina bifida probands and three out of thirteen family members carried a variant in either EPHA2 (rs147977279), EPHB6 (rs780569137) or EFNB1 (rs772228172). Analysis of public databases shows that these variants are rare. In exome datasets of the probands and parents of the probands with Eph-ephrin variants, the genotypes of spina bifida-related genes were compared to investigate the probability of the gene–gene interaction in relation to environmental risk factors. We report the presence of Eph-ephrin gene variants that are prevalent in a small cohort of spina bifida patients in Malaysian families.
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Goyal A, Kumawat M, Vashisth M, Gill PS, Sing I, Dhaulakhandi DB. Study of C677T Methylene Tetrahydrofolate Reductase Gene Polymorphism as a Risk Factor for Neural Tube Defects. Asian J Neurosurg 2021; 16:554-561. [PMID: 34660368 PMCID: PMC8477844 DOI: 10.4103/ajns.ajns_372_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/08/2020] [Accepted: 03/26/2021] [Indexed: 11/04/2022] Open
Abstract
Introduction Various genetic and environmental factors contribute to the development of neural tube defects (NTDs) which are a group of neurulation defects resulting from failure of closure of embryonic neural tube. Among genetic factors is polymorphism in methylene tetrahydrofolate reductase (MTHFR) gene, giving rise to a gene variant or mutant. However, in most studies directed at finding an association between MTHFR variants and NTD, there is no clear evidence of a cause-and-effect relationship. Materials and Methods Forty diagnosed cases of NTDs and forty healthy individuals were investigated in a case-control study for presence of C677T MTHFR gene polymorphism. Serum folate and Vitamin B12 levels were estimated and MTHFR gene polymorphism was detected by polymerase chain reaction-restriction fragment length polymorphism. Results It was found that 32 cases were homozygous with CC genotype and eight were heterozygous with CT genotype, whereas 35 controls had CC genotype and five had CT genotype. TT genotype was absent in both the groups. There was no statistically significant difference between both the groups. No evidence of association between MTHFR C677T polymorphism and NTDs was found. Conclusion Although there was no evidence of association between MTHFR C677T polymorphism and NTDs, our study does not rule out the impact of MTHFR gene mutation on folate metabolism. The reason for absence of TT genotype and no association could be a small sample size. Larger, comprehensive, and well-designed multicentric but feasible studies involving proper subjects and appropriate and adequate controls from several hospitals may provide more meaningful data.
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Affiliation(s)
- Anjalika Goyal
- Department of Biochemistry, PGIMS, Pandit Bhagwat Dayal Sharma University of Health Sciences, Rohtak, Haryana, India
| | - Manjulata Kumawat
- Department of Biochemistry, PGIMS, Pandit Bhagwat Dayal Sharma University of Health Sciences, Rohtak, Haryana, India
| | - Minakshi Vashisth
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Paramjit Singh Gill
- Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Ishwar Sing
- Department of Neurosurgery, PGIMS, Pandit Bhagwat Dayal Sharma University of Health Sciences, Rohtak, Haryana, India
| | - Dhara B Dhaulakhandi
- Department of Biotechnology and Molecular Medicine, PGIMS, Pandit Bhagwat Dayal Sharma University of Health Sciences, Rohtak, Haryana, India
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Singh BK, Maria A, Bandyopadhyay T, Choudhary SK. Clinico-epidemiological profile and outcomes of babies with neural tube defects in a tertiary care center in Northern India. J Matern Fetal Neonatal Med 2021; 35:7052-7057. [PMID: 34121591 DOI: 10.1080/14767058.2021.1937102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Neural tube defects constitute a major source of disability among children. Proper management requires accurate diagnosis, an assessment of the severity of the lesion, a decision whether intervention is warranted, the nature of the intervention, and educating the family of the need for lifelong medical care. But to do so, reliable data regarding presentation and outcome is very crucial. AIM OF THE STUDY To discuss the clinical epidemiological profile and outcome of babies admitted with neural tube defects (NTDs). MATERIAL AND METHODS Retrospective observational study was done by extracting data from case notes and follow-up files in Department of Neonatology, PGIMER and Dr. RML Hospital, New Delhi over a period from March 2015 to July 2020. RESULTS A total of 25 babies were included in the study. Majority of babies were born to mother at a median age group of 24 (19-36) yrs and nearly one-third of them were illiterate. The history of maternal periconceptional folic acid intake was seen in only five babies (21%). Two third of babies were male (64%) and the median age at admission was at 9 (1-27) days of life. Majority of the cases were open types of NTDs with most common type being meningomyelocele (88%) followed by occipital encephalocele (12%) and there was one case of closed type of neural tube defect having lipomeningomyelocele (4%). The most common associated anomaly was hydrocephalus (76%) followed by Arnold chiari malformation (56%). Motor weakness in form of paraparesis or paraplegia was present in 21 (84%) babies and sensory deficit was present in 44% babies. Bowel and bladder dysfuntion was present in 48% of cases. Ventriculitis was the most common associated morbidity (38%). Meningomyelocele (MMC) repair was the most commonly performed primary surgery (33%) followed by Ventriculo-peritoneal (VP) shunt repair (24%). Twelve babies (48%) were discharged while 2 (8%) expired and 11 (44%) babies left against medical advice. CONCLUSION Neural tube defect is a congenital disorder with significant morbidity. The clinical severity of the NTDs and the uncertainty in their cause makes this a priority for further research. National policies for prevention, in utero diagnosis, and early surgical intervention are required for a better prognosis.
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Affiliation(s)
- Bhawana Komal Singh
- Department of Neonatology, Dr Ram Manohar Lohia Hospital and Post Graduate Institute of Medical Education and Research, New Delhi, India, Atal Bihari Vajpayi Institute of Medical Sciences (ABVIMS) and Dr Ram Manohar Lohia Hospital, New Delhi, India
| | - Arti Maria
- Department of Neonatology, Dr Ram Manohar Lohia Hospital and Post Graduate Institute of Medical Education and Research, New Delhi, India, Atal Bihari Vajpayi Institute of Medical Sciences (ABVIMS) and Dr Ram Manohar Lohia Hospital, New Delhi, India
| | - Tapas Bandyopadhyay
- Department of Neonatology, Dr Ram Manohar Lohia Hospital and Post Graduate Institute of Medical Education and Research, New Delhi, India, Atal Bihari Vajpayi Institute of Medical Sciences (ABVIMS) and Dr Ram Manohar Lohia Hospital, New Delhi, India
| | - Sushil Kumar Choudhary
- Department of Neonatology, Dr Ram Manohar Lohia Hospital and Post Graduate Institute of Medical Education and Research, New Delhi, India, Atal Bihari Vajpayi Institute of Medical Sciences (ABVIMS) and Dr Ram Manohar Lohia Hospital, New Delhi, India
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Fedota O, Sadovnychenko I, Chorna L, Roshcheniuk L, Vorontsov V, Ryzhko P, Haybonyuk I, Belyaev S, Belozorov I, Makukh H. The Effects of Polymorphisms in One-carbon Metabolism Genes on Manifestation of Ichthyosis Vulgaris. Open Access Maced J Med Sci 2021. [DOI: 10.3889/oamjms.2021.6004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND: Ichthyosis vulgaris is the most common type of Mendelian disorders of cornification, caused by loss-of-function mutations in the gene encoding epidermal protein filaggrin (FLG), namely R501X and 2282del4. FLG 2282del4 mutation in heterozygotes is incompletely penetrant. Polymorphisms in one-carbon metabolism genes could be associated with clinical manifestation of ichthyosis vulgaris.
AIM: The purpose of the present study was to analyze the effects of MTHFR, MTR and MTRR polymorphisms in patients with ichthyosis vulgaris.
METHODS: 31 patients with ichthyosis vulgaris, 7 their FLG heterozygous relatives without symptoms of disorder, and 150 healthy controls were enrolled in study. FLG null mutations —R501X (rs61816761) and 2282del4 (rs558269137) — and one-carbon metabolism gene polymorphisms — MTHFR C677T (rs1801133), MTHFR A1298C (rs1801131), MTR A2756G (rs1805087) and MTRR A66G (rs1801394) — were analyzed by a polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) assay.
RESULTS: Among patients with ichthyosis, heterozygous for FLG 2282del4 mutation, the distributions of genotypes for folate metabolism genes were: MTHFR C677T CC:CT:TT —29.4%:70.6%:0.0%; MTHFR A1298C AA:AC:CC — 52.9%:47.1%:0.0%; MTR A2756G AA:AG:GG — 70.3%:23.5%:5.9%; MTRR A66G AA:AG:GG — 23.4%:52.9%:23.5%. The frequencies of MTR 2756AA and MTRR 66GG genotypes were 1.4–1.6 times higher in affected individuals heterozygous for 2282del4 than in patients with other FLG genotypes. In affected 2282del4 heterozygotes, the frequency of MTR 2756AA genotype was 1.6 times greater than in healthy controls (p<0.01). The strongest association was found between MTHFR 677CT/MTHFR 1298AA/MTR 2756AA/MTRR 66AG genotype and ichthyosis — OR=11.23 (95% CI 2.51−50.21, p=0.002).
CONCLUSIONS: Various genotypes of one-carbon metabolism genes increase the risk of ichthyosis in heterozygotes for the FLG 2282del4 mutation (OR 2.799‑11.231). The most probable predisposing genotype is 677CT/1298AA/2756AA+AG/66AG.
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Sadhukhan S, Maity S, Chakraborty S, Paul S, Munian D, Kumar Pattanayak A, Jana B, Das M. Structural insight into the effect of polymorphic variation on the functional dynamics of methionine synthase reductase: Implications in neural tube defects. Chem Biol Drug Des 2020; 97:283-292. [PMID: 32812692 DOI: 10.1111/cbdd.13780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/26/2020] [Accepted: 08/09/2020] [Indexed: 12/31/2022]
Abstract
Neural tube defects (NTDs), one of the most common birth defects, are strongly associated with the variations of several single nucleotide polymorphisms (SNPs) in the MTRR gene. The gene codes a key enzyme that is involved in the rejuvenation of methionine synthase activity. An allelic variant of the protein leads to missense mutation at 49th position from isoleucine to methionine (I49M) is associated with higher disease prevalence in different populations. Here, extensive molecular dynamics simulations and interaction network analysis reveal that the 49th isoleucine is a crucial residue that allosterically regulates the dynamics between the flavin mononucleotide (FMN) and NADP(H) binding domains. I49M variation alters the functional dynamics in a way that might impede the electron transport chain along the NADP(H) → flavin adenine dinucleotide → FMN pathway. The present study provides functional insights into the effect of the genetic variations of the MTRR gene on the NTDs disease pathogenesis.
