B-vitamins, genotype and disease causality: Symposium on ‘Genetic polymorphisms and disease risk’

Comparison of TCN-2 (776C>G) Gene Polymorphism and Vitamin B12 Status with Different Body Mass Index among Saudi Adults

BACKGROUND

Overweight and obesity (OO) are significant public health issues, and many elements, including genetics, epigenetics, sedentary lifestyle, comorbid conditions, psychological and environmental pressures, have been linked to OO. More than 2 billion people are presently impacted by the global obesity epidemic, which is still advancing relentlessly. It is a significant public health concern and a major contributor to healthcare costs, because it increases the chance of developing conditions such as heart disease, stroke, type 2 diabetes, and chronic kidney disease (CKD). Using the ranges of 18.5-25 for normality, 25-30 for overweight, and 30 for obesity, BMI (in kg/m²) is used to identify obesity. Vitamin deficiency is one of the causative factors associated with the increasing trend of obesity. Altered vitamin B12 status is a multifactorial trait; changes in B12 status are produced by several single nucleotide polymorphisms (SNPs) in various genes that interact with the environment. They also support coordinated efforts to alter the built environment that is causing the obesity pandemic. Therefore, the present study aimed to evaluate the TCN-2 (776C>G) gene alteration and vitamin B12 levels with respect to different body mass index, as well as associating BMI with other biochemical parameters.

METHODS

250 individuals were involved in the study; among them, 100 were in the healthy weight range category (BMI: 18.5 to <25 kg/m²), 100 were overweight (BMI: 25.0 to <30 kg/m²), and 50 were obese (BMI: >30 kg/m²). Participants visited during the screening program were subjected to blood pressure measurement, and further peripheral blood samples were drawn from all the participants in plain as well as in EDTA vials for biochemical (lipid profile and vitamin B12 level) analysis and single nucleotide polymorphism studies. Extracted DNA from whole blood collected in EDTA vials using kit protocol was used for genotyping by PCR-RFLP.

RESULTS

The levels of systolic (p < 0.0001) and diastolic blood pressures (p < 0.0001), HDL (p < 0.0001), LDL (p = 0.04), TG (p < 0.0001), cholesterol (p < 0.0001), and VLDL (p < 0.0001) showed significant differences between healthy controls, overweight, and obese groups. The healthy control TCN-2 (776C>G) genotypes were compared with those of overweight and obese participants, and compared to the healthy controls it was observed that overweight (p = 0.01) and obese (p = 0.002) subjects had significant differences in TCN-2 (776C>G) genotypes. For genotypes CG and GG, the odds ratio was 1.61 (0.87-2.95; p = 0.12), and 3.81 (1.47-9.88; p = 0.005) for overweight participants, respectively, and obese participants' calculated odds ratios were 2.49 (1.16-5.36; p = 0.01) and 5.79 (1.93-17.35; p = 0.001), respectively. The relative risk for genotypes CG and GG, was 1.25 (0.93-1.68; p = 0.12), 2.17 (1.12-4.17; p = 0.02) for overweight participants, while the obese participants' calculated relative risks were 1.31 (1.03-1.68; p = 0.01) and 2.02 (1.12-3.65; p = 0.001), respectively. Vitamin B12 levels were analyzed, and it was observed that a significant difference existed among overweight (305.5 pmol/L, p < 0.0001) and obese patients (229 pmol/L, p < 0.0001), respectively, as compared to healthy controls (385.5 pmol/L). Correlation analysis showed a significant association of vitamin B12 level with TG, cholesterol and VLDL; it showed a negative correlation, suggesting that decreases in B12 levels may impact the lipid profile.

CONCLUSION

The study concluded that a predisposition to the GG genotype of TCN-2 gene polymorphism (776C>G) may increase susceptibility to obesity and the related complications, and higher odds and relative risk for the GG genotype may increase the risk of having obesity and further related complications. Lower vitamin B12 levels were linked with obesity and overweight, and impaired lipid parameters suggested that lower vitamin B12 may impact the altered lipid profile.

