Thursday, July 23, 2020

What's on your plate - nutrition, dark matter and health

Graham Lawton at New Scientist magazine has written a nice feature on the hidden elements of human nutrition. There is so much that we do not know about the effects of thousands of molecular compounds present in the foods we eat. He explores that topic fairly well in his article.

That article mentions some software - PhyteByte - colleagues and I designed and published in BMC Bioinformatics. The software is designed to identify food compounds with potential to have pharmacological properties. I'll share details on how all that came to be in another post. As that article was wending its way through the finals stages of editorial review, I was asked to contribute a blog to accompany the PhyteByte article. You can find what I wrote on the “dark matter” of nutrition – just what are you eating here.

Tuesday, July 21, 2020

AMY1 copy number variation

Amylase comes in two forms - salivary and pancreatic - encoded by the AMY1 and AMY2 gene clusters, respectively. These genes - AMY2B, AMY2A, AMY1A, AMY1B, AMY1C - map to human chromosome 1p21.1 and form a tight five-gene group of ~206 kbp. The genes, especially the AMY1 cluster, have garnered added interest because of the findings that they show extensive copy number variation. In some studies, copy number variation (CNV) has been determined to be influenced at least in part by selection, or adaptation to available food sources.

The first step in the digestion of dietary starch and glycogen is cleavage of the 1,4-alpha-glucoside bond. This cleavage is catalyzed by amylase. Hence, this is an important enzyme for the extraction of energy from food.

Because the AMY1 gene cluster CNV mediates salivary α-amylase levels and is linked to postprandial phenotypes relevant to type 2 diabetes, we initiated a study to examine if AMY1-CNV is associated with age-mediated change in insulin resistance. We noted positive associations of insulin resistance with age among participants of two cohorts with low AMY1-copy-numbers. Type 2 diabetes was correlated with age in those with low AMY1-copy-numbers but not with high AMY1-copy-numbers.

This work recently was published in Clinical Chemistry in an article titled "Salivary AMY1 copy number variation modifies age-related type 2 diabetes risk, by Liu, et al."

Tuesday, December 30, 2014

FTO, cohort of birth and body mass index

In a recently accepted article in PNAS, entitled "Cohort of birth modifies the association between FTO genotype and BMI," the association of FTO variant rs993609 with body mass index is described as having essentially zero influence for study participants born before 1942 and increasing influence on this obesity phenotype as participants were born in increasingly more recent years. That long-range enhancers within the FTO region recapitulate aspects of IRX3 expression implies that the obesity-associated interval serves to regulate IRX3. Consistent with this, obesity-associated SNPs are associated with expression of IRX3, but not FTO, in human brains. Nonetheless, this is an important obesity locus, be it FTO or IRX3 as the functional unit. 
The authors rightly suggest that gene-environment interactions (GxEs) coupled with changes to the environment of the participants could alter the FTO-BMI association. 

FTO is subject to exercise-induced changes in DNA methylation. See, for example, table 5 (and reference 3) of  Rönn, Volkov, et al. We have cataloged a large number of genetic variants that show the type of GxEs suggested by the recent PNAS article. That catalog shows that some nine different studies observed modulating effects of physical activity on the FTO-BMI association. (In most populations of European ancestry, for example, in which many of these studies were conducted, the variants analyzed are in relatively strong to very strong linkage disequilibrium.) Other lifestyle choices also modulated the effects of FTO variants, including macronutrient intakes of carbohydrate, and fatty acids such as saturated fat, MUFA (mono-unsaturated fatty acid) and PUFAs (poly-unsaturated fatty acids). Whether time spent engaged in physical activity shrank as the birth cohorts became more recent, or diet changed, or some combination of this, is difficult to ascertain. But a list of known FTO-BMI GxEs would be a good place to begin such an analysis.

Thursday, December 18, 2014

CardioGxE analysis would not be so rich without the help of students

In late October we published a paper on a catalog of cardiometabolic gene-environment interactions pulled from over 380 publications. That paper is entitled "CardioGxE, a catalog of gene-environment interactions for cardiometabolic traits" and represents, among many other aspects of my research, the benefit and satisfaction of giving first-year nutrition graduate students the opportunity to engage in research and contribute important results to a larger research effort.

Lately, I have had several opportunities to guide students of the Tufts Friedman School of Nutrition Science and Policy during a practicum or directed study. I often try hard to find a project that will contribute directly to something we have ongoing that also has good potential to be published in the near future. That does not always come to be, but for our CardioGxE paper such was the case. Four of my co-authors were first-year grad students, and another three were more senior. Particularly for these four younger students, they each made unique and important contributions to the analyses we present in the paper. Our paper would not have the impact it is currently enjoying nor be as complete in showing the utility of gene-environment interactions without their work. Thank you to you all!

Which brings me to my main point: Consider well the abilities that a group of students can bring to your project. Engaging them as equals, as true colleagues, could very well facilitate a project's completion and publication. And, if those students are now authors, say on their first paper, that makes it very nice all around.

Tuesday, September 9, 2014

NuGO Week: Mediterranean diet and the Nordic diet

Yesterday began the 11th NuGO Week conference on “Nutrigenomics of Food” with a debate on Mediterranean diet and the Nordic diet. The Mediterranean diet (MD) is well known if not precisely defined - little to no dairy in Spain, but feta and other cheeses in Greece. We heard of results from PREDIMED and the view from Spain. The Nordic diet (ND) is a contemporary adaptation of healthy and traditional food choices from Nordic countries.

Both diets show health benefits in the respective examined populations. These benefits were described as mainly pertaining to cardiovascular disease, including glycemic measures, and to chronic inflammation.

What we heard was much more compare and contrast (of data) than a debate. There was only very brief mention of conducting the same experiment for both diets (a metabolomics assessment of blood and urine from subjects taking the diet of the respective area (Spain and Norway, e.g.). But no one offered putting Spaniards on a Nordic diet and Norwegians on a Mediterranean diet.

One thing I will like to see is an analysis of the response to the MD in PREDIMED based on an analysis of the genetic ancestry of the individuals. There are sufficient data to be able to classify the subjects by genetic ancestry along norther-southern European axes. Then, we can address if those persons with greater northern European ancestry show a weaker or equal beneficial response to the MD. 

Similarly, the ND projects would do well to engage more subjects - although I fully realize that the population of Spain is likely larger than that of all five Nordic countries combined - and incorporate genetics and other large data sets.