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Affiliation(s)
| | - Subhajit Maity
- Department of Zoology, University of Calcutta, Kolkata, India.,Department of Endocrinology, Institute of Post Graduate Medical Education Research (IPGMER), Kolkata, India
| | | | - Silpita Paul
- Department of Zoology, University of Calcutta, Kolkata, India.,Department of Molecular Medicine, Bose Institute, Kolkata, India
| | - Dinesh Munian
- Department of Neonatology, Institute of Post Graduate Medical Education Research (IPGMER), Kolkata, India
| | | | - Biman Jana
- School of Chemical Sciences, Indian Association for Cultivation of Science, Kolkata, India
| | - Madhusudan Das
- Department of Zoology, University of Calcutta, Kolkata, India
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Pharmacogenomic Markers of Methotrexate Response in the Consolidation Phase of Pediatric Acute Lymphoblastic Leukemia Treatment. Genes (Basel) 2020; 11:genes11040468. [PMID: 32344632 PMCID: PMC7230684 DOI: 10.3390/genes11040468] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 02/06/2023] Open
Abstract
Methotrexate (MTX) is one of the staples of pediatric acute lymphoblastic leukemia (ALL) treatment. MTX targets the folate metabolic pathway (FMP). Abnormal function of the enzymes in FMP, due to genetic aberrations, leads to adverse drug reactions. The aim of this study was to investigate variants in pharmacogenes involved in FMP and their association with MTX pharmacokinetics (MTX elimination profile) and toxicity in the consolidation therapy phase of pediatric ALL patients. Eleven variants in the thymidylate synthetase (TYMS), methylenetetrahydrofolate reductase (MTHFR), dihydrofolate reductase (DHFR), SLC19A1 and SLCO1B genes were analyzed in 148 patients, using PCR- and sequencing-based methodology. For the Serbian and European control groups, data on allele frequency distribution were extracted from in-house and public databases. Our results show that the A allele of SLC19A1 c.80 variant contributes to slow MTX elimination. Additionally, the AA genotype of the same variant is a predictor of MTX-related hepatotoxicity. Patients homozygous for TYMS 6bp deletion were more likely to experience gastrointestinal toxicity. No allele frequency dissimilarity was found for the analyzed variants between Serbian and European populations. Statistical modelling did not show a joint effect of analyzed variants. Our results indicate that SLC19A1 c.80 variant and TYMS 6bp deletion are the most promising pharmacogenomic markers of MTX response in pediatric ALL patients.
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Nasri K, Midani F, Kallel A, Ben Jemaa N, Aloui M, Boulares M, Lassoued M, Ben Halima M, Ben Wafi S, Soussi M, Mahjoubi I, Baara A, Ben Fradj MK, Omar S, Feki M, Jemaa R, Gaigi SS, Marrakchi R. Association of MTHFR C677T, MTHFR A1298C, and MTRR A66G Polymorphisms with Neural Tube Defects in Tunisian Parents. Pathobiology 2019; 86:190-200. [PMID: 31238314 DOI: 10.1159/000499498] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 03/11/2019] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE This study aims to investigate the association of 5,10-methylenetetrahydrofolate reductase (MTHFR C677T and A1298C) and methionine synthase reductase (MTRR A66G) gene polymorphisms with neural tube defects (NTDs) in a Tunisian population. METHODS Genotyping was performed by polymerase chain reaction with restriction fragment length polymorphisms (PCR-RFLPs) using the restriction enzymes. Allele and genotype frequencies were compared between mothers and fathers of fetuses with NTDs with matched controls based on an association analysis using SPSS software. RESULTS MTHFR (C677T, A1298C) and MTRR A66G polymorphisms were found to be protector factors for NTD fetuses in the mother group. In addition, a combination of the three wild-type alleles C677/A1298/A66 has increased four-fold the incidence of NTDs (p = 0.004, OR = 3.96, 95% CI: 1.53-10.23). In the father group, MTHFR C677T was a risk factor for NTDs. However, no association was found between MTHFR A1298C, MTRR A66G, and the occurrence of this anomaly. The analysis of MTHFR C677T and MTRR A66G polymorphisms has demonstrated a significant difference in vitamin B12 levels between recessive and dominant genotypes in case mothers (p < 0.05). CONCLUSION Additional studies are required to better understand the roles of parental gene polymorphisms related to folate-homocysteine metabolism in the pathogenesis of NTD.
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Affiliation(s)
- Kaouther Nasri
- Faculté des Sciences de Bizerte, Université de Carthage, Bizerte, Tunisia, .,UR 06/ SP14 Troubles du développement embryo-fœtal et placentaire, Service d'embryo-fœtopathologie, Centre de Maternité et de Néonatologie La Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia,
| | - Fatma Midani
- UR 05/08-08, Département de biochimie, Hôpital la Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Amani Kallel
- UR 05/08-08, Département de biochimie, Hôpital la Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Nadia Ben Jemaa
- UR 06/ SP14 Troubles du développement embryo-fœtal et placentaire, Service d'embryo-fœtopathologie, Centre de Maternité et de Néonatologie La Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Mariem Aloui
- Faculté des Sciences de Bizerte, Université de Carthage, Bizerte, Tunisia.,UR 06/ SP14 Troubles du développement embryo-fœtal et placentaire, Service d'embryo-fœtopathologie, Centre de Maternité et de Néonatologie La Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Miryam Boulares
- Faculté des Sciences de Bizerte, Université de Carthage, Bizerte, Tunisia.,CERTE -Technopole de Borj-Cedria Laboratoire de Traitement et Valorisation des Rejets Hydriques, Soliman, Tunisia
| | - Mehdi Lassoued
- UR 05/08-08, Département de biochimie, Hôpital la Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Meriam Ben Halima
- UR 05/08-08, Département de biochimie, Hôpital la Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Safa Ben Wafi
- UR 05/08-08, Département de biochimie, Hôpital la Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Mariem Soussi
- UR 05/08-08, Département de biochimie, Hôpital la Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Imen Mahjoubi
- UR 05/08-08, Département de biochimie, Hôpital la Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Abir Baara
- UR 05/08-08, Département de biochimie, Hôpital la Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Mohamed Kacem Ben Fradj
- UR 05/08-08, Département de biochimie, Hôpital la Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Souhail Omar
- Laboratoire de Biologie clinique, Institut National Mongi Ben Hmida de Neurologie, Rue Jebbari La Rabta, Tunis, Tunisia
| | - Moncef Feki
- UR 05/08-08, Département de biochimie, Hôpital la Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Riadh Jemaa
- UR 05/08-08, Département de biochimie, Hôpital la Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Soumeya Siala Gaigi
- UR 06/ SP14 Troubles du développement embryo-fœtal et placentaire, Service d'embryo-fœtopathologie, Centre de Maternité et de Néonatologie La Rabta et de la Faculté de Médecine de Tunis, Université El Manar II, Tunis, Tunisia
| | - Raja Marrakchi
- Laboratoire de génétique, immunologie et pathologie humaine, faculté des sciences de Tunis, Université El Manar II, Tunis, Tunisia
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Paul S, Sadhukhan S, Munian D, Bankura B, Das M. Association of FOLH1, DHFR, and MTHFR gene polymorphisms with susceptibility of Neural Tube Defects: A case control study from Eastern India. Birth Defects Res 2018; 110:1129-1138. [PMID: 30120883 DOI: 10.1002/bdr2.1365] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/07/2018] [Accepted: 06/12/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Silpita Paul
- Department of Zoology; University of Calcutta, Kolkata; West Bengal India
| | - Susanta Sadhukhan
- Department of Zoology; University of Calcutta, Kolkata; West Bengal India
| | - Dinesh Munian
- Department of Neonatology; Institute of Post Graduate Medical Education & Research, Kolkata; West Bengal India
| | | | - Madhusudan Das
- Department of Zoology; University of Calcutta, Kolkata; West Bengal India
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11
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K Rebekah P, Tella S, Buragadda S, Tiruvatturu MK, Akka J. Interaction between Maternal and Paternal SHMT1 C1420T Predisposes to Neural Tube Defects in the Fetus: Evidence from Case-Control and Family-Based Triad Approaches. Birth Defects Res 2018; 109:1020-1029. [PMID: 28762673 DOI: 10.1002/bdr2.23623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/19/2016] [Accepted: 12/22/2016] [Indexed: 12/25/2022]
Abstract
BACKGROUND Neural tube defects (NTDs) are caused by the failure of neural tube formation which occurs during early embryonic development. NTDs are the most severe and leading cause of fetal mortality. Serine hydroxymethyl transferase (SHMT1) provides one-carbon units necessary for embryogenesis and defects in one-carbon production result in specific pathological conditions during pregnancy. The present study is aimed to evaluate the association of SHMT1 C1420T with NTD risk in the fetus using fetal, maternal and paternal groups by applying both case-control and family-based triad approaches. METHODS A total of 924 subjects including 124 NTD case-parent trios (n = 124 × 3 = 372) and 184 healthy control-parent trios (n = 184 × 3 = 552) from Telangana State, South India were analyzed. DNA from umbilical cord tissues and parental blood samples were extracted, and genotyped by polymerase chain reaction-restriction fragment length polymorphism. Statistical analysis used were SPSS, parent-of-origin effect (POE) analysis. RESULTS Case-control study design demonstrated fetuses with homozygous variant genotype (TT) to be at risk toward spina bifida subtype (p = 0.022). Among parents, fathers with TT genotype were associated with anencephaly (p = 0.018) and spina bifida subtypes (p = 0.027) in the offspring. Of interest, maternal-paternal-offspring genotype incompatibility revealed maternal CT genotype in combination with paternal TT genotype increased risk for NTDs in the fetus (CTxTT = TT; p = 0.021). Family-based parent-of-origin effect linkage analysis revealed significant maternal over-transmission of variant allele to NTD fetuses (p < 0.01). CONCLUSION The present study, using both case-control and family-based triad approach is the first report to demonstrate parental association of SHMT1 C1420T variant in conferring NTD risk in the fetus. Birth Defects Research 109:1020-1029, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Prasoona K Rebekah
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana State, India
| | - Sunitha Tella
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana State, India
| | - Srinadh Buragadda
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana State, India
| | | | - Jyothy Akka
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana State, India
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12
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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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13
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Au KS, Findley TO, Northrup H. Finding the genetic mechanisms of folate deficiency and neural tube defects-Leaving no stone unturned. Am J Med Genet A 2017; 173:3042-3057. [PMID: 28944587 PMCID: PMC5650505 DOI: 10.1002/ajmg.a.38478] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 08/11/2017] [Accepted: 08/21/2017] [Indexed: 12/21/2022]
Abstract
Neural tube defects (NTDs) occur secondary to failed closure of the neural tube between the third and fourth weeks of gestation. The worldwide incidence ranges from 0.3 to 200 per 10,000 births with the United States of American NTD incidence at around 3-6.3 per 10,000 dependent on race and socioeconomic background. Human NTD incidence has fallen by 35-50% in North America due to mandatory folic acid fortification of enriched cereal grain products since 1998. The US Food and Drug Administration has approved the folic acid fortification of corn masa flour with the goal to further reduce the incidence of NTDs, especially among individuals who are Hispanic. However, the genetic mechanisms determining who will benefit most from folate enrichment of the diet remains unclear despite volumes of literature published on studies of association of genes with functions related to folate metabolism and risk of human NTDs. The advances in omics technologies provides hypothesis-free tools to interrogate every single gene within the genome of NTD affected individuals to discover pathogenic variants and methylation targets throughout the affected genome. By identifying genes with expression regulated by presence of folate through transcriptome profiling studies, the genetic mechanisms leading to human NTDs due to folate deficiency may begin to be more efficiently revealed.