Contribution of genetic ancestry and polygenic risk score in meeting vitamin B12 needs in healthy Brazilian children and adolescents

Polymorphisms in genes related to the metabolism of vitamin B12 haven’t been examined in a Brazilian population. To (a) determine the correlation between the local genetic ancestry components and vitamin B12 levels using ninety B12-related genes; (b) determine associations between these genes and their SNPs with vitamin B12 levels; (c) determine a polygenic risk score (PRS) using significant variants. This cross-sectional study included 168 children and adolescents, aged 9–13 years old. Total cobalamin was measured in plasma. Genotyping arrays and whole exome data were combined to yield ~ 7000 SNPs in 90 genes related to vitamin B12. The Efficient Local Ancestry Inference was used to estimate local ancestry for African (AFR), Native American, and European (EUR). The association between the genotypes and vitamin B12 levels were determined with generalized estimating equation. Vitamin B12 levels were driven by positive (EUR) and negative (AFR, AMR) correlations with genetic ancestry. A set of 36 variants were used to create a PRS that explained 42% of vitamin level variation. Vitamin B12 levels are influenced by genetic ancestry and a PRS explained almost 50% of the variation in plasma cobalamin in Brazilian children and adolescents.

Ethnicity influences total serum vitamin B12 concentration: a study of Black, Asian and White patients in a primary care setting

AIMS

A growing body of evidence suggests that ethnicity and race influence vitamin B₁₂ metabolism and status yet clinical awareness of this is poor, causing doubts regarding diagnosis and treatment. Moreover, deficiency and insufficiency cut-offs are universally applied for this test in most diagnostic settings. The objective of this study was to assess serum vitamin B₁₂ concentrations in Black, Asian and White primary care patients in London, UK, particularly in patients of Black or Black British ethnic origin and establish if there is a need for specific reference ranges.

METHODS

Serum B₁₂ results from 49 414 patients were processed between January 2018 and November 2019 using the Architect assay (Abbott Diagnostics) at St. Thomas' Hospital, London, UK. Age, sex and ethnicity data were collected from the laboratory Health Informatics Team.

RESULTS

Black patients (n=13 806) were found to have significantly higher serum vitamin B₁₂ concentration across all age groups and both sexes, especially Nigerian patients (median B₁₂ 505 pmol/L,IQR: 362-727, n=891), compared with Asian and White ethnic groups (p<0.001). Binary logistic regression analysis revealed that the Black or Black British ethnic group had the strongest association with elevated serum B₁₂ (>652 pmol/L) (adjusted OR 3.38, 95% CI 3.17 to 3.61, p<0.0001).

CONCLUSIONS

It is likely that a combination of genetic and acquired/environmental factors are responsible for the ethnic differences in serum B₁₂. This suggests that there is a need for ethnic-specific reference ranges with indications for the incorporation of age and sex too.

Cubilin, the Intrinsic Factor-Vitamin B12 Receptor in Development and Disease

Gp280/Intrinsic factor-vitamin B12 receptor/Cubilin (CUBN) is a large endocytic receptor serving multiple functions in vitamin B12 homeostasis, renal reabsorption of protein or toxic substances including albumin, vitamin D-binding protein or cadmium. Cubilin is a peripheral membrane protein consisting of 8 Epidermal Growth Factor (EGF)-like repeats and 27 CUB (defined as Complement C1r/C1s, Uegf, BMP1) domains. This structurally unique protein interacts with at least two molecular partners, Amnionless (AMN) and Lrp2/Megalin. AMN is involved in appropriate plasma membrane transport of Cubilin whereas Lrp2 is essential for efficient internalization of Cubilin and its ligands. Observations gleaned from animal models with Cubn deficiency or human diseases demonstrate the importance of this protein. In this review addressed to basic research and medical scientists, we summarize currently available data on Cubilin and its implication in renal and intestinal biology. We also discuss the role of Cubilin as a modulator of Fgf8 signaling during embryonic development and propose that the Cubilin-Fgf8 interaction may be relevant in human pathology, including in cancer progression, heart or neural tube defects. We finally provide experimental elements suggesting that some aspects of Cubilin physiology might be relevant in drug design.

Nutrigenomic Information in the openEHR Data Set

BACKGROUND

The traditional concept of personalized nutrition is based on adapting diets according to individual needs and preferences. Discussions about personalized nutrition have been on since the Human Genome Project, which has sequenced the human genome. Thenceforth, topics such as nutrigenomics have been assessed to help in better understanding the genetic variation influence on the dietary response and association between nutrients and gene expression. Hence, some challenges impaired the understanding about the nowadays important clinical data and about clinical data assumed to be important in the future.

