Apolipoprotein A-IV-2 allele: association of its worldwide distribution with adult persistence of lactase and speculation on its function and origin

CardioGxE, a catalog of gene-environment interactions for cardiometabolic traits

Background

Genetic understanding of complex traits has developed immensely over the past decade but remains hampered by incomplete descriptions of contribution to phenotypic variance. Gene-environment (GxE) interactions are one of these contributors and in the guise of diet and physical activity are important modulators of cardiometabolic phenotypes and ensuing diseases.

Results

We mined the scientific literature to collect GxE interactions from 386 publications for blood lipids, glycemic traits, obesity anthropometrics, vascular measures, inflammation and metabolic syndrome, and introduce CardioGxE, a gene-environment interaction resource. We then analyzed the genes and SNPs supporting cardiometabolic GxEs in order to demonstrate utility of GxE SNPs and to discern characteristics of these important genetic variants. We were able to draw many observations from our extensive analysis of GxEs. 1) The CardioGxE SNPs showed little overlap with variants identified by main effect GWAS, indicating the importance of environmental interactions with genetic factors on cardiometabolic traits. 2) These GxE SNPs were enriched in adaptation to climatic and geographical features, with implications on energy homeostasis and response to physical activity. 3) Comparison to gene networks responding to plasma cholesterol-lowering or regression of atherosclerotic plaques showed that GxE genes have a greater role in those responses, particularly through high-energy diets and fat intake, than do GWAS-identified genes for the same traits. Other aspects of the CardioGxE dataset were explored.

Conclusions

Overall, we demonstrate that SNPs supporting cardiometabolic GxE interactions often exhibit transcriptional effects or are under positive selection. Still, not all such SNPs can be assigned potential functional or regulatory roles often because data are lacking in specific cell types or from treatments that approximate the environmental factor of the GxE. With research on metabolic related complex disease risk embarking on genome-wide GxE interaction tests, CardioGxE will be a useful resource.

Latitude, sunshine, and human lactase phenotype distributions may contribute to geographic patterns of modern disease: the inflammatory bowel disease model

Countries with high lactase nonpersistence (LNP) or low lactase persistence (LP) populations have lower rates of some "western" diseases, mimicking the effects of sunshine and latitude. Inflammatory bowel disease (IBD), ie, Crohn's disease and ulcerative colitis, is putatively also influenced by sunshine. Recent availability of worldwide IBD rates and lactase distributions allows more extensive comparisons. The aim of this study was to evaluate the extent to which modern day lactase distributions interact with latitude, sunshine exposure, and IBD rates. National IBD rates, national distributions of LP/LNP, and population-weighted average national annual ultraviolet B exposure were obtained, estimated, or calculated from the literature. Negative binomial analysis was used to assess the relationship between the three parameters and IBD rates. Analyses for 55 countries were grouped in three geographic domains, ie, global, Europe, and non-Europe. In Europe, both latitude and ultraviolet B exposure correlate well with LP/LNP and IBD. In non-Europe, latitude and ultraviolet B exposure correlate weakly with LP/LNP, but the latter retains a more robust correlation with IBD. In univariate analysis, latitude, ultraviolet B exposure, and LP/LNP all had significant relationships with IBD. Multivariate analysis showed that lactase distributions provided the best model of fit for IBD. The model of IBD reveals the evolutionary effects of the human lactase divide, and suggests that latitude, ultraviolet B exposure, and LP/LNP mimic each other because LP/LNP follows latitudinal directions toward the equator. However, on a large scale, lactase patterns also follow lateral polarity. The effects of LP/LNP in disease are likely to involve complex interactions.

Genetic epidemiology of health disparities in allergy and clinical immunology

The striking racial and ethnic disparities in disease prevalence for common disorders, such as allergic asthma, cannot be explained entirely by environmental, social, cultural, or economic factors, and genetic factors should not be ignored. Unfortunately, genetic studies in underserved minorities are hampered by disagreements over the biologic construct of race and logistic issues, including admixture of different races and ethnicities. Current observations suggest that the frequency of high-risk variants in candidate genes can differ between African Americans, Puerto Ricans, and Mexican Americans, and this might contribute to the differences in disease prevalence. Maintenance of certain allelic variants in the population over time might reflect selective pressures in previous generations. For example, significant associations between markers in certain candidate genes (eg, STAT6, ADRB2, and IFNGR1) for traits such as high total IgE levels observed in resistance to extracellular parasitic disease in one population and atopic asthma in another supports the common disease/common variant model for disease. Herein is a discussion of how genetic variants might explain, at least in part, the marked disparities observed in risk to allergic asthma.

Genetic determinants and ethnic disparities in sepsis-associated acute lung injury

Acute lung injury (ALI) is a common and devastating illness that occurs in the context of sepsis and other systemic inflammatory disorders. In systemic illnesses like sepsis, only a subset of patients develops ALI even when pathologic stimuli are apparently equivalent, suggesting that there are genetic features that may influence its onset. Considerable obstacles in defining the exact nature of the pathogenesis of ALI include substantial phenotypic variance, incomplete penetrance, complex gene-environment interactions and a strong potential for locus heterogeneity. Moreover, ALI arises in a critically ill population with diverse precipitating factors and appropriate controls that best match the reference population have not been agreed upon. The sporadic nature of ALI precludes conventional approaches such as linkage mapping for the elucidation of candidate genes, but tremendous progress has been made in combining robust, genomic tools such as high-throughput, expression profiling with case-control association studies in well characterized populations. Similar to trends observed in common, complex traits such as hypertension and diabetes, some of these studies have highlighted differences in allelic variant frequencies between European American and African American ALI patients for novel genes which may explain, in part, the complex interplay between ethnicity, sepsis and the development of ALI. In trying to understand the basis for contemporary differences in allelic frequency, which may lead to differences in susceptibility, the potential role of positive selection for genetic variants in ancestral populations is considered.