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Affiliation(s)
- KS Au
- Division of Medical Genetics, Department of Pediatrics, University of Texas Health Science Houston – McGovern Medical School, Houston, TX
| | - TO Findley
- Division of Neonatology, Department of Pediatrics, University of Texas Health Science Houston – McGovern Medical School, Houston, TX
| | - H Northrup
- Division of Medical Genetics, Department of Pediatrics, University of Texas Health Science Houston – McGovern Medical School, Houston, TX
- Shriners Hospitals for Children - Houston, Houston, TX
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Findley TO, Tenpenny JC, O'Byrne MR, Morrison AC, Hixson JE, Northrup H, Au KS. Mutations in folate transporter genes and risk for human myelomeningocele. Am J Med Genet A 2017; 173:2973-2984. [PMID: 28948692 DOI: 10.1002/ajmg.a.38472] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 07/21/2017] [Accepted: 08/21/2017] [Indexed: 11/09/2022]
Abstract
The molecular mechanisms linking folate deficiency and neural tube defect (NTD) risk in offspring remain unclear. Folate transporters (SLC19A1, SLC46A1, SLC25A32, and FOLH1) and folate receptors (FOLR1, FOLR2, and FOLR3) are suggested to play essential roles in transporting folate from maternal intestinal lumen to the developing embryo. Loss of function variants in these genes may affect folate availability and contribute to NTD risk. This study examines whether variants within the folate transporter and receptor genes are associated with an increased risk for myelomeningocele (MM). Exons and their flanking intron sequences of 348 MM subjects were sequenced using the Sanger sequencing method and/or next generation sequencing to identify variants. Frequencies of alleles of single nucleotide polymorphisms (SNPs) in MM subjects were compared to those from ethnically matched reference populations to evaluate alleles' associated risk for MM. We identified eight novel variants in SLC19A1 and twelve novel variants in FOLR1, FOLR2, and FOLR3. Pathogenic variants include c.1265delG in SLC19A1 resulting in an early stop codon, four large insertion deletion variants in FOLR3, and a stop_gain variant in FOLR3. No new variants were identified in SLC46A1, SLC25A32, or FOLH1. In SLC19A1, c.80A>G (rs1051266) was not associated with our MM cohort; we did observe a variant allele G frequency of 61.7%, higher than previously reported in other NTD populations. In conclusion, we discovered novel loss of function variants in genes involved in folate transport in MM subjects. Our results support the growing evidence of associations between genes involved in folate transport and susceptibility to NTDs.
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Affiliation(s)
- Tina O Findley
- Division of Neonatology, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Joy C Tenpenny
- Division of Neonatology, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Michelle R O'Byrne
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas
| | - James E Hixson
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.,Shriners Hospital for Children, Houston, Texas
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
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Zhang J, Dai XL, Liu GC, Wang J, Ren XY, Jin MH, Mi NN, Wang SQ. An Inframe Trinucleotide Deletion in MTRR Exon 1 is Associated with the Risk of Spina Bifida. Neuromolecular Med 2017; 19:387-394. [PMID: 28712006 DOI: 10.1007/s12017-017-8452-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/10/2017] [Indexed: 11/26/2022]
Abstract
Maternal genetic variants of enzymes in folate-homocysteine metabolic network are significantly correlative with the risk of spina bifida. To survey the genetic causality, the genotypes of three women having spina bifida fetuses from two unrelated Chinese families were screened in candidate alleles. Polymerase chain reaction, capillary electrophoresis and Sanger sequencing were employed to recognize the allelic variation. A trinucleotide deletion (c.4_6delAGG) was identified in the first exon of MTRR. All the three women showed the novel clinical variation including one heterozygous and two homozygous. The siblings who had healthy babies from the same families did not harbor the variation. In the unaffected control individuals, the variant was also not observed. Eukaryotic expression and bioinformatics techniques were utilized to explore the molecular pathogenesis of the potential genetic risk of developing spina bifida. Exceptionally, the functional examination revealed that the Arg2del variant kept subcellular localization unaltered with catalytic activity intact, but failed to efficiently activate MTR compared with the wild type. Genetic disorder of folate and homocysteine metabolism during pregnancy is believed to be associated with folate-sensitive neural tube defects. The report highlights that the inframe deletion in MTRR exon 1 could be a high risk factor susceptibility to spina bifida.
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Affiliation(s)
- Jun Zhang
- Institute of Molecular Medicine and Oncology, Chongqing Medical University, Yuzhong District, Chongqing City, 400016, China.
| | - Xiao-Lu Dai
- Institute of Molecular Medicine and Oncology, Chongqing Medical University, Yuzhong District, Chongqing City, 400016, China
| | - Gui-Cen Liu
- Institute of Molecular Medicine and Oncology, Chongqing Medical University, Yuzhong District, Chongqing City, 400016, China
| | - Juan Wang
- Institute of Molecular Medicine and Oncology, Chongqing Medical University, Yuzhong District, Chongqing City, 400016, China
| | - Xue-Yi Ren
- Genetics Department, Chongqing Institute for Food and Drug Control, Chongqing, 400121, China
| | - Mu-Hua Jin
- Institute of Molecular Medicine and Oncology, Chongqing Medical University, Yuzhong District, Chongqing City, 400016, China
| | - Nan-Nan Mi
- Institute of Molecular Medicine and Oncology, Chongqing Medical University, Yuzhong District, Chongqing City, 400016, China
| | - Shu-Qin Wang
- Institute of Molecular Medicine and Oncology, Chongqing Medical University, Yuzhong District, Chongqing City, 400016, China
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16
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K Rebekah P, Tella S, Buragadda S, Tiruvatturu MK, Akka J. Interaction between Maternal and Paternal SHMT1 C1420T Predisposes to Neural Tube Defects in the Fetus: Evidence from Case-Control and Family-Based Triad Approaches. Birth Defects Res 2017. [PMID: 28411382 DOI: 10.1002/bdra.23623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/19/2016] [Accepted: 12/22/2016] [Indexed: 11/06/2022]
Abstract
BACKGROUND Neural tube defects (NTDs) are caused by the failure of neural tube formation which occurs during early embryonic development. NTDs are the most severe and leading cause of fetal mortality. Serine hydroxymethyl transferase (SHMT1) provides one-carbon units necessary for embryogenesis and defects in one-carbon production result in specific pathological conditions during pregnancy. The present study is aimed to evaluate the association of SHMT1 C1420T with NTD risk in the fetus using fetal, maternal and paternal groups by applying both case-control and family-based triad approaches. METHODS A total of 924 subjects including 124 NTD case-parent trios (n = 124 × 3 = 372) and 184 healthy control-parent trios (n = 184 × 3 = 552) from Telangana State, South India were analyzed. DNA from umbilical cord tissues and parental blood samples were extracted, and genotyped by polymerase chain reaction-restriction fragment length polymorphism. Statistical analysis used were SPSS, parent-of-origin effect (POE) analysis. RESULTS Case-control study design demonstrated fetuses with homozygous variant genotype (TT) to be at risk toward spina bifida subtype (p = 0.022). Among parents, fathers with TT genotype were associated with anencephaly (p = 0.018) and spina bifida subtypes (p = 0.027) in the offspring. Of interest, maternal-paternal-offspring genotype incompatibility revealed maternal CT genotype in combination with paternal TT genotype increased risk for NTDs in the fetus (CTxTT = TT; p = 0.021). Family-based parent-of-origin effect linkage analysis revealed significant maternal over-transmission of variant allele to NTD fetuses (p < 0.01). CONCLUSION The present study, using both case-control and family-based triad approach is the first report to demonstrate parental association of SHMT1 C1420T variant in conferring NTD risk in the fetus. Birth Defects Research, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Prasoona K Rebekah
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana State, India
| | - Sunitha Tella
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana State, India
| | - Srinadh Buragadda
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana State, India
| | | | - Jyothy Akka
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana State, India
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17
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Sun K, Song J, Liu K, Fang K, Wang L, Wang X, Li J, Tang X, Wu Y, Qin X, Wu T, Gao P, Chen D, Hu Y. Associations between homocysteine metabolism related SNPs and carotid intima-media thickness: a Chinese sib pair study. J Thromb Thrombolysis 2017; 43:401-410. [PMID: 27822905 PMCID: PMC5337241 DOI: 10.1007/s11239-016-1449-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Carotid intima-media thickness (CIMT) is a good surrogate for atherosclerosis. Hyperhomocysteinemia is an independent risk factor for cardiovascular diseases. We aim to investigate the relationships between homocysteine (Hcy) related biochemical indexes and CIMT, the associations between Hcy related SNPs and CIMT, as well as the potential gene–gene interactions. The present study recruited full siblings (186 eligible families with 424 individuals) with no history of cardiovascular events from a rural area of Beijing. We examined CIMT, intima-media thickness for common carotid artery (CCA-IMT) and carotid bifurcation, tested plasma levels for Hcy, vitamin B6 (VB6), vitamin B12 (VB12) and folic acid (FA), and genotyped 9 SNPs on MTHFR, MTR, MTRR, BHMT, SHMT1, CBS genes. Associations between SNPs and biochemical indexes and CIMT indexes were analyzed using family-based association test analysis. We used multi-level mixed-effects regression model to verify SNP-CIMT associations and to explore the potential gene–gene interactions. VB6, VB12 and FA were negatively correlated with CIMT indexes (p < 0.05). rs2851391 T allele was associated with decreased plasma VB12 levels (p = 0.036). In FABT, CBS rs2851391 was significantly associated with CCA-IMT (p = 0.021) and CIMT (p = 0.019). In multi-level mixed-effects regression model, CBS rs2851391 was positively significantly associated with CCA-IMT (Coef = 0.032, se = 0.009, raw p < 0.001) after Bonferoni correction (corrected α = 0.0056). Gene–gene interactions were found between CBS rs2851391 and BHMT rs10037045 for CCA-IMT (p = 0.011), as well as between CBS rs2851391 and MTR rs1805087 for CCA-IMT (p = 0.007) and CIMT (p = 0.022). Significant associations are found between Hcy metabolism related genetic polymorphisms, biochemical indexes and CIMT indexes. There are complex interactions between genetic polymorphisms for CCA-IMT and CIMT.
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Affiliation(s)
- Kexin Sun
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, 38 Xueyuan Road, Beijing, 100191, China
| | - Jing Song
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, 38 Xueyuan Road, Beijing, 100191, China
| | - Kuo Liu
- Department of Epidemiology and Biostatistics, Capital Medical University, 10 You'anmenwai Xitoutiao, Beijing, 100069, China
| | - Kai Fang
- Beijing Center for Disease Prevention and Control, No.16 He Pingli Middle Street, Dongcheng District, Beijing, 100013, China
| | - Ling Wang
- Pingshan New District Center for Disease Control and Prevention, Shenzhen, 518118, Guangdong, China
| | - Xueyin Wang
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, 38 Xueyuan Road, Beijing, 100191, China
| | - Jing Li
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, 38 Xueyuan Road, Beijing, 100191, China
| | - Xun Tang
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, 38 Xueyuan Road, Beijing, 100191, China
| | - Yiqun Wu
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, 38 Xueyuan Road, Beijing, 100191, China
| | - Xueying Qin
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, 38 Xueyuan Road, Beijing, 100191, China
| | - Tao Wu
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, 38 Xueyuan Road, Beijing, 100191, China
| | - Pei Gao
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, 38 Xueyuan Road, Beijing, 100191, China
| | - Dafang Chen
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, 38 Xueyuan Road, Beijing, 100191, China
| | - Yonghua Hu
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, 38 Xueyuan Road, Beijing, 100191, China.