OBJECTIVE

Finding the main clinical statements in the personalized nutrition field (nutrigenomics) to create the future-proof health information system to the openEHR server based on archetypes, as well as a specific nutrigenomic template.

METHODS

A systematic literature search was conducted in electronic databases such as PubMed. The aim of this systemic review was to list the chief clinical statements and create archetype and templates for openEHR modeling tools, namely, Ocean Archetype Editor and Ocean Template Design.

RESULTS

The literature search led to 51 articles; however, just 26 articles were analyzed after all the herein adopted inclusion criteria were assessed. Of these total, 117 clinical statements were identified, as well as 27 archetype-friendly concepts. Our group modeled four new archetypes (waist-to-height ratio, genetic test results, genetic summary, and diet plan) and finally created the specific nutrigenomic template for nutrition care.

CONCLUSION

The archetypes and the specific openEHR template developed in this study gave dieticians and other health professionals an important tool to their nutrigenomic clinical practices, besides a set of nutrigenomic data to clinical research.

Modulation of hepatic gene expression profiles by vitamin B1, vitamin B2, and niacin supplementation in mice exposed to acute hypoxia

This study was aimed to observe the effects of vitamin B₁, vitamin B₂, and niacin supplementation on hepatic gene expression profiles in mice exposed to acute hypoxia. Thirty mice were randomly divided into normal, acute hypoxia, and acute hypoxia plus vitamin B₁, vitamin B₂, and niacin supplementation groups and fed corresponding diets for 2 weeks and then exposed to a simulated altitude of 6000 m for 8 h. Hepatic gene expression profiles were analyzed using a microarray technique. Several biochemical markers were also assayed. The results showed that a total of 2476 genes were expressed differentially after acute hypoxia exposure (1508 upregulated genes and 968 downregulated genes). Compared with the acute hypoxia group, there were 1382 genes differentially expressed (626 upregulated genes and 756 downregulated genes) in the acute hypoxia plus vitamin B₁, vitamin B₂, and niacin supplementation group. Pathway analysis indicated that carbohydrate, lipid, and amino acid metabolism, as well as electron transfer chain, were improved to some extent after vitamin B₁, vitamin B₂, and niacin supplementation. Supportive results were obtained from biochemical assays. Our findings suggest that the supplementation of vitamin B₁, vitamin B₂, and niacin is beneficial in improving nutritional metabolism partly via gene expression under acute hypoxia condition.

An update on vitamin B12-related gene polymorphisms and B12 status

Background

Vitamin B12 is an essential micronutrient in humans needed for health maintenance. Deficiency of vitamin B12 has been linked to dietary, environmental and genetic factors. Evidence for the genetic basis of vitamin B12 status is poorly understood. However, advancements in genomic techniques have increased the knowledge-base of the genetics of vitamin B12 status. Based on the candidate gene and genome-wide association (GWA) studies, associations between genetic loci in several genes involved in vitamin B12 metabolism have been identified.

Objective

The objective of this literature review was to identify and discuss reports of associations between single-nucleotide polymorphisms (SNPs) in vitamin B12 pathway genes and their influence on the circulating levels of vitamin B12.

Methods

Relevant articles were obtained through a literature search on PubMed through to May 2017. An article was included if it examined an association of a SNP with serum or plasma vitamin B12 concentration. Beta coefficients and odds ratios were used to describe the strength of an association, and a P < 0.05 was considered as statistically significant. Two reviewers independently evaluated the eligibility for the inclusion criteria and extracted the data.

Results

From 23 studies which fulfilled the selection criteria, 16 studies identified SNPs that showed statistically significant associations with vitamin B12 concentrations. Fifty-nine vitamin B12-related gene polymorphisms associated with vitamin B12 status were identified in total, from the following populations: African American, Brazilian, Canadian, Chinese, Danish, English, European ancestry, Icelandic, Indian, Italian, Latino, Northern Irish, Portuguese and residents of the USA.

Conclusion

Overall, the data analyzed suggests that ethnic-specific associations are involved in the genetic determination of vitamin B12 concentrations. However, despite recent success in genetic studies, the majority of identified genes that could explain variation in vitamin B12 concentrations were from Caucasian populations. Further research utilizing larger sample sizes of non-Caucasian populations is necessary in order to better understand these ethnic-specific associations.