Further evidence for the association between obesity-related traits and the apolipoprotein A-IV gene

OBJECTIVE

To investigate associations and gene-environment interactions of APOA-IV gene polymorphisms with obesity-related phenotypes in a Brazilian population.

METHODS

A total of 391 individuals (171 men and 220 women) were genotyped for Xbal, Thr347Ser and Gln360His polymorphisms by PCR-RFLP methods. Adjusted body mass index (BMI) and waist circumference (WC) were compared among genotypes/haplotypes by unpaired t-test or analysis of variance. Gene-environment interactions were tested by analysis of variance using a general linear model.

RESULTS

Analysis of the APOA-IV gene variants separately showed that X*2 and 347Ser alleles were associated with higher BMI (P=0.02 for both polymorphisms). Haplotype analysis confirmed this association. For these polymorphisms, the effect on BMI appeared to depend on smoking status (test for interaction, P=0.007 and 0.02, respectively), the Thr347Ser variant was associated with a BMI increase in smokers only (P=0.002). At the single-locus level no association was observed between 360His allele and BMI; however, haplotype analyses showed an association of this gene variant and higher BMI. A trend for association with WC (P=0.05) was observed in male carriers of the 360His allele. The effect of this polymorphism also depended on smoking status (test for interaction, P=0.018). Nonsmoker male carriers of the 360His allele had a larger waist circumference than homozygotes for the Gln allele (P=0.003).

CONCLUSION

Our data suggest that the APOA-IV gene polymorphisms investigated are associated with obesity-related traits. The effects of X*2 and 347Ser variants on BMI and the 360His variant on waist circumference depended on smoking status.

Genetic polymorphisms and lipoprotein responses to diets

While human diets have markedly evolved since their origin, the human genome has only marginally changed. Nevertheless, polymorphisms of common genes are widespread. It has been substantiated that most major diseases (including cardiovascular disease, diabetes, obesity and cancers) result from the interaction between genetic susceptibility and environmental factors, including diet. In the field of lipoprotein metabolism and cardiovascular disease several gene polymorphisms for key proteins, such as apoproteins (apo) E, B, A-IV and C-III, LDL receptor, microsomal transfer protein (MTP), fatty acid-binding protein (FABP), cholesteryl ester transfer protein (CETP), lipoprotein lipase and hepatic lipase, have been identified and linked to variable responses to diets. We are carrying out an intervention study (RIVAGE) in Marseille dedicated to investigating the interactions between diets (Mediterranean or low-fat types v. standard Western type), risk factors for cardiovascular disease and gene polymorphisms in about 300 patients randomized into two groups over periods of 3 and 12 months. Some data obtained in about 100 patients after 3 months of dietary change are available. Among single nucleotide polymorphisms (SNP) already studied (apoE (epsilon2, epsilon3, epsilon4), apoB (-516C/T), apoC-III (SstI), apoA-IV (Ser347Thr), MTP (-493G/T), intestinal FABP (Ala54Thr), CETP (TaqIB) and hepatic lipase (-480C/T)), some SNP showed interactions with diets in relation to changes in particular variables after 3 months on the dietary regimens. This was the case for apoE and LDL-cholesterol and triacylglycerols, apoA-IV and LDL-cholesterol, MTP and LDL-cholesterol, intestinal FABP and triacylglycerols. These data provide evidence of the interaction between some SNP and the metabolic response to diets.

Apolipoprotein A-IV polymorphisms and diet-gene interactions

Apolipoprotein A-IV is a 46kDa glycoprotein that is synthesized by intestinal enterocytes and is incorporated into the surface of nascent chylomicrons. Considerable evidence suggests that apolipoprotein A-IV plays a role in intestinal lipid absorption and chylomicron assembly. We have proposed that polymorphisms that alter the interfacial behavior of apolipoprotein A-IV may modulate the physical properties and metabolic fate of plasma chylomicrons. Of the reported genetic polymorphisms of apolipoprotein A-IV, two, Q360H and T347S, are known to occur at high frequencies among the world populations. Biophysical studies have established that the Q360H isoprotein displays higher lipid affinity; conversely the T347S isoprotein is predicted to be less lipid avid. Recent studies have shown that the Q360H polymorphism is associated with increased postprandial hypertriglyceridemia, a reduced low-density lipoprotein response to dietary cholesterol in the setting of a moderate fat intake, an increased high-density lipoprotein response to changes in total dietary fat content, and lower body mass and adiposity; the T347S polymorphism appears to confer the opposite effects. Studies on the diet-gene interactions of other apolipoprotein A-IV alleles are needed, as are studies on the interactions between apolipoprotein A-IV alleles and other apolipoprotein polymorphisms.