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Mirgal D, Ghosh K, Mahanta J, Dutta P, Shetty S. Possible selection of host folate pathway gene polymorphisms in patients with malaria from a malaria endemic region in North East India. Trans R Soc Trop Med Hyg 2016; 110:294-8. [PMID: 27198213 DOI: 10.1093/trstmh/trw026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 03/23/2016] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Recent studies in experimental mice have shown that mild deficiency of methylenetetrahydrofolate reductase (MTHFR) enzyme confers protection against malaria, thus providing an important basis for the hypothesis that MTHFR polymorphism, i.e. C677T, might have been subjected to selection pressure against malaria. The present study was undertaken in a malaria endemic region in North East India to assess whether a similar selection advantage exists for other genes in folate metabolism pathway. METHODS A total of 401 subjects including 131 symptomatic malaria, 97 asymptomatic malaria and 173 normal healthy controls were analysed for nine polymorphisms (single-nucleotide polymorphisms [SNPs] in eight genes and insertion/deletion in one gene): MTHFR C677T, methionine synthase reductase (MTRR) A66G, glutamate carboxypeptidase II (GCPII) C1561T, cystathionine beta-synthase (CBS) 844ins68, reduced folate carrier-1 (RFC-1) G80A, serine hydroxymethyltransferase (SHMT) C1420T, methionine synthase (MTR) A2756G, MTHFR G1793A (D 919G), glycine N-methyltransferase (GNMT) 1289 by PCR-RFLP technique. Differences in frequencies of genotype distribution of each polymorphic marker between these groups were evaluated. RESULTS MTRR A2756G, SHMT C1420T, GCPII C1561T, MTRR A2756G and GNMT C1289T and RFC1 G80A polymorphisms showed significantly different prevalence between different groups analyzed. No significant differences were seen in the distribution of other polymorphisms. CONCLUSIONS The study gives a clue for the possible selection of specific polymorphisms in the genes involved in the folate metabolism pathway by malaria parasite.
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Affiliation(s)
- Darshana Mirgal
- Department of Hemostasis and Thrombosis, National Institute of Immunohaematology (ICMR), New Multistoreyed Building, KEM Hospital, Parel, Mumbai
| | | | | | - Prafulla Dutta
- Regional Medical Research Centre (ICMR), Dibrugarh, Assam
| | - Shrimati Shetty
- Department of Hemostasis and Thrombosis, National Institute of Immunohaematology (ICMR), New Multistoreyed Building, KEM Hospital, Parel, Mumbai
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19
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Functional variant in methionine synthase reductase intron-1 is associated with pleiotropic congenital malformations. Mol Cell Biochem 2015; 407:51-6. [DOI: 10.1007/s11010-015-2453-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/16/2015] [Indexed: 01/03/2023]
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20
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Yang Y, Chen J, Wang B, Ding C, Liu H. Association between MTHFR C677T polymorphism and neural tube defect risks: A comprehensive evaluation in three groups of NTD patients, mothers, and fathers. ACTA ACUST UNITED AC 2015; 103:488-500. [PMID: 25808073 DOI: 10.1002/bdra.23361] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND The C677T polymorphism in the methylenetetrahydrofolate reductase gene (MTHFR) gene has been reported to play a critical role in the pathogenesis of neural tube defects (NTDs). The association of the C677T polymorphism in the MTHFR gene and NTD susceptibility has been widely demonstrated, but the results are inconclusive. In this study, we performed a meta-analysis in three groups to investigate the association between the MTHFR C677T polymorphism and NTD risk. METHODS A computer retrieval of PubMed, Cochrane Library, CBM, and Embase for papers on the MTHFR C677T polymorphism and NTD risk was performed. All data were analyzed with STATA (Version 13.0). Odds ratios (ORs) with 95% confidence intervals (CIs) were estimated to assess the association. A test for heterogeneity, a sensitivity analysis, and an assessment of publication bias were performed in our meta-analysis. RESULTS Forty articles were included in this meta-analysis: 13 studies for Group A: 1329 NTD patients versus 2965 healthy controls; 34 studies for Group B: 3018 mothers with NTD progeny versus 8746 healthy controls; three studies for Group C: 157 fathers with NTD progeny versus 705 healthy controls. The analysis results show: allele contrast in NTD patients: OR = 1.445, 95% CI [1.186, 1.760]; allele contrast in mothers: OR = 1.342, 95% CI [1.166, 1.544]; allele contrast in fathers: OR = 1.062, 95% CI [0.821, 1.374]. CONCLUSION We found no association between any of the fathers' genotypes and NTDs, whereas a significant correlation between MTHFR C677T polymorphism and NTD risk was found in NTD patients and in their mother.
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Affiliation(s)
- Yi Yang
- West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Jie Chen
- West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Beiyu Wang
- West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Chen Ding
- West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Hao Liu
- West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
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21
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Yadav U, Kumar P, Yadav SK, Mishra OP, Rai V. "Polymorphisms in folate metabolism genes as maternal risk factor for neural tube defects: an updated meta-analysis". Metab Brain Dis 2015; 30:7-24. [PMID: 25005003 DOI: 10.1007/s11011-014-9575-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/05/2014] [Indexed: 02/02/2023]
Abstract
Epidemiological studies have evaluated the association between maternal methylenetetrahydrofolate reductase (MTHFR) C677T, A1298C and methionine synthase reductase (MTRR) A66G polymorphisms and risk of neural tube defects (NTDs) in offspring. However, the results from the published studies on the association between these three polymorphisms and NTD risk are conflicting. To derive a clearer picture of association between these three maternal polymorphisms and risk of NTD, we performed meta-analysis. A comprehensive search was conducted to identify all case-control studies of maternal MTHFR and MTRR polymorphisms and NTD risk. We used odds ratios (ORs) with 95% confidence intervals (CIs) to assess the strength of the association. Overall, we found that maternal MTHFR C677T polymorphism (OR(TvsC) =1.20; 95% CI = 1.13-1.28) and MTRR A66G polymorphism (OR(GvsA) = 1.21; 95% CI = 0.98-1.49) were risk factors for producing offspring with NTD but maternal MTHFR A1298C polymorphism (OR(CvsA) = 0.91; 95% CI = 0.78-1.07) was not associated with NTD risk. However, in stratified analysis by geographical regions, we found that the maternal C677T polymorphism was significantly associated with the risk of NTD in Asian (OR(TvsC) = 1.43; 95% CI: 1.05-1.94), European (OR(TvsC) = 1.13; 95% CI: 1.04-1.24) and American (OR(TvsC) = 1.26; 95% CI: 1.13-1.41) populations. In conclusion, present meta-analysis supports that the maternal MTHFR C677T and MTRR A66G are polymorphisms contributory to risk for NTD.
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Affiliation(s)
- Upendra Yadav
- Human Molecular Genetics Laboratory, Department of Biotechnology, VBS Purvanchal University, Jaunpur, 222 003, UP, India
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22
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Luo L, Chen Y, Wang L, Zhuo G, Qiu C, Tu Q, Mei J, Zhang W, Qian X, Wang X. Polymorphisms of Genes Involved in the Folate Metabolic Pathway Impact the Occurrence of Unexplained Recurrent Pregnancy Loss. Reprod Sci 2014; 22:845-51. [PMID: 25544674 DOI: 10.1177/1933719114565033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Low levels of folate combined with high levels of homocysteine may cause unexplained recurrent pregnancy loss (URPL). However, the relationships between polymorphisms in genes of the folate metabolic pathway and URPL remain controversial. We conducted a case-control study to explore polymorphisms of the major folate pathway genes, including methylenetetrahydrofolate reductase (MTHFR) 677C>T, MTHFR 1298A>C, methionine synthase (MTR) 2756A>G, methionine synthase reductase (MTRR) 66A>G and reduced folate carrier 1 (RFC-1) 80A>G, and their associations with URPL. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to determine the distributions of MTHFR, MTR and RFC-1 polymorphisms, and the results were validated using direct sequencing. The polymorphisms in MTRR were determined using direct sequencing. Haplotypes were analyzed using SHEsis, an online tool for biological analysis. We found that the MTHFR 677T allele and the 677T/1298A/2756A/66A/80G haplotype were risk factors for URPL, while the MTR 2756G allele and the 677C/1298A/2756A/66A/80A haplotype exhibited protective effects on susceptibility to URPL in a Chinese Han population from the Hangzhou area.
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Affiliation(s)
- Li Luo
- School of Laboratory Medicine & Life Science, Wenzhou Medical University, Wenzhou, China
| | - Yueming Chen
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, China
| | - Li Wang
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, China
| | - Guangchao Zhuo
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, China
| | - Chunning Qiu
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, China
| | - Qiaofeng Tu
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, China
| | - Jin Mei
- Department of Obstetrics/Gynaecology and Genetics, Hangzhou First People's Hospital, Hangzhou, China
| | - Wen Zhang
- Department of Obstetrics/Gynaecology and Genetics, Hangzhou First People's Hospital, Hangzhou, China
| | - Xia Qian
- Department of Obstetrics/Gynaecology and Genetics, Hangzhou First People's Hospital, Hangzhou, China
| | - Xianjun Wang
- School of Laboratory Medicine & Life Science, Wenzhou Medical University, Wenzhou, China Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, China
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Pangilinan F, Molloy AM, Mills JL, Troendle JF, Parle-McDermott A, Kay DM, Browne ML, McGrath EC, Abaan HO, Sutton M, Kirke PN, Caggana M, Shane B, Scott JM, Brody LC. Replication and exploratory analysis of 24 candidate risk polymorphisms for neural tube defects. BMC MEDICAL GENETICS 2014; 15:102. [PMID: 25293959 PMCID: PMC4411759 DOI: 10.1186/s12881-014-0102-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 08/19/2014] [Indexed: 12/14/2022]
Abstract
Background Neural tube defects (NTDs), which are among the most common congenital malformations, are influenced by environmental and genetic factors. Low maternal folate is the strongest known contributing factor, making variants in genes in the folate metabolic pathway attractive candidates for NTD risk. Multiple studies have identified nominally significant allelic associations with NTDs. We tested whether associations detected in a large Irish cohort could be replicated in an independent population. Methods Replication tests of 24 nominally significant NTD associations were performed in racially/ethnically matched populations. Family-based tests of fifteen nominally significant single nucleotide polymorphisms (SNPs) were repeated in a cohort of NTD trios (530 cases and their parents) from the United Kingdom, and case–control tests of nine nominally significant SNPs were repeated in a cohort (190 cases, 941 controls) from New York State (NYS). Secondary hypotheses involved evaluating the latter set of nine SNPs for NTD association using alternate case–control models and NTD groupings in white, African American and Hispanic cohorts from NYS. Results Of the 24 SNPs tested for replication, ADA rs452159 and MTR rs10925260 were significantly associated with isolated NTDs. Of the secondary tests performed, ARID1A rs11247593 was associated with NTDs in whites, and ALDH1A2 rs7169289 was associated with isolated NTDs in African Americans. Conclusions We report a number of associations between SNP genotypes and neural tube defects. These associations were nominally significant before correction for multiple hypothesis testing. These corrections are highly conservative for association studies of untested hypotheses, and may be too conservative for replication studies. We therefore believe the true effect of these four nominally significant SNPs on NTD risk will be more definitively determined by further study in other populations, and eventual meta-analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12881-014-0102-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Faith Pangilinan
- Molecular Pathogenesis Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Room 5306, 50 South Drive, Bethesda, MD, 20892-8004, USA.
| | - Anne M Molloy
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland.
| | - James L Mills
- Division of Epidemiology, Statistics and Prevention Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - James F Troendle
- Office of Biostatistics Research, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | | | - Denise M Kay
- New York State Department of Health, Division of Genetics, Wadsworth Center, Albany, NY, 12201, USA.
| | - Marilyn L Browne
- New York State Department of Health, Congenital Malformations Registry, Troy, NY, 12180, USA. .,Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, NY, 12144, USA.
| | - Emily C McGrath
- New York State Department of Health, Division of Genetics, Wadsworth Center, Albany, NY, 12201, USA.
| | - Hatice Ozel Abaan
- Molecular Pathogenesis Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Room 5306, 50 South Drive, Bethesda, MD, 20892-8004, USA.
| | - Marie Sutton
- Evidence Centre, Health Research Board, Dublin, Ireland.
| | - Peadar N Kirke
- Child Health Epidemiology Unit, Health Research Board, Dublin, Ireland.
| | - Michele Caggana
- New York State Department of Health, Division of Genetics, Wadsworth Center, Albany, NY, 12201, USA.
| | - Barry Shane
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, 94720-3104, USA.
| | - John M Scott
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
| | - Lawrence C Brody
- Molecular Pathogenesis Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Room 5306, 50 South Drive, Bethesda, MD, 20892-8004, USA.