Genetic and environmental factors associated with vitamin B12status in Amazonian children

Objective

To evaluate the prevalence of vitamin B12deficiency and factors associated with vitamin B12status in Amazonian children.

Design

Genetic risk score (GRS), socio-economic and nutritional status, and morbidity data were the independent variables used in multiple linear regression models to evaluate factors associated with vitamin B12status in a population-based cross-sectional study. GRS was created by summing a number of known risk alleles for low serum vitamin B12.

Setting

Acrelândia, western Brazilian Amazon.

Subjects

Children (n988) aged <10 years.

Results

Overall prevalence of vitamin B12deficiency (<150 pmol/l) was 4·2 (95 % CI 3·0, 5·6) % and was highest in children aged <24 months: 13·6 (95 % CI % 8·8, 19·7) %. For children <24 months, wealth index (β=0·017,P=0·030) and animal protein intake(β=0·219,P=0·003) were positively associated with vitamin B12status. GRS (β=−0·114,P<0·001) and serum homocysteine (β=–0·049,P<0·001) were negatively associated. Among children aged ≥24 months, vitamin B12status was positively associated with wealth index (β=0·012,P<0·001), height-for-ageZ-score (β=0·024, P=0·033) and serum vitamin A (β=0·089,P<0·001). Age≥60 months(β=–0·118,P<0·001), GRS (β=–0·048, P<0·001), maternal schooling <5 years (β=–0·083,P<0·001), low intake of animal-derived foods (β=–0·050,P=0·030), serum homocysteine (β=–0·053,P<0·001), serum folate ≥23·6 nmol/l (β=–0·055,P=0·012) and geohelminth infection (β=–0·141,P=0·017) were negatively associated with vitamin B12status.

Conclusions

GRS, poverty, low intake of animal-derived foods, geohelminth infection, vitamin A and folate status were important factors associated with vitamin B12status of children in our study.

B vitamin polymorphisms and behavior: evidence of associations with neurodevelopment, depression, schizophrenia, bipolar disorder and cognitive decline

The B vitamins folic acid, vitamin B12 and B6 are essential for neuronal function, and severe deficiencies have been linked to increased risk of neurodevelopmental disorders, psychiatric disease and dementia. Polymorphisms of genes involved in B vitamin absorption, metabolism and function, such as methylene tetrahydrofolate reductase (MTHFR), cystathionine β synthase (CβS), transcobalamin 2 receptor (TCN2) and methionine synthase reductase (MTRR), have also been linked to increased incidence of psychiatric and cognitive disorders. However, the effects of these polymorphisms are often quite small and many studies failed to show any meaningful or consistent associations. This review discusses previous findings from clinical studies and highlights gaps in knowledge. Future studies assessing B vitamin-associated polymorphisms must take into account not just traditional demographics, but subjects' overall diet, relevant biomarkers of nutritional status and also analyze related genetic factors that may exacerbate behavioral effects or nutritional status.

Vitamin B12 and methionine deficiencies induce genome damage measured using the cytokinesis-block micronucleus cytome assay in human B lymphoblastoid cell lines

One-carbon metabolism is a network of interrelated biochemical reactions that has 2 major functions: DNA methylation and DNA synthesis. Methionine (Met), an essential amino acid, is converted to S-adenosyl-methionine (SAM), the body's main methyl group donor, which is converted to S-adenosylhomocysteine during methylation reactions. Vitamin B12 (B12) acts as a coenzyme of methionine synthase, which is required for the synthesis of Met and SAM. To determine the effects of Met and B12, we used the cytokinesis-block micronucleus assay in GM13705 and GM12593 cell line cultures exposed to 13 unique combinations of B12 and Met concentrations over 9 days. The nutrient levels chosen span the normal physiological ranges in humans. The Met-B12 concentration significantly and negatively correlated with all markers of genotoxicity in the 2 cell lines tested. In both cell lines, all markers of genotoxicity were significantly higher when treated with 15 μM Met than when treated with 50 μM Met, regardless of the B12 treatment level. Genotoxicity was significantly reduced in the group treated with 50 μM Met and 600 pM B12. Concentrations of 50 μM Met and 600 pM B12 are an optimal combination for stabilizing the genome. It is advisable to acquire adequate amounts of Met and B12 for maintaining genome stability.

