Kris Richardson et al. (including Larry Parnell and Jose Ordovas who are on Twitter) give a fascinating example of a gene-diet interaction yesterday in PLoS One (press release); the variant on a mRNA region allows microRNA to bind (miR; short chain non-coding RNA) that is of relevance to nutrition.

The perilipins (PLIN1 – 5) are proteins coat the surfaces of lipid droplets in adipocytes where triacylglycerols are stored.  PLIN4 facilitates free fatty acid uptake, whereas PLIN1 and other perilipins regulate trig storage and lipolysis, and thus have been a focus of intense study.

Since the PLIN1 and PLIN4 gene promoters contain PPAR response-elements, existing research focused on variants of these genes as PPARs are sensitive to diet, especially by unsaturated fatty acids.  The authors cite research associating variants of PLIN1 to obesity related phenotypes in women as well as gene x environment interactions between PLIN1, a TZD (diabetic drug) and weight gain and one between PLIN1 and a high saturated fat diet that influences risk of insulin resistance.  The PLIN1 knockout mouse model is also lean and obesity resistant.

To add a new layer of complexity, the experiments described in this new paper focused on a different region, at the post-transcriptional level: the 3′UTR on mRNA where miR bind.  Variants here may influence the amount of protein produced.  PLIN4 was the gene under study here.

Here is a brief summary of their experiments:

First, they genotyped 7 PLIN4 SNPs from 1,740 subjects from populations in the Framingham Offspring Study (FOS) and the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) and recorded corresponding anthropometrics and other relevant measurements (e.g. glucose, insulin resistance, trigs, HDL-C, total n-3 and n-6 PUFA, total calories, physical activity score, etc).  Then they performed a meta-analyses to test the association of the PLIN4 variants with relevant phenotypes, which showed one between minor (A) allele carriers of rs8887 (the SNP on the 3′UTR) and elevated BMI, weight, and waist circumference.  rs8887 explained 0.4% and 0.33% of BMI variance in FOS and GOLDN populations.  (Note: rs8887 is on the 23andme chip; I have 1 copy of the minor allele).

A subsequent meta-analysis between the PLIN4 SNPs and n-3 and n-6 PUFA intakes. Subjects who consumed greater amounts of n-3 PUFA with minor alleles of rs8887 had reduced BMI, weight, and waist circumference compared to non-carriers.  rs8887 and n-3 intake explained 0.48% and 0.77% of BMI variance in FOS and GOLDN. At another SNP, rs884164 (also in 23andme; I have 2 copies of minor allele), minor (C) allele carriers who consumed greater n-3 had reduced BMI, weight, waist circumference, glucose, and trigs.  This SNP also had an association with a greater n-6 PUFA intake and lower HDL and increased trigs, again among minor allele carriers.  rs884164 and n-3 intake explained 0.17% and 0.13% of BMI variance in FOS and GOLDN.

An analysis between visceral fat and subcutaneous fat and the PLIN4 SNPs was performed from the FOS population, and minor allele carriers of rs8887 had more of both.  rs8887 explained 0.75% of the variance in visceral fat and 0.56% variance in subcutaneous fat.

Since rs8887 and rs884164 had the most consistent associations, they performed analyses to see if they were functional variants.  miR-522 was predicted to bind to a seed site in the PLIN4 mRNA with the minor allele.  miR-522 hadn’t been previously demonstrated to be expressed in adipose tissue, so they tested and confirmed it.  They also confirmed that miR-522 binds in the PLIN4 3′UTR region when the minor allele is present.  rs884164 was predicted to fall in an NFkB motif; NFkB has been shown to elevate PLIN1 in other research and n-3 can alter its expression.  Since NFkB is central to inflammation and insulin resistance, it may be important for further study.

So in summary, these experiments found that the minor allele on rs8887 in the 3′UTR region of PLIN4 mRNA creates a miR recognition element (MRE) which can bind miR-522.  This would result in a lesser expression of PLIN4 in minor allele carriers which may explain the associations between the elevated obesity related phenotypes and the rs8887 SNP in the 2 populations examined.  This is very interesting; recall that minor allele carriers with increased n-3 PUFA intake did not experience these phenotypes, suggesting that there are subgroups that would benefit from optimizing certain dietary characteristics based on 3′UTR variants.  For n-3 PUFA, this may occur through PPARs, however there is no direct evidence for n-3 altering PLIN4 expression yet.  This would need to be considered in future studies on n-3 supplementation and weight.

These findings are also important because:

to date, there are few known examples of genetic variation in miR-target sites contributing to phenotypic variation.

Larry Parnell also pointed me to this Nature paper that was published just a few days ago that shows another nice example with regard to allele-specific miRNA binding in the HLA-C gene, which effects susceptibility to HIV.

So this research represents the tip of the iceberg.

Finally, they examined the genetic drift of the PLIN4 3′UTR by constructing a phylogenetic tree with interesting results:

The PLIN4 3′UTR has undergone significant change from mouse to primate and furthermore that change is ongoing even among recently diverged primates such as neandertal and human.

Further analysis across human populations indicates that it is currently undergoing drift.

If the appearance of variation at the rs8887 position is recent to human, it is tempting to speculate that the genesis of the rs8887 minor A allele may have contributed to the phenotypic diversification distinguishing humans from other primates as it is thought that the gain, or loss, of genetic regulatory mechanisms are critical for the evolutionary process [34]. That this interaction may have contributed to the evolution of the human brain is food for thought [35].

It is intriguing to what extent other variants like this influence other nutrition related interactions and phenotypes, and how they will add to our understanding of evolutionary processes!

Reference

Kris Richardson, Qiong Louie-Gao, Donna K. Arnett, Laurence D. Parnell, Chao-Qiang Lail, Alberto Davalos, Caroline S. Fox, Serkalem Demissie, L. Adrienne Cupples, Carlos Fernandez-Hernando, & Jose M. Ordovas (2011). The PLIN4 Variant rs8887 Modulates Obesity Related Phenotypes in Humans through Creation of a Novel miR-522 Seed Site
PLoS One : 10.1371/journal.pone.0017944