Complexity of type 2 diabetes mellitus data sets emerging from nutrigenomic research: a case for dimensionality reduction?

Association between TGF-β/BMP signaling pathway polymorphisms and the risk of primary ovarian insufficiency in Korean women

BACKGROUND

Primary ovarian insufficiency (POI) is one of the leading female infertility diseases in which ovarian function stops before the age of 40. Reports that POI is associated with transforming growth factor (TGF)-β/bone morphogenetic protein (BMP) signaling pathway-associated genes (e.g., TGF-β, and BMP15) have been continuous since publication that the TGF-β superfamily acts as important regulators for ovary and placenta function in humans. Mechanistically, the secretion of follicle-stimulating hormone, progesterone, and estrogen is affected by the TGF-β superfamily in granulosa cells, which are involved in the development of theca cells, oocytes, and granulosa cells.

OBJECTIVE

This study aimed to identify the association between genes related to the TGF-β/BMP signaling pathway and the risk of POI pathogenesis.

METHODS

Possible associations between six gene polymorphisms and POI susceptibility were examined in 139 patients with POI and 345 control subjects.

RESULTS

Allele combination of TGFBR1 rs334348 G > A and TGFBR3 rs1805110G > A exhibited association with decreased POI risk (adjusted odds ratio [AOR] = 0.165; 95% confidence interval [CI] 0.032-0.847; P = 0.031). Also, TGFBR1 rs1590 G > T and rs334348 G > A and TGFBR3 rs1805110 G > A allele combination exhibited association with decreased POI risk (OR = 0.553; 95% CI 0.374-0.816; P = 0.003).

CONCLUSION

This study suggests that polymorphisms in the TGF-β signaling pathway genes can be useful biomarkers for POI diagnosis and treatment.

Nutrigenomics: Perceptions of South African Dietitians and General Practitioners

INTRODUCTION

Although investigations into the emerging field of nutrigenomics are relatively limited and more research in this field is required, experts agree that there is potential for it to be incorporated into health care practice. If health care professionals can promote healthy dietary behavior based on nutrigenomic testing, it can assist in addressing the health consequences of poor diet and lightning the strain on the South African health care system.

METHODS

Registered dietitians (RDs) and general practitioners (GPs) registered with the Health Professions Council of South Africa (HPCSA) who obtained their qualification in South Africa (SA) were eligible to participate in this cross-sectional study. Participants were identified using convenience and snowball sampling. A self-administered electronic survey using EvaSys Software® was completed by those that agreed to participate.

RESULTS

Nearly all RDs (97.3%), but less than a third of GPs (30.4%), had heard of the term nutrigenomics. Approximately three-quarters of RDs (74.7%) and GPs (73.9%) had or would personally consider undergoing genetic testing. More than 40% (43.5%) of RDs ranked direct-to-consumer genetic testing companies as the most equipped, while 31.8% of GPs ranked RDs as the most equipped to provide patients with nutrigenomic services. Both RDs and GPs ranked similar reasons as "strongly agree" for why consumers were motivated to make use of nutrigenomic services, which included "motivated by a desire to prevent or manage disease" (56.7%), "prevent a disease based on family history" (65.9%), "control health outcomes based on family history" (54.9%), and "improve overall health-related quality of life" (48.6%). Cost concerns were reported as the greatest barrier to implementing nutrigenomic services (75.7%). Other barriers included confidentiality issues (47.8%) and moral concerns (37.3%). Greater individualization of diet prescription (66.5%), stronger foundations for nutrition recommendations (62.4%), and dietary prescriptions that would manage or prevent certain diseases more effectively (59.0%) were all perceived as benefits of including nutrigenomics in practice.

CONCLUSION

This study identified perceived consumer motivators and barriers that might affect the willingness to seek nutrigenomic services in SA. In addition, the need for more nutrigenomic training opportunities, including the planning of personalized diets based on genetic testing results and interpretation of results, was confirmed. However, both RDs and GPs felt that the emerging field of nutrigenomics needs further development before it can be applied effectively in routine private and public health care in SA.

Overview of genomics and post-genomics research on type 2 diabetes mellitus: Future perspectives and a framework for further studies

In this review, we briefly outlined salient features of pathophysiology and results of the genetic association studies hitherto conducted on type 2 diabetes. Primarily focusing on the current status of genomic research, we briefly discussed the limited progress made during the post-genomic era and tried to identify the limitations of the post-genomic research strategies. We suggested reanalysis of the existing genomic data through advanced statistical and computational methods and recommended integrated genomics-metabolomics approaches for future studies to facilitate understanding of the gene-environment interactions in the manifestation of the disease. We also propose a framework for research that may be apt for determining the effects of urbanization and changing lifestyles in the manifestation of complex genetic disorders like type 2 diabetes in the Indian populations and offset the confounding effects of both genetic and environmental factors in the natural way.