Common variant in FUT2 gene is associated with levels of vitamin B(12) in Indian population

Vitamin B(12) is an essential micronutrient synthesized by microorganisms. Mammals including humans have evolved ways for transport and absorption of this vitamin. Deficiency of vitamin B(12) (either due to low intake or polymorphism in genes involved in absorption and intracellular transport of this vitamin) has been associated with various complex diseases. Genome-wide association studies have recently identified several common single nucleotide polymorphisms (SNPs) in fucosyl transferase 2 gene (FUT2) to be associated with levels of vitamin B(12)-the strongest association was with a non-synonymous SNP rs602662 in this gene. In the present study, we attempted to replicate the association of this SNP (rs602662) in an Indian population since a significant proportion has been reported to have low levels of vitamin B(12) in this population. A total of 1146 individuals were genotyped for this SNP using a single base extension method and association with levels of vitamin B(12) was assessed in these individuals. Regression analysis was performed to analyze the association considering various confounding factors like for age, sex, diet, hypertension, diabetes mellitus and coronary artery disease status. We found that the SNP rs602662 was significantly associated with the levels of vitamin B(12) (p value<0.0001). We also found that individuals adhering to a vegetarian diet with GG (homozygous major genotype) have significantly lower levels of vitamin B(12) in these individuals. Thus, our study reveals that vegetarian diet along with polymorphism in the FUT2 gene may contribute significantly to the high prevalence of vitamin B(12) deficiency in India.

The challenges for molecular nutrition research 1: linking genotype to healthy nutrition

Nutrition science finds itself at a major crossroad. On the one hand we can continue the current path, which has resulted in some substantial advances, but also many conflicting messages which impair the trust of the general population, especially those who are motivated to improve their health through diet. The other road is uncharted and is being built over the many exciting new developments in life sciences. This new era of nutrition recognizes the complex relation between the health of the individual, its genome, and the life-long dietary exposure, and has lead to the realisation that nutrition is essentially a gene-environment interaction science. This review on the relation between genotype, diet and health is the first of a series dealing with the major challenges in molecular nutrition, analyzing the foundations of nutrition research. With the unravelling of the human genome and the linking of its variability to a multitude of phenotypes from "healthy" to an enormously complex range of predispositions, the dietary modulation of these propensities has become an area of active research. Classical genetic approaches applied so far in medical genetics have steered away from incorporating dietary effects in their models and paradoxically, most genetic studies analyzing diet-associated phenotypes and diseases simply ignore diet. Yet, a modest but increasing number of studies are accounting for diet as a modulator of genetic associations. These range from observational cohorts to intervention studies with prospectively selected genotypes. New statistical and bioinformatics approaches are becoming available to aid in design and evaluation of these studies. This review discusses the various approaches used and provides concrete recommendations for future research.

Transcriptomics and functional genetic polymorphisms as biomarkers of micronutrient function: focus on selenium as an exemplar

Micronutrients are essential for optimal human health. However, in some cases, raising intake by supplementation has not proven to be beneficial and there is even some evidence that supplementation may increase disease risk, highlighting the importance of assessing the functional status of micronutrients. Techniques such as gene microarrays and single-nucleotide polymorphism analysis have the potential to examine effects of micronutrient intake on patterns of gene expression and inter-individual variation in micronutrient metabolism. Recent genomic research related to selenium (Se) provides examples illustrating how studies of functional single-nucleotide polymorphism and gene expression patterns can reveal novel biomarkers of micronutrient function. Both in vitro and in vivo experiments show that there are functionally relevant polymorphisms in genes encoding glutathione peroxidases 1, 3 and 4, selenoprotein P, selenoprotein S and the 15 kDa selenoprotein. Disease association studies investigating these gene variants have so far been relatively small but an association of a polymorphism in the selenoprotein S gene with colorectal cancer risk has been replicated in two distinct populations. Future disease association studies should examine effects of multiple variants in combination with nutritional status. Gene microarray studies indicate that changes in Se intake alter expression of components of inflammatory, stress response and translation pathways. Our hypothesis is that Se intake and genetic factors have linked effects on stress response, inflammation and apoptotic pathways. Combining such data in a systems biology approach has the potential to identify both biomarkers of micronutrients status and sub-group populations at particular risk.

