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Good News From Nutrigenomics: Vitamins Can Compensate for Disadvantaged Genes
An interview with Dr. Nicholas J. Marini
By Richard A. Passwater, Ph.D.
Recently, we have been discussing the paradigm shift in nutritional science facilitated by nutrigenomics. The Rubicon has been crossed and there is good news. For decades, we have been learning that much of our health is influenced by our genes, but, more recently, we began to understand that good nutrition can often override bad genes. Now, it has been shown that supplemental vitamins can compensate for disadvantaged genes that compromise health because they produce inferior biochemicals in our bodies.
This month, we will chat with Dr. Nicholas Marini, Ph.D., who was the lead scientist in the University of California, Berkeley group that published what I feel is one of the two most outstanding scientific studies in recent memory. Their research report, published in June in the prestigious Proceedings of the National Academy of Science (PNAS), was widely hailed in scientific circles (1).
Science Daily noted this importance in their article entitled, “Good News in our DNA: Defects You Can Fix with Vitamins and Minerals”: “University of California, Berkeley scientists have found a welcome reason to delve into your genetic heritage: to find the slight genetic flaws that can be fixed with remedies as simple as vitamin or mineral supplements” (2). What is particularly exciting about their research is that it not only confirms that increasing the appropriate nutrients in a person with a disadvantaged gene overcomes the biochemical problems caused by this genetic defect. But, this research also provides a methodology to rigorously study many, if not all, such disadvantaged genes and their nutrient interactions. Dr. Marini’s research helps provide a methodology to assess gene function as well as nutrient interactions.
It is well known that certain disadvantaged genes called single nucleotide polymorphisms (SNPs) lead to higher incidence, earlier onset and greater severity of certain diseases, as well as lower responses to treatment, and thus, lower survival rates than the general population (3).
Dr. Marini is a research scientist at the University of California at Berkeley. For the past four years, he has been the lead scientist in studies identifying genetic variants in vitamin-dependent enzymes that affect function, yet may be amenable to vitamin remediation. Dr. Marini is currently involved in two projects aimed at elucidating the potential health and fitness benefits of characterizing and nutritionally correcting such alleles (genetic variations). The first project, in collaboration with scientists at Children’s Hospital Oakland Research Institute, is looking at folate pathway genetics as determinants for certain birth defects. The second project, which is being funded by the Department of Defense, is to evaluate the impact of genetic variation on peak physical and cognitive performance. Before UC, Berkeley, Dr. Marini spent nine years in the biotechnology industry where he was primarily involved in developing genomic technologies to enable more efficient drug discovery and screening processes. Dr. Marini received his bachelor’s degree from Georgetown University, his Ph.D. in molecular biology from The Johns Hopkins University and completed post-doctoral work at The Scripps Research Institute in La Jolla, CA.
Passwater: Why did you choose to be a research geneticist? What “hooked” you and when were you “hooked?”
Marini: It was a combination of two things. First, ever since I was young I always enjoyed the “Scientific Method” (though I had no idea that’s what it was called)—trying to figure out a problem or how something worked by making guesses and testing them. Second, I loved looking into a microscope. That’s what pushed me into life sciences. I settled into genetics because early in my graduate career, the field of molecular genetics was exploding with promise and excitement. It still is.
Passwater: What drew you to nutrigenomics or did you just “evolve” into the field as your research progressed?
Marini: Even though nutrigenomics is a relatively new field, I’m relatively new to nutrigenomics. My academic training was in classical microbial genetics and before starting this program, I worked in the biotechnology industry for several genomic technology companies. As the sequencing of the human genome was completed and the genomics fields advanced, genetic diagnostic capabilities increased. However, much of these diagnoses provide information that raise a lot of fear and do not offer many options (such as ovarian cancer and cystic fibrosis). It seemed that for the general public to embrace the value of the Human Genome Project, we as geneticists should be able to provide a class of personal genetic information that was actionable and not frightening or loaded with privacy concerns. The idea behind nutrigenomics—that nutrient intakes can act as genetic modifiers and that nutritional balance can be individually tuned based on one’s genotype—provided the ideal place to look for such genetic information.