Nutrigenetics and nutrigenomics insights into diabetes etiopathogenesis

Diabetes mellitus (DM) is considered a global pandemic, and the incidence of DM continues to grow worldwide. Nutrients and dietary patterns are central issues in the prevention, development and treatment of this disease. The pathogenesis of DM is not completely understood, but nutrient-gene interactions at different levels, genetic predisposition and dietary factors appear to be involved. Nutritional genomics studies generally focus on dietary patterns according to genetic variations, the role of gene-nutrient interactions, gene-diet-phenotype interactions and epigenetic modifications caused by nutrients; these studies will facilitate an understanding of the early molecular events that occur in DM and will contribute to the identification of better biomarkers and diagnostics tools. In particular, this approach will help to develop tailored diets that maximize the use of nutrients and other functional ingredients present in food, which will aid in the prevention and delay of DM and its complications. This review discusses the current state of nutrigenetics, nutrigenomics and epigenomics research on DM. Here, we provide an overview of the role of gene variants and nutrient interactions, the importance of nutrients and dietary patterns on gene expression, how epigenetic changes and micro RNAs (miRNAs) can alter cellular signaling in response to nutrients and the dietary interventions that may help to prevent the onset of DM.

Association of miR-146aC>G, miR-196a2T>C, and miR-499A>G polymorphisms with risk of premature ovarian failure in Korean women

We investigated whether microRNA (miRNA) polymorphisms (miR-146aC>G, miR-196a2T>C, and miR-499A>G) confer risk of premature ovarian failure (POF) in Korean women. DNA samples from 136 patients with POF and 234 controls were genotyped for the 3 miRNA single-nucleotide polymorphisms by polymerase chain reaction-restriction fragment length polymorphism. The miR-146aCG/miR-196a2TC combined genotype was less frequent in patients than in controls (P < .05), conferring less susceptibility. Using haplotype-based multifactor dimensionality reduction analysis, the C-C-A and G-T-A inferred haplotypes (miR-146a/miR-196a2/miR-499) were less frequent in patients, suggesting protective effects (P < .05 for each), whereas the C-T-A and G-C-A haplotypes were more frequent in patients (P < .05 for each). The C-T and G-C haplotypes (miR-146a/miR-196a2) were more frequent in patients, whereas the C-C and G-T haplotypes were less frequent in patients (P < .05 for each). However, none of the 3 miRNA polymorphisms alone was associated with POF risk. Our findings suggest that putative gene-gene interaction between miR-146 and miR-196a2 may be involved in POF development.

Insulin signaling regulating genes: effect on T2DM and cardiovascular risk

Type 2 diabetes mellitus (T2DM) is a complex disorder that has a heterogeneous genetic and environmental background. In this Review, we discuss the role of relatively infrequent polymorphisms of genes that regulate insulin signaling (including the K121Q polymorphism of ENPP1, the G972R polymorphism of IRS1 and the Q84R polymorphism of TRIB3) in T2DM and other conditions related to insulin resistance. The biological relevance of these three polymorphisms has been very thoroughly characterized both in vitro and in vivo and the available data indicate that they all affect insulin signaling and action as well as insulin secretion. They also affect insulin-mediated regulation of endothelial cell function. In addition, several reports indicate that the effects of all three polymorphisms on the risk of T2DM and cardiovascular diseases related to insulin resistance depend on the clinical features of the individual, including their body weight and age at disease onset. Thus, these polymorphisms might be used to demonstrate how difficult it is to ascertain the contribution of relatively infrequent genetic variants with heterogeneous effects on disease susceptibility. Unraveling the role of such variants might be facilitated by improving disease definition and focusing on specific subsets of patients.

The on-line promotion and sale of nutrigenomic services

PURPOSE

Nutrigenomic researchers hope to improve health through personalized nutrition, but many consider the sale of nutrigenomic services to be premature. Few studies have evaluated the promotion and sales practices of organizations hosting nutrigenomic websites.

METHODS

Systematic search and analysis of websites promoting nutrigenomic services in October 2006.

RESULTS

Of the 64 organizations hosting websites, 29 organizations offered (24 of 29) or promoted (5 of 29) at-home testing and 26 organizations sold services on-line (17 of 26) or provided a direct link to on-line sales (9 of 26). A lack of transparency made it difficult to identify unique tests; however, three organizations were linked to 56% of all test mentions. Most organizations were healthcare/wellness service providers (50%) or laboratories/biotech companies (27%). Few organizations provided on-line information about laboratory certifications (20%), nutrigenomic test or research limitations (13%), test validity or utility (11%), or genetic counseling (9%). Affiliation opportunities were offered by 15 organizations.