Nutritional influence on epigenetics and effects on longevity

PURPOSE OF REVIEW

This review synthesizes recently published information regarding nutrition and its impact upon epigenetically mediated mechanisms involved in longevity and aging.

RECENT FINDINGS

Recent studies enriched considerably our understanding of the relationship between aging and gene-nutrient interactions that continuously shape our phenotype. Epigenetic mechanisms play an important role in mediating between the nutrient inputs and the ensuing phenotypic changes throughout our entire life and seem to be responsible, in part, for the biological changes that occur during aging. Less is known about the epigenetic role that nutrients have in directly influencing longevity and aging. However, recent studies clearly indicated that because nutrition modulates epigenetic events associated with various diseases (e.g., cancer, obesity, and diabetes), there is at least an indirect epigenetic link between nutrition and longevity and, therefore, biologic plausibility to hypothesize the epigenetic role of nutrition in altering longevity. Apart from limited human studies, promising animal studies brought us much closer to understanding how nutrition could have such an impact upon longevity and aging.

SUMMARY

Complex epigenetic mechanisms are involved in aging and longevity, directly or indirectly via disease mechanisms. Nutrition has a strong impact upon epigenetic processes and, therefore, holds promise in having important roles in regulating longevity and aging.

A network approach to micronutrient genetics: interactions with lipid metabolism

PURPOSE OF REVIEW

Although interactions between fat soluble micronutrients and lipid metabolism in relation to absorption, status and body composition have been well described, there is new evidence to suggest that key genes have profound effects on how micronutrients and lipids are handled in a range of cells and organs. This review highlights the importance of genetic variation in folate, selenium, zinc and carotenoid metabolism and the recent findings of micro-macro nutrient interactions.

RECENT FINDINGS

Although the methylenetetrahydrofolate reductase gene has been linked to CVD for some time, recent findings indicate that single-nucleotide polymorphisms (SNPs) in this gene are also linked to diabetes and may influence the pathogenesis of this disease through elevated alanine amino transferase concentrations. A recent selenium supplementation trial showed that SNPs can affect responses of GPx4, GPx1 and GPx3 protein expression or activity in response to Se supplementation or withdrawal. There is convincing evidence to suggest that the high variability of plasma carotenoids seen in human populations is at least partly caused by multiple genetic variations in genes involved in lipoprotein metabolism and lipid transfer. The most striking evidence of an interaction between carotenoid and lipid metabolism, however, comes from the observation that BCMO1 mice develop liver steatosis independent of the vitamin A content of the diet, and the discovery of common SNPs in this gene indicates that this interaction might be of clinical significance.

SUMMARY

Knowledge of genetic variants that affect micronutrient metabolism and responses to micronutrient supplementation were until recently largely limited to methylenetetrahydrofolate reductase. However, identification of novel functional SNPs in BCMO1, the critical enzyme of beta-carotene metabolism, and in several key selenoproteins indicates the potential importance of micronutrient-gene interactions.

Genome-wide association study of vitamin B6, vitamin B12, folate, and homocysteine blood concentrations

The B vitamins are components of one-carbon metabolism (OCM) that contribute to DNA synthesis and methylation. Homocysteine, a by-product of OCM, has been associated with coronary heart disease, stroke and neurological disease. To investigate genetic factors that affect circulating vitamin B6, vitamin B12, folate and homocysteine, a genome-wide association analysis was conducted in the InCHIANTI (N = 1175), SardiNIA (N = 1115), and BLSA (N = 640) studies. The top loci were replicated in an independent sample of 687 participants in the Progetto Nutrizione study. Polymorphisms in the ALPL gene (rs4654748, p = 8.30 x 10(-18)) were associated with vitamin B6 and FUT2 (rs602662, [corrected] p = 2.83 x 10(-20)) with vitamin B12 serum levels. The association of MTHFR, a gene consistently associated with homocysteine, was confirmed in this meta-analysis. The ALPL gene likely influences the catabolism of vitamin B6 while FUT2 interferes with absorption of vitamin B12. These findings highlight mechanisms that affect vitamin B6, vitamin B12 and homocysteine serum levels.