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Zhang Q, Bai B, Liu X, Miao C, Li H. Association of folate metabolism genes MTHFR and MTRR with multiple complex congenital malformation risk in Chinese population of Shanxi. Transl Pediatr 2014; 3:259-67. [PMID: 26835343 PMCID: PMC4729852 DOI: 10.3978/j.issn.2224-4336.2014.07.10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Birth defects are common, serious malformations with a complex etiology that suggests involvement of both genetic and environmental factors. Low dietary folate and polymorphisms in genes of folate metabolism can influence risk for birth defects. In the present study 250 Chinese birth defects cases who suffered 1-8 types of birth defect disease phenotypes were subjected and two genetic variants in two folate metabolism key enzymes, rs1801394 of methionine synthase reductase (MTRR) and rs1801133 of methylenetetrahydrofolate reductase (MTHFR) were genotyped by using SNaPshot method. The results indicated that rs1801394 and rs1801133 were associated with multiple birth defects. According to homology of organogenesis, the disease phenotypes were classified into ectoderm-, mesoderm-, and endoderm-developed groups. Genetic analysis results displayed that as protective factors, genetic variants of rs1801133 and rs1801394 were associated with the risk of ectoderm-, and endoderm-developed malformations, but only the variant of rs1801394 was associated with the risk of mesoderm-developed malformations. Our present study first related nutrition metabolism related gene variants to germ layers and provided a novel understanding of an implication of earlier causation of birth defects pathogenesis in humans.
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Affiliation(s)
- Qin Zhang
- Beijing Municipal Key Laboratory of Child Development Nutrigenomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Baoling Bai
- Beijing Municipal Key Laboratory of Child Development Nutrigenomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Xiaozhen Liu
- Beijing Municipal Key Laboratory of Child Development Nutrigenomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Chunyue Miao
- Beijing Municipal Key Laboratory of Child Development Nutrigenomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Huili Li
- Beijing Municipal Key Laboratory of Child Development Nutrigenomics, Capital Institute of Pediatrics, Beijing 100020, China
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A genetic association study detects haplotypes associated with obstructive heart defects. Hum Genet 2014; 133:1127-38. [PMID: 24894164 DOI: 10.1007/s00439-014-1453-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/20/2014] [Indexed: 10/25/2022]
Abstract
The development of congenital heart defects (CHDs) involves a complex interplay between genetic variants, epigenetic variants, and environmental exposures. Previous studies have suggested that susceptibility to CHDs is associated with maternal genotypes, fetal genotypes, and maternal-fetal genotype (MFG) interactions. We conducted a haplotype-based genetic association study of obstructive heart defects (OHDs), aiming to detect the genetic effects of 877 SNPs involved in the homocysteine, folate, and transsulfuration pathways. Genotypes were available for 285 mother-offspring pairs with OHD-affected pregnancies and 868 mother-offspring pairs with unaffected pregnancies. A penalized logistic regression model was applied with an adaptive least absolute shrinkage and selection operator (lasso), which dissects the maternal effect, fetal effect, and MFG interaction effects associated with OHDs. By examining the association between 140 haplotype blocks, we identified 9 blocks that are potentially associated with OHD occurrence. Four haplotype blocks, located in genes MGMT, MTHFS, CBS, and DNMT3L, were statistically significant using a Bayesian false-discovery probability threshold of 0.8. Two blocks in MGMT and MTHFS appear to have significant fetal effects, while the CBS and DNMT3L genes may have significant MFG interaction effects.
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Lucock M, Yates Z, Martin C, Choi JH, Boyd L, Tang S, Naumovski N, Furst J, Roach P, Jablonski N, Chaplin G, Veysey M. Vitamin D, folate, and potential early lifecycle environmental origin of significant adult phenotypes. EVOLUTION MEDICINE AND PUBLIC HEALTH 2014; 2014:69-91. [PMID: 24699387 PMCID: PMC4001294 DOI: 10.1093/emph/eou013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Solar radiation early in pregnancy interacts with light sensitive vitamins to influence an embryo's genetic profile. This influences both adult disease risk and may play a role in the evolution of skin colour. Background and objectives: Vitamin D and folate are highly UV sensitive, and critical for maintaining health throughout the lifecycle. This study examines whether solar irradiance during the first trimester of pregnancy influences vitamin D receptor (VDR) and nuclear folate gene variant occurrence, and whether affected genes influence late-life biochemical/clinical phenotypes. Methodology: 228 subjects were examined for periconceptional exposure to solar irradiance, variation in vitamin D/folate genes (polymerase chain reaction (PCR)), dietary intake (food frequency questionnaire (FFQ)) and important adult biochemical/clinical phenotypes. Results: Periconceptional solar irradiance was associated with VDR-BsmI (P = 0.0008wk7), TaqI (P = 0.0014wk7) and EcoRV (P = 0.0030wk6) variant occurrence between post-conceptional weeks 6–8, a period when ossification begins. Similar effects were detected for other VDR gene polymorphisms. Periconceptional solar irradiance was also associated with 19 bp del-DHFR (P = 0.0025wk6), and to a lesser extent C1420T-SHMT (P = 0.0249wk6), a folate-critical time during embryogenesis. These same genes were associated with several late-life phenotypes: VDR-BsmI, TaqI and ApaI determined the relationship between dietary vitamin D and both insulin (P < 0.0001/BB, 0.0007/tt and 0.0173/AA, respectively) and systolic blood pressure (P = 0.0290/Bb, 0.0299/Tt and 0.0412/AA, respectively), making them important early and late in the lifecycle. While these and other phenotype associations were found for the VDR variants, folate polymorphism associations in later-life were limited to C1420T-SHMT (P = 0.0037 and 0.0297 for fasting blood glucose and HbA1c levels, respectively). We additionally report nutrient–gene relationships with body mass index, thiol/folate metabolome, cognition, depression and hypertension. Furthermore, photoperiod at conception influenced occurrence of VDR-Tru9I and 2R3R-TS genotypes (P = 0.0120 and 0.0360, respectively). Conclusions and implications: Findings identify environmental and nutritional agents that may interact to modify gene–phenotype relationships across the lifecycle, offering new insight into human ecology. This includes factors related to both disease aetiology and the evolution of skin pigmentation.
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Affiliation(s)
- Mark Lucock
- School of Environmental and Life Sciences, Biomedical Sciences and Pharmacy, Maths and Physical Sciences, University of Newcastle, PO Box 127, Brush Road, Ourimbah, NSW 2258, Australia, The Pennsylvania State University, Anthropology Department, 409 Carpenter Building, University Park, PA 16802, USA, and Teaching and Research Unit, Central Coast Local Health District, PO Box 361, Gosford, NSW 2250, Australia
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Li M, Erickson SW, Hobbs CA, Li J, Tang X, Nick TG, Macleod SL, Cleves MA. Detecting maternal-fetal genotype interactions associated with conotruncal heart defects: a haplotype-based analysis with penalized logistic regression. Genet Epidemiol 2014; 38:198-208. [PMID: 24585533 DOI: 10.1002/gepi.21793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/18/2013] [Accepted: 01/02/2014] [Indexed: 01/10/2023]
Abstract
Nonsyndromic congenital heart defects (CHDs) develop during embryogenesis as a result of a complex interplay between environmental exposures, genetics, and epigenetic causes. Genetic factors associated with CHDs may be attributed to either independent effects of maternal or fetal genes, or the intergenerational interactions between maternal and fetal genes. Detecting gene-by-gene interactions underlying complex diseases is a major challenge in genetic research. Detecting maternal-fetal genotype (MFG) interactions and differentiating them from the maternal/fetal main effects has presented additional statistical challenges due to correlations between maternal and fetal genomes. Traditionally, genetic variants are tested separately for maternal/fetal main effects and MFG interactions on a single-locus basis. We conducted a haplotype-based analysis with a penalized logistic regression framework to dissect the genetic effect associated with the development of nonsyndromic conotruncal heart defects (CTD). Our method allows simultaneous model selection and effect estimation, providing a unified framework to differentiate maternal/fetal main effect from the MFG interaction effect. In addition, the method is able to test multiple highly linked SNPs simultaneously with a configuration of haplotypes, which reduces the data dimensionality and the burden of multiple testing. By analyzing a dataset from the National Birth Defects Prevention Study (NBDPS), we identified seven genes (GSTA1, SOD2, MTRR, AHCYL2, GCLC, GSTM3, and RFC1) associated with the development of CTDs. Our findings suggest that MFG interactions between haplotypes in three of seven genes, GCLC, GSTM3, and RFC1, are associated with nonsyndromic conotruncal heart defects.
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Affiliation(s)
- Ming Li
- Department of Pediatrics University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
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28
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Ouyang S, Liu Z, Li Y, Ma F, Wu J. Cystathionine beta-synthase 844ins68 polymorphism is unrelated to susceptibility to neural tube defects. Gene 2014; 535:119-23. [DOI: 10.1016/j.gene.2013.11.052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 11/04/2013] [Accepted: 11/22/2013] [Indexed: 01/05/2023]
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Murthy J, Lakkakula S, Gurramkonda VB, Pathapati RM, Maram R, Lakkakula BVKS. CBS c.844ins68 Polymorphism Frequencies in Control Populations: Implications on Nonsyndromic Cleft Lip With or Without Cleft Palate. Cleft Palate Craniofac J 2014; 52:49-53. [PMID: 24437588 DOI: 10.1597/13-051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common birth defect with substantial clinical and social impact. Folate deficiency is one of the factors that have been associated with increased risk for NSCLP. Polymorphisms in folate and homocysteine pathway genes may act as susceptibility factors. OBJECTIVE The objective of this study was to evaluate prevalence estimates of cystathionine beta-synthase (CBS) insertion of 68-bp (c.844ins68) polymorphisms and their correlation with NSCLP. MATERIAL AND METHODS A total of 236 unrelated individuals from seven Indian populations and an additional 355 cases with NSCLP and 357 controls without NSCLP were included in this study. We investigated the CBS c.844ins68 polymorphism in all samples. Genotyping was performed with polymerase chain reaction and electrophoresis. The data were statistically analyzed using the chi-square test. RESULTS The CBS c.844ins68 allele is present in six of the seven populations analyzed, and allele frequencies range from 1.5% in Balija to 9.1% in Sugali populations. The CBS c.844ins68 polymorphism showed a significant protective effect on NSCLP at both genotype (WW versus WI: odds ratio [OR] = 0.54, 95% confidence interval [CI] = 0.31 to 0.95, P = .149) and allele levels (W versus I: OR = 0.56, 95% CI = 0.32 to 0.96, P = .033). CONCLUSIONS The current study observed significant differences in the frequency of the CBS 844ins68 allele across populations. There is a significant association between CBS c.844ins68 polymorphism and cleft lip and palate in the Indian population. Additional studies are warranted to identify the functional variants in the genes controlling homocysteine as etiological contributors to the formation of oral clefts.