CONCLUSIONS

Organizations did not provide adequate information about nutrigenomic services and at-home genetic testing. Affiliation opportunities and distribution agreements suggest the promotion and sale of nutrigenomic services will continue, increasing the importance of consumer and provider education. In absence of federal regulation, organizations promoting nutrigenomic services should equate websites to product labels and include information to facilitate informed decision-making.

Genes, diet and inflammatory bowel disease

Inflammatory bowel disease (IBD) arises in part from a genetic predisposition, through the inheritance of a number of contributory genetic polymorphisms. These variant forms of genes may be associated with an abnormal response to normal luminal bacteria. A consistent observation across most populations is that any of three polymorphisms of the Caspase-activated recruitment domain (CARD15) gene are more prevalent in IBD patients as compared with unaffected controls. Similar aberrant responses to bacteria are associated with variants in Autophagy-related 16-like 1 (ATG16L1) and human defensin (HBD-2, -3 and -4) genes. The defective bacterial signal in turn leads to an excessive immune response, presenting as chronic gut inflammation in susceptible individuals. Inconsistent population reports implicate the major histocompatability complex (MHC), that encodes a number of human leukocyte antigens (HLA), MHC class I chain-related gene A (MICA) or cytokines, such as tumour necrosis factor-alpha (TNF-alpha). Toll-like receptors encoded by the TLR4 or TLR9 genes may also play a role. Recent whole genome scans suggest that a rare variant in the interleukin-23 receptor (IL23R) gene may actually protect against IBD. Other implicated genes may affect mucosal cell polarity (Drosophila discs large homologue 5, DLG5) or mucosal transporter function (sodium dependent organic cation transporters, SLC22A4 and SLC22A5). A variant in ABCB1 (ATP-binding cassette subfamily B member 1) may be especially associated with increased risk of UC. While pharmacogenetics is increasingly being used to predict and optimise clinical response to therapy, nutrigenetics may have even greater potential. In many cases, IBD can be controlled through prescribing an elemental diet, which appears to act through modulating cytokine response and changing the gut microbiota. More generally, no single group of dietary items is beneficial or detrimental to all patients, and elimination diets have been used to individualise dietary requirements. However, recognising the nature of the genes involved may suggest a more strategic approach. Pro- or prebiotics will directly influence the microbial flora, while immunonutrition, including omega-3 fatty acids and certain polyphenols, may reduce the symptoms of gut inflammation. The expression of gut transporters may be modulated through various herbal remedies including green tea polyphenols. Such approaches would require that the gene of interest is functioning normally, other than its expression being up or down-regulated. However, new approaches are being developed to overcome the effects of polymorphisms that affect the function of a gene. A combination of human correlation studies with experimental models could provide a rational strategy for optimising nutrigenetic approaches to IBD.

Nutrigenomics and gut health

Recognition of the interplay between genes and diet in development of disease and for maintenance of optimal metabolism has led to nutrigenomic or nutrigenetic approaches to personalising or individualising nutrition, with the potential of preventing, delaying, or reducing the symptoms of chronic diseases. Some of the development work has focussed on cardiovascular disease or type II diabetes mellitus, where various groups have identified potential diet-gene interactions. However, the available studies also emphasise the exponential increase in numbers of subjects necessary to recruit for clinical evaluation if we are to successfully provide informative high-dimensional datasets of genetic, nutrient, metabolomic (clinical), and other variables. There is also a significant bioinformatics challenge to analyze these. To add to the complexity, many of the pioneering studies had assumed that single nucleotide polymorphisms (SNPs) were the main source of human variability, but an increasing evidence base suggests the importance of more subtle gene regulatory mechanisms, including copy number variants. As an example, the risk of Inflammatory Bowel Disease (IBD) is associated with the inheritance of a number of contributory SNPs as well as with copy number variants of certain other genes. The variant forms of genes often result in disruptions to bacterial homeostasis mechanisms or to signal transduction of the intestinal epithelial cell of the host, and thereby to altered intestinal barrier function, and/or adaptive immune responses. The human gut microbiota is altered in individuals suffering from disorders such as IBD, and probiotic or prebiotic therapies or elemental diets may be beneficial to a high proportion of individuals through modifying the gut microbiota, and also modulating immune responses. New putative foods or dietary therapies may be identified through novel tissue culture screens, followed by further testing with in vivo animal models of human disease. A scientifically based rationale for developing novel foods related to genotype might use a combination of food fractionation, testing in tissue culture models and validation through animal models, before moving into human populations. However, the field of nutrigenomics raises ethical, legal and social issues, and will be of genuine benefit to human health only if developed in linkage with adequately trained health professionals. Such training will widen public understanding, and permit dialogue with regulatory officials to responsibly develop, apply and progress this new field.