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Salih MA, Murshid WR, Seidahmed MZ. Classification, clinical features, and genetics of neural tube defects. Saudi Med J 2014; 35 Suppl 1:S5-S14. [PMID: 25551113 PMCID: PMC4362100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Neural tube defects (NTDs) constitute a major health burden (0.5-2/1000 pregnancies worldwide), and remain a preventable cause of still birth, neonatal, and infant death, or significant lifelong handicaps. The malformations result from failure of the neural folds to fuse in the midline, and form the neural tube between the third and the fourth week of embryonic development. This review article discusses their classification, clinical features, and genetics. Most NTDs are sporadic and both genetic, and non-genetic environmental factors are involved in its etiology. Consanguinity was suggested to contribute to the high incidence of NTDs in several countries, including Saudi Arabia. Syndromes, often associated with chromosomal anomalies, account for <10% of all NTDs; but a higher proportion (20%) has been documented in Saudi Arabia. Genetic predisposition constitutes the major underlying risk factor, with a strong implication of genes that regulate folate one-carbon metabolism and planar cell polarity.
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Affiliation(s)
- Mustafa A. Salih
- From the Division of Pediatric Neurology (Salih), Department of Pediatrics, the Division of Neurosurgery (Murshid), Department of Surgery, College of Medicine, King Saud University, and the Neonatology Unit (Seidahmed), Department of Pediatrics, Security Forces Hospital, Riyadh, Kingdom of Saudi Arabia.,Address correspondence and reprint request to: Prof. Mustafa A. M. Salih, Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, PO Box 2925, Riyadh 11461, Kingdom of Saudi Arabia. E-mail:
| | - Waleed R. Murshid
- From the Division of Pediatric Neurology (Salih), Department of Pediatrics, the Division of Neurosurgery (Murshid), Department of Surgery, College of Medicine, King Saud University, and the Neonatology Unit (Seidahmed), Department of Pediatrics, Security Forces Hospital, Riyadh, Kingdom of Saudi Arabia.
| | - Mohammed Z. Seidahmed
- From the Division of Pediatric Neurology (Salih), Department of Pediatrics, the Division of Neurosurgery (Murshid), Department of Surgery, College of Medicine, King Saud University, and the Neonatology Unit (Seidahmed), Department of Pediatrics, Security Forces Hospital, Riyadh, Kingdom of Saudi Arabia.
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Soldano KL, Garrett ME, Cope HL, Rusnak JM, Ellis NJ, Dunlap KL, Speer MC, Gregory SG, Ashley-Koch AE. Genetic association analyses of nitric oxide synthase genes and neural tube defects vary by phenotype. ACTA ACUST UNITED AC 2013; 98:365-73. [PMID: 24323870 DOI: 10.1002/bdrb.21079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/12/2013] [Indexed: 12/12/2022]
Abstract
Neural tube defects (NTDs) are caused by improper neural tube closure during the early stages of embryonic development. NTDs are hypothesized to have a complex genetic origin and numerous candidate genes have been proposed. The nitric oxide synthase 3 (NOS3) G594T polymorphism has been implicated in risk for spina bifida, and interactions between that single nucleotide polymorphism (SNP) and the methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism have also been observed. To evaluate other genetic variation in the NO pathway in the development of NTDs, we examined all three NOS genes: NOS1, NOS2, and NOS3. Using 3109 Caucasian samples in 745 families, we evaluated association in the overall dataset and within specific phenotypic subsets. Haplotype tagging SNPs in the NOS genes were tested for genetic association with NTD subtypes, both for main effects as well as for the presence of interactions with the MTHFR C677T polymorphism. Nominal main effect associations were found with all subtypes, across all three NOS genes, and interactions were observed between SNPs in all three NOS genes and MTHFR C677T. Unlike the previous report, the most significant associations in our dataset were with cranial subtypes and the AG genotype of rs4795067 in NOS2 (p = 0.0014) and the interaction between the rs9658490 G allele in NOS1 and MTHFR 677TT genotype (p = 0.0014). Our data extend the previous findings by implicating a role for all three NOS genes, independently and through interactions with MTHFR, in risk not only for spina bifida, but all NTD subtypes.
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Affiliation(s)
- Karen L Soldano
- Center for Human Genetics, Duke University Medical Center, Durham, North Carolina
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Imbard A, Benoist JF, Blom HJ. Neural tube defects, folic acid and methylation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2013; 10:4352-89. [PMID: 24048206 PMCID: PMC3799525 DOI: 10.3390/ijerph10094352] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 08/30/2013] [Accepted: 09/03/2013] [Indexed: 12/17/2022]
Abstract
Neural tube defects (NTDs) are common complex congenital malformations resulting from failure of the neural tube closure during embryogenesis. It is established that folic acid supplementation decreases the prevalence of NTDs, which has led to national public health policies regarding folic acid. To date, animal studies have not provided sufficient information to establish the metabolic and/or genomic mechanism(s) underlying human folic acid responsiveness in NTDs. However, several lines of evidence suggest that not only folates but also choline, B12 and methylation metabolisms are involved in NTDs. Decreased B12 vitamin and increased total choline or homocysteine in maternal blood have been shown to be associated with increased NTDs risk. Several polymorphisms of genes involved in these pathways have also been implicated in risk of development of NTDs. This raises the question whether supplementation with B12 vitamin, betaine or other methylation donors in addition to folic acid periconceptional supplementation will further reduce NTD risk. The objective of this article is to review the role of methylation metabolism in the onset of neural tube defects.
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Affiliation(s)
- Apolline Imbard
- Biochemistry-Hormonology Laboratory, Robert Debré Hospital, APHP, 48 bd Serrurier, Paris 75019, France; E-Mail:
- Metabolic Unit, Department of Clinical Chemistry, VU Free University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands; E-Mail:
| | - Jean-François Benoist
- Biochemistry-Hormonology Laboratory, Robert Debré Hospital, APHP, 48 bd Serrurier, Paris 75019, France; E-Mail:
| | - Henk J. Blom
- Metabolic Unit, Department of Clinical Chemistry, VU Free University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands; E-Mail:
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Moreno-Garcia MA, Rosenblatt DS, Jerome-Majewska LA. Vitamin B(12) metabolism during pregnancy and in embryonic mouse models. Nutrients 2013; 5:3531-50. [PMID: 24025485 PMCID: PMC3798919 DOI: 10.3390/nu5093531] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/10/2013] [Accepted: 08/23/2013] [Indexed: 11/16/2022] Open
Abstract
Vitamin B(12) (cobalamin, Cbl) is required for cellular metabolism. It is an essential coenzyme in mammals for two reactions: the conversion of homocysteine to methionine by the enzyme methionine synthase and the conversion of methylmalonyl-CoA to succinyl-CoA by the enzyme methylmalonyl-CoA mutase. Symptoms of Cbl deficiency are hematological, neurological and cognitive, including megaloblastic anaemia, tingling and numbness of the extremities, gait abnormalities, visual disturbances, memory loss and dementia. During pregnancy Cbl is essential, presumably because of its role in DNA synthesis and methionine synthesis; however, there are conflicting studies regarding an association between early pregnancy loss and Cbl deficiency. We here review the literature about the requirement for Cbl during pregnancy, and summarized what is known of the expression pattern and function of genes required for Cbl metabolism in embryonic mouse models.
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Affiliation(s)
- Maira A. Moreno-Garcia
- Department of Human Genetics, McGill University, 1205 Avenue Docteur Penfield, N5/13,Montreal, Quebec, Canada H3A 1B1; E-Mails: (M.A.M.-G.); (D.S.R.)
| | - David S. Rosenblatt
- Department of Human Genetics, McGill University, 1205 Avenue Docteur Penfield, N5/13,Montreal, Quebec, Canada H3A 1B1; E-Mails: (M.A.M.-G.); (D.S.R.)
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada H3H 1P3
| | - Loydie A. Jerome-Majewska
- Department of Human Genetics, McGill University, 1205 Avenue Docteur Penfield, N5/13,Montreal, Quebec, Canada H3A 1B1; E-Mails: (M.A.M.-G.); (D.S.R.)
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada H3H 1P3
- McGill University Health Centre, 4060 Ste. Catherine West, PT 420, Montreal, Quebec, Canada H3Z 2Z3
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-514-412-4400 (ext. 23279); Fax: +1-514-412-4331
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Rai V, Yadav U, Kumar P, Yadav SK. Analysis of methionine synthase reductase polymorphism (A66G) in Indian Muslim population. INDIAN JOURNAL OF HUMAN GENETICS 2013; 19:183-7. [PMID: 24019620 PMCID: PMC3758725 DOI: 10.4103/0971-6866.116123] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND AND OBJECTIVES: Methionine synthase reductase (MTRR) is a vital enzyme of homocysteine/methionine metabolic pathway and is required for the conversion of inactive form of methionine synthase (MTR) to its active form. A clinically important allelic variant of MTRR A66G, with less enzymatic activity is reported with worldwide prevalence rate of ~ 30%. The present study was designed to determine the frequency of MTRR A66G polymorphism in rural Sunni Muslim population of Eastern Uttar Pradesh. MATERIALS AND METHODS: Total 56 subjects were analyzed for MTRR A66G polymorphism. A66G mutation analysis was carried out according to the polymerase chain reaction-restriction fragment length polymorphism method of Wilson et al.
[1] amplification with MTRR specific primers followed by amplicon digestion with NdeI enzyme was used for the identification of different MTRR genotypes in subjects. RESULTS AND DISCUSSION: The AA genotype was found in 5 subjects, AG in 23 subjects, and GG genotype in 28 subjects. Genotype frequencies of AA, AG, and GG were 0.089, 0.41, and 0.5 respectively. The allele frequency of A allele was found to be 0.298 and G allele was 0.705. CONCLUSION: It is evident from the present study that the percentage of homozygous genotype GG and frequency of G allele is high in the target Muslim population.
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Affiliation(s)
- Vandana Rai
- Human Molecular Genetics Laboratory, Department of Biotechnology, VBS Purvanchal University, Jaunpur, Uttar Pradesh, India
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Zhang T, Lou J, Zhong R, Wu J, Zou L, Sun Y, Lu X, Liu L, Miao X, Xiong G. Genetic variants in the folate pathway and the risk of neural tube defects: a meta-analysis of the published literature. PLoS One 2013; 8:e59570. [PMID: 23593147 PMCID: PMC3617174 DOI: 10.1371/journal.pone.0059570] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 02/18/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Neural Tube Defects (NTDs) are among the most prevalent and most severe congenital malformations worldwide. Polymorphisms in key genes involving the folate pathway have been reported to be associated with the risk of NTDs. However, the results from these published studies are conflicting. We surveyed the literature (1996-2011) and performed a comprehensive meta-analysis to provide empirical evidence on the association. METHODS AND FINDINGS We investigated the effects of 5 genetic variants from 47 study populations, for a total of 85 case-control comparisons MTHFR C677T (42 studies; 4374 cases, 7232 controls), MTHFR A1298C (22 studies; 2602 cases, 4070 controls), MTR A2756G (9 studies; 843 cases, 1006 controls), MTRR A66G (8 studies; 703 cases, 1572 controls), and RFC-1 A80G (4 studies; 1107 cases, 1585 controls). We found a convincing evidence of dominant effects of MTHFR C677T (OR 1.23; 95%CI 1.07-1.42) and suggestive evidence of RFC-1 A80G (OR 1.55; 95%CI 1.24-1.92). However, we found no significant effects of MTHFR A1298C, MTR A2756G, MTRR A66G in risk of NTDs in dominant, recessive or in allelic models. CONCLUSIONS Our meta-analysis strongly suggested a significant association of the variant MTHFR C677T and a suggestive association of RFC-1 A80G with increased risk of NTDs. However, other variants involved in folate pathway do not demonstrate any evidence for a significant marginal association on susceptibility to NTDs.
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Affiliation(s)
- Ti Zhang
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiao Lou
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Wu
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Zou
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Sun
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuzai Lu
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guanglian Xiong
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Ouyang S, Liu Z, Li Y, Wu J. Meta-analyses on the association of MTR A2756G and MTRR A66G polymorphisms with neural tube defect risks in Caucasian children. J Matern Fetal Neonatal Med 2013; 26:1166-70. [PMID: 23425389 DOI: 10.3109/14767058.2013.777699] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Methionine synthase (MTR) and MTR reductase (MTRR) genes have been considered to be implicated in the development of neural tube defects (NTDs). The associations between MTR A2756G and MTRR A66G polymorphisms and NTD risk in children have been investigated in many studies. However, results are inconsistent. Accordingly, we conducted meta-analyses to further investigate such associations. METHODS Published literatures were obtained from PubMed and Embase databases. All studies evaluating the association between MTR A2756G or MTRR A66G polymorphism and infant NTDs were included. Pooled odds ratio with a 95% confidence interval was calculated using fixed or random-effects model. RESULTS A total of 13 studies (1298 cases and 2237 controls) on MTR A2756G polymorphism and 10 studies (1358 cases and 2169 controls) on MTRR A66G polymorphism were included. Meta-analyses reveal no significant association of MTR A2756G and MTRR A66G polymorphisms with risk for NTDs in Caucasian children in either the genetic model or allele model. CONCLUSIONS The present meta-analyses indicate that MTR A2756G and MTRR A66G polymorphism are not associated with NTD risks in Caucasian children.
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Affiliation(s)
- Shengrong Ouyang
- Department of Biochemistry, Capital Institute of Pediatrics, Beijing 100020, China
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Ouyang S, Li Y, Liu Z, Chang H, Wu J. Association between MTR A2756G and MTRR A66G polymorphisms and maternal risk for neural tube defects: A meta-analysis. Gene 2013; 515:308-12. [DOI: 10.1016/j.gene.2012.11.070] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Revised: 07/13/2012] [Accepted: 11/29/2012] [Indexed: 01/16/2023]
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Abstract
Genetic disturbances in folate metabolism may increase risk for congenital heart defects. We examined the association of heart defects with four polymorphisms in folate-related genes (methylenetetrahydrofolate reductase (MTHFR) c.677C.T, MTHFR c.1298A.C, methionine synthase reductase (MTRR) c.66A.G, and reduced folate carrier (SLC19A1) c.80A.G) in a case-control study of children (156 patients, 69 controls) and mothers of children with heart defects (181 patients, 65 controls), born before folic acid fortification. MTRR c.66A.G in children modified odds ratios for overall heart defects, specifically ventricular septal defect and aortic valve stenosis (p-value below 0.05). The 66GG and AG genotypes were associated with decreased odds ratios for heart defects (0.42, 95% confidence interval (0.18-0.97) and 0.39 (0.18-0.84), respectively). This overall association was driven by decreased risk for ventricular septal defect for 66GG and AG (odds ratio 0.32 (0.11-0.91) and 0.25 (0.09-0.65)) and decreased odds ratio for aortic valve stenosis for 66AG (0.27 (0.09-0.79)). The association of ventricular septal defect and 66AG remained significant after correction for multiple testing (p = 0.0044, multiple testing threshold p = 0.0125). Maternal MTHFR 1298AC genotype was associated with increased odds ratio for aortic valve stenosis (2.90 (1.22-6.86), p = 0.0157), but this association did not meet the higher multiple testing threshold. No association between MTHFR c.677C.T or SLC19A1 c.80A.G and heart defect risk was found. The influence of folate-related polymorphisms may be specific to certain types of heart defects; larger cohorts of mothers and children with distinct sub-classes are required to adequately address risk.
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Kirsch SH, Herrmann W, Obeid R. Genetic defects in folate and cobalamin pathways affecting the brain. Clin Chem Lab Med 2013. [DOI: 10.1515/cclm-2012-0673] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Yan L, Zhao L, Long Y, Zou P, Ji G, Gu A, Zhao P. Association of the maternal MTHFR C677T polymorphism with susceptibility to neural tube defects in offsprings: evidence from 25 case-control studies. PLoS One 2012; 7:e41689. [PMID: 23056169 PMCID: PMC3463537 DOI: 10.1371/journal.pone.0041689] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 06/25/2012] [Indexed: 01/06/2023] Open
Abstract
Background Methylenetetrahydrofolate reductase (MTHFR) is a critical enzyme in folate metabolism and is involved in DNA methylation, DNA synthesis, and DNA repair. In addition, it is a possible risk factor in neural tube defects (NTDs). The association of the C677T polymorphism in the MTHFR gene and NTD susceptibility has been widely demonstrated, but the results remain inconclusive. In this study, we performed a meta-analysis with 2429 cases and 3570 controls to investigate the effect of the MTHFR C677T polymorphism on NTDs. Methods An electronic search of PubMed and Embase database for papers on the MTHFR C677T polymorphism and NTD risk was performed. All data were analysed with STATA (version 11). Odds ratios (ORs) with 95% confidence intervals (CIs) were estimated to assess the association. Sensitivity analysis, test of heterogeneity, cumulative meta-analysis, and assessment of bias were performed in our meta-analysis. Results A significant association between the MTHFR C677T polymorphism and NTD susceptibility was revealed in our meta-analysis ( TT versus CC: OR = 2.022, 95% CI: 1.508, 2.712; CT+TT versus CC: OR = 1.303, 95% CI: 1.089, 1.558; TT versus CC+CT: OR = 1.716, 95% CI: 1.448, 2.033; 2TT+CT versus 2CC+CT: OR = 1.330, 95% CI: 1.160, 1.525). Moreover, an increased NTD risk was found after stratification of the MTHFR C677T variant data by ethnicity and source of controls. Conclusion The results suggested the maternal MTHFR C677T polymorphism is a genetic risk factor for NTDs. Further functional studies to investigate folate-related gene polymorphisms, periconceptional multivitamin supplements, complex interactions, and the development of NTDs are warranted.
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Affiliation(s)
- Lifeng Yan
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lin Zhao
- Department of Neurosurgery, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Yan Long
- Department of Pharmacology, China Pharmaceutical University, Nanjing, China
| | - Peng Zou
- Department of Neurosurgery, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Guixiang Ji
- Nanjing Institute of Environmental Sciences/Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Ministry of Environmental Protection, Nanjing, China
| | - Aihua Gu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
- * E-mail: (AG); (PZ)
| | - Peng Zhao
- Department of Neurosurgery, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
- * E-mail: (AG); (PZ)
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Alfarra HY, Alfarra SR, Sadiq MF. Neural tube defects between folate metabolism and genetics. INDIAN JOURNAL OF HUMAN GENETICS 2012; 17:126-31. [PMID: 22345982 PMCID: PMC3276979 DOI: 10.4103/0971-6866.92082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Neural tube defects (NTDs) are the second most common severely disabling human congenital defects. Worldwide, NTDs incidence is approximately one per 1000 live births and varies between 0.78 and 12 per 1000 births in general populations. NTDs causation involves multiple genes, nutritional and environmental factors. Research in the next stage should include bigger populations and bigger studies that would be suitable to detect significant links and conclusions with relatively minor risk factors; analysis of multiple candidate genes to detect potential gene-gene interactions; detailed analysis of patient samples stratified by phenotype.
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Affiliation(s)
- Helmi Y Alfarra
- Department of Biological Sciences, Yarmouk University, Irbid, Jordan
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Wang HG, Wang JL, Zhang J, Zhao LX, Zhai GX, Xiang YZ, Chang P. Reduced folate carrier A80G polymorphism and susceptibility to neural tube defects: a meta-analysis. Gene 2012; 510:180-4. [PMID: 22975209 DOI: 10.1016/j.gene.2012.02.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 02/08/2012] [Accepted: 02/16/2012] [Indexed: 10/27/2022]
Abstract
The reduced folate carrier (RFC1) plays a crucial role in mediating folate delivery into a variety of cells. RFC1 polymorphism (A80G) has been reported to be associated with increased risk of neural tube defects (NTDs). However, results derived from individually underpowered studies are conflicting. We performed a systematic search of MEDLINE and EMBASE databases and carried out a meta-analysis on the association between RFC1 polymorphism (A80G) and NTDs risk. Overall, a significant correlation between RFC1 A80G polymorphism and NTDs risk was found neither in infants nor in maternal (allele contrast in infants: OR(RE)=1.15, 95% CI: 0.92-1.45; allele contrast in mothers: OR(RE)=1.24, 95% CI: 0.98-1.56). The present meta-analysis failed to support a positive association between RFC1 A80G polymorphism and susceptibility to NTDs. It is important to realize, however, that socio-economic factors, and gene-environment and gene-gene interactions, could have influenced the outcome of our meta-analysis. For this reason, a relationship between the A80G polymorphism and NTD risk cannot be entirely discounted.
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Affiliation(s)
- Hai-Gang Wang
- Department of Pharmacy, Qilu Hospital, Shandong University, Jinan, China
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Pangilinan F, Molloy AM, Mills JL, Troendle JF, Parle-McDermott A, Signore C, O'Leary VB, Chines P, Seay JM, Geiler-Samerotte K, Mitchell A, VanderMeer JE, Krebs KM, Sanchez A, Cornman-Homonoff J, Stone N, Conley M, Kirke PN, Shane B, Scott JM, Brody LC. Evaluation of common genetic variants in 82 candidate genes as risk factors for neural tube defects. BMC MEDICAL GENETICS 2012; 13:62. [PMID: 22856873 PMCID: PMC3458983 DOI: 10.1186/1471-2350-13-62] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 07/13/2012] [Indexed: 12/17/2022]
Abstract
BACKGROUND Neural tube defects (NTDs) are common birth defects (~1 in 1000 pregnancies in the US and Europe) that have complex origins, including environmental and genetic factors. A low level of maternal folate is one well-established risk factor, with maternal periconceptional folic acid supplementation reducing the occurrence of NTD pregnancies by 50-70%. Gene variants in the folate metabolic pathway (e.g., MTHFR rs1801133 (677 C > T) and MTHFD1 rs2236225 (R653Q)) have been found to increase NTD risk. We hypothesized that variants in additional folate/B12 pathway genes contribute to NTD risk. METHODS A tagSNP approach was used to screen common variation in 82 candidate genes selected from the folate/B12 pathway and NTD mouse models. We initially genotyped polymorphisms in 320 Irish triads (NTD cases and their parents), including 301 cases and 341 Irish controls to perform case-control and family based association tests. Significantly associated polymorphisms were genotyped in a secondary set of 250 families that included 229 cases and 658 controls. The combined results for 1441 SNPs were used in a joint analysis to test for case and maternal effects. RESULTS Nearly 70 SNPs in 30 genes were found to be associated with NTDs at the p < 0.01 level. The ten strongest association signals (p-value range: 0.0003-0.0023) were found in nine genes (MFTC, CDKN2A, ADA, PEMT, CUBN, GART, DNMT3A, MTHFD1 and T (Brachyury)) and included the known NTD risk factor MTHFD1 R653Q (rs2236225). The single strongest signal was observed in a new candidate, MFTC rs17803441 (OR = 1.61 [1.23-2.08], p = 0.0003 for the minor allele). Though nominally significant, these associations did not remain significant after correction for multiple hypothesis testing. CONCLUSIONS To our knowledge, with respect to sample size and scope of evaluation of candidate polymorphisms, this is the largest NTD genetic association study reported to date. The scale of the study and the stringency of correction are likely to have contributed to real associations failing to survive correction. We have produced a ranked list of variants with the strongest association signals. Variants in the highest rank of associations are likely to include true associations and should be high priority candidates for further study of NTD risk.
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Affiliation(s)
- Faith Pangilinan
- Molecular Pathogenesis Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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McKay JA, Groom A, Potter C, Coneyworth LJ, Ford D, Mathers JC, Relton CL. Genetic and non-genetic influences during pregnancy on infant global and site specific DNA methylation: role for folate gene variants and vitamin B12. PLoS One 2012; 7:e33290. [PMID: 22479380 PMCID: PMC3316565 DOI: 10.1371/journal.pone.0033290] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 02/06/2012] [Indexed: 01/17/2023] Open
Abstract
Inter-individual variation in patterns of DNA methylation at birth can be explained by the influence of environmental, genetic and stochastic factors. This study investigates the genetic and non-genetic determinants of variation in DNA methylation in human infants. Given its central role in provision of methyl groups for DNA methylation, this study focuses on aspects of folate metabolism. Global (LUMA) and gene specific (IGF2, ZNT5, IGFBP3) DNA methylation were quantified in 430 infants by Pyrosequencing®. Seven polymorphisms in 6 genes (MTHFR, MTRR, FOLH1, CβS, RFC1, SHMT) involved in folate absorption and metabolism were analysed in DNA from both infants and mothers. Red blood cell folate and serum vitamin B12 concentrations were measured as indices of vitamin status. Relationships between DNA methylation patterns and several covariates viz. sex, gestation length, maternal and infant red cell folate, maternal and infant serum vitamin B12, maternal age, smoking and genotype were tested. Length of gestation correlated positively with IGF2 methylation (rho = 0.11, p = 0.032) and inversely with ZNT5 methylation (rho = −0.13, p = 0.017). Methylation of the IGFBP3 locus correlated inversely with infant vitamin B12 concentration (rho = −0.16, p = 0.007), whilst global DNA methylation correlated inversely with maternal vitamin B12 concentrations (rho = 0.18, p = 0.044). Analysis of common genetic variants in folate pathway genes highlighted several associations including infant MTRR 66G>A genotype with DNA methylation (χ2 = 8.82, p = 0.003) and maternal MTHFR 677C>T genotype with IGF2 methylation (χ2 = 2.77, p = 0.006). These data support the hypothesis that both environmental and genetic factors involved in one-carbon metabolism influence DNA methylation in infants. Specifically, the findings highlight the importance of vitamin B12 status, infant MTRR genotype and maternal MTHFR genotype, all of which may influence the supply of methyl groups for DNA methylation. In addition, gestational length appears to be an important determinant of infant DNA methylation patterns.
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Affiliation(s)
- Jill A McKay
- Institute for Ageing and Health, Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, Tyne and Wear, United Kingdom.
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Wang XW, Luo YL, Wang W, Zhang Y, Chen Q, Cheng YL. Association between MTHFR A1298C polymorphism and neural tube defect susceptibility: a metaanalysis. Am J Obstet Gynecol 2012; 206:251.e1-7. [PMID: 22265089 DOI: 10.1016/j.ajog.2011.12.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 11/29/2011] [Accepted: 12/19/2011] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To determine whether 5,10-methylenetetrahydrofolate reductase A1298C polymorphism is associated with neural tube defect susceptibility. STUDY DESIGN Computerized literature searches of the PubMed, Embase, and Medline database were conducted to identify all eligible articles. Study subjects were classified as neural tube defect patients, mothers with neural tube defect offspring and fathers with neural tube defect offspring. The pooled odds ratios with 95% confidence interval (CI) were calculated by fixed-effects model or random-effects model. RESULTS Twenty-three case-control studies were finally included. The pooled results showed no significant association between 5,10-methylenetetrahydrofolate reductase A1298C polymorphism and neural tube defect susceptibility in any genetic contrast among the 3 groups, except 1 (AC vs AA in neural tube defect patients: odds ratio, 1.16; 95% CI, 1.10-1.32; P = .03), which, however, turned out to be of no statistical significance in the subgroup of the white population (odds ratio, 1.14; 95% CI, 0.98-1.31; P = .08). CONCLUSION This metaanalysis suggests that 5,10-methylenetetrahydrofolate reductase A1298C polymorphism is not associated with neural tube defect susceptibility in the white population.
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Köşüş N, Köşüş A, Hızlı D, Bitirgen EÜ, Turhan NÖ. Can serum ferritin, vitamin B12and folic acid levels affect serum screening tests during pregnancy? J Matern Fetal Neonatal Med 2012; 25:1674-7. [DOI: 10.3109/14767058.2012.657276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Effect on risk of anencephaly of gene-nutrient interactions between methylenetetrahydrofolate reductase C677T polymorphism and maternal folate, vitamin B12 and homocysteine profile. Public Health Nutr 2012; 15:1419-28. [PMID: 22230335 DOI: 10.1017/s136898001100334x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
OBJECTIVE To evaluate the effects on anencephaly risk of the interaction between the maternal profile of folate, vitamin B12 and homocysteine and the 677C→T polymorphism in the gene encoding methylenetetrahydrofolate reductase (MTHFR). DESIGN Case-control study paired (1:1) on maternity clinic, date of birth and state of residence. Cases of anencephaly were identified using the Registry of the Mexican Neural Tube Defect Epidemiological Surveillance System. Case and control mothers were selected from the same maternity departments. All mothers completed a structured questionnaire and blood samples were obtained to determine the MTHFR 677C→T polymorphism and biochemical profile. SETTING Mexico, Puebla and Guerrero states, Mexico. SUBJECTS A total of 151 mothers of cases and controls were enrolled from March 2000 to February 2001. We had complete information on biochemical profile and MTHFR C677T polymorphism for ninety-eight mothers of cases and ninety-one mothers of controls. RESULTS The adjusted models show that the risk of anencephaly in mothers with 677TT genotype was reduced by 18 % (OR = 0·82; 95 % CI 0·72, 0·94) for each 1 ng/ml increment in serum folate. In terms of tertiles, mothers with 677TT genotype with serum folate levels in the upper tertile (>14·1 ng/ml) had a 95 % lower risk to have a child with anencephaly than mothers with serum folate levels in the first and second tertiles (P trend = 0·012). CONCLUSIONS Our data agree with the hypothesis of a gene-nutrient interaction between MTHFR 677C→T polymorphism and folate status. We observed a protective effect on anencephaly risk only in mothers with 677TT genotype as serum folate levels increased.
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Weiner AS, Boyarskikh UA, Voronina EN, Selezneva IA, Sinkina TV, Lazarev AF, Petrova VD, Filipenko ML. Polymorphisms in the folate-metabolizing genes MTR, MTRR, and CBS and breast cancer risk. Cancer Epidemiol 2012; 36:e95-e100. [PMID: 22236648 DOI: 10.1016/j.canep.2011.11.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/28/2011] [Accepted: 11/30/2011] [Indexed: 01/14/2023]
Abstract
Alterations in the nucleotide sequences of folate-metabolizing genes can increase the risk of malignant transformation. The aim of our study was to investigate the association of three single-nucleotide polymorphisms (SNPs) in the folate-metabolizing genes - A2756G MTR, A66G MTRR, and 844ins68 CBS - which have putative functional significance in breast cancer risk. The allele and genotype frequencies of the SNPs were determined in a case group (840 women with sporadic breast cancer) and a control group (770 women). No statistically significant association of studied SNPs with breast cancer was revealed. A meta-analysis, which included data obtained from the literature and the present research, did not reveal any statistically significant associations of these SNPs with breast cancer. The results obtained provide evidence that these SNPs are not involved in the development of breast cancer.
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Affiliation(s)
- Alexandra S Weiner
- Institute of Chemical Biology and Fundamental Medicine, Group of Pharmacogenomics, Novosibirsk, Russia.
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Tokuda Y, Yagi T, Yoshii K, Ikeda Y, Fuwa M, Ueno M, Nakano M, Omi N, Tanaka M, Mori K, Kageyama M, Nagasaki I, Yagi K, Kinoshita S, Tashiro K. An approach to predict the risk of glaucoma development by integrating different attribute data. SPRINGERPLUS 2012; 1:41. [PMID: 23961367 PMCID: PMC3725912 DOI: 10.1186/2193-1801-1-41] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 10/15/2012] [Indexed: 11/10/2022]
Abstract
Primary open-angle glaucoma (POAG) is one of the major causes of blindness worldwide and considered to be influenced by inherited and environmental factors. Recently, we demonstrated a genome-wide association study for the susceptibility to POAG by comparing patients and controls. In addition, the serum cytokine levels, which are affected by environmental and postnatal factors, could be also obtained in patients as well as in controls, simultaneously. Here, in order to predict the effective diagnosis of POAG, we developed an “integration approach” using different attribute data which were integrated simply with several machine learning methods and random sampling. Two data sets were prepared for this study. The one is the “training data set”, which consisted of 42 POAG and 42 controls. The other is the “test data set” consisted of 73 POAG and 52 controls. We first examined for genotype and cytokine data using the training data set with general machine learning methods. After the integration approach was applied, we obtained the stable accuracy, using the support vector machine method with the radial basis function. Although our approach was based on well-known machine learning methods and a simple process, we demonstrated that the integration with two kinds of attributes, genotype and cytokines, was effective and helpful in diagnostic prediction of POAG.
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Affiliation(s)
- Yuichi Tokuda
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kajiicho 465, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto, 602-8566 Japan
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Abstract
The vitamin folate functions within the cell as a carrier of one-carbon units. The requirement for one-carbon transfers is ubiquitous and all mammalian cells carry out folate dependent reactions. In recent years, low folate status has been linked to risk of numerous adverse health conditions throughout life from birth defects and complications of pregnancy to cardiovascular disease, cancer and cognitive dysfunction in the elderly. In many instances inadequate intake of folate seems to be the primary contributor but there is also evidence that an underlying genetic susceptibility can play a modest role by causing subtle alterations in the availability, metabolism or distribution of intermediates in folate related pathways. Folate linked one-carbon units are essential for DNA synthesis and repair and as a source of methyl groups for biological methylation reactions. The notion of common genetic variants being linked to risk of disease was relatively novel in 1995 when the first functional folate-related polymorphism was discovered. Numerous polymorphisms have now been identified in folate related genes and have been tested for functionality either as a modifier of folate status or as being associated with risk of disease. Moreover, there is increasing research into the importance of folate-derived one-carbon units for DNA and histone methylation reactions, which exert crucial epigenetic control over cellular protein synthesis. It is thus becoming clear that genetic aspects of folate metabolism are wide-ranging and may touch on events as disparate as prenatal imprinting to cancer susceptibility. This chapter will review the current knowledge in this area.
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Affiliation(s)
- Anne M Molloy
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland,
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