Passwater: Indeed, our readers are very interested in the science verifying that nutrients can be “tuned” to one’s individual biochemistry to compensate for disadvantaged genes. Which came first: your interest in doing research at Berkeley or your interest in nutrigenomics? Was there a research team, researcher or program at Berkeley that attracted you?
Marini: Primarily, it was my colleague in these studies, Dr. Jasper Rine, a professor of genetics at Berkeley. It was Jasper who spearheaded the notion that we need to be looking for “good news” (his words) in the human genome and convinced me that this would be worthwhile. In addition, Dr. Bruce Ames (who has appeared several times in this column) has quite a legacy at Berkeley and has long been a proponent of the need to tailor micronutrient levels based on genetics and age (4, 5). I should also mention that we were fortunate to find a corporate partner (Applied Biosystems) that had the foresight to see the value in nutrigenomics and helped with seed funding.
Passwater: Nutrigenomics is a relatively young field. Is it coming of age and are we starting to see practical benefits from the basic science?
Marini: Here, I would like to make a distinction between what I see as nutrigenomics as opposed to what I would call nutrigenetics. The existence of individual gene-nutrient interactions has been known for several decades and has long been providing practical health benefits. For example, there are nutritional therapies for PKU and many rare metabolic genetic defects that are now part of newborn screening programs in most states. On the other hand, I see nutrigenomics as more comprehensively integrating genetic variation on the pathway—or even the genome scale. Thus, nutrigenomics will cover many disciplines including nutrition science, epidemiology, molecular genetics, genomics, metabolic profiling, bioinformatics and systems biology. Obviously, this is really complicated and much technology and data management/analysis methodologies are still being worked out. Nevertheless, genomic approaches have already shed light on genetics underlying diabetes and obesity. I am encouraged by the attention the field is getting, the fact that people are appreciating its potential in delivering significant health benefits safely and inexpensively, and that many researchers are thinking about ways to advance the field.
Passwater: In your June PNAS article, you discussed the gene that produces the methylene tetrahydrofolate reductase (MTHFR) enzyme. What is the role of this enzyme and what is the importance of having a normal MTHFR enzyme as opposed to a disadvantaged enzyme?
Marini: The MTHFR enzyme catalyzes a reaction that modifies a reduced form of folic acid. The product of the MTHFR reaction (5-methyl-tetrahydrofolate) is a critical coenzyme necessary for the synthesis of the amino acid, methionine, as well as the metabolite, S-adenosyl-methionine (SAMe), which is the major methyl donor for cellular methylation reactions. This latter function is really critical since methylation is a very widespread modification of proteins, lipids and DNA and can affect the function of all these. With respect to DNA, methylation patterns can influence genome-wide patterns of gene expression. Thus, the efficiency of the MTHFR reaction has a significant impact on cell physiology.
Passwater: So, folate plays many roles in maintaining human health: it’s been linked to preterm birth and birth defects, as well as to cardiovascular disease, stroke and colorectal cancer. Folate is a generic term referring to many related compounds.
Folates function as a coenzyme in single-carbons transfers. In food, folate is usually in the form of polyglutamates. In supplements, it is usually in the form of folic acid. The recommended daily intake (RDI) is written in terms of dietary folate equivalents (DFE).
Food consists of a complex mixture of polyglutamated tetrahydrofolates (typically 3–11) called pteroylpolyglutamates, characterized according two their carbon one attachments such as formyl (-CHO), methylene (-CH2-) and methyl (-CH3).
These polyglutamated folates are converted to a monoglutamated form of 5-methyltetrahydrofolate (methylfolate) at the brush border membrane of the jejunal mucosa by pteroylpolygutamate hydrolase (conjugase).
Most nutritionists have been taught that the active form of folate is tetrahydrofolic acid (THFA). Newer science shows that methylfolate (also called Metafolin or 5-methyl-tetrahydrofolate) is actually the most active form, as it is loosely bound to plasma proteins and more readily available for carbon transfer. About 80% of folate in the blood is as methylfolate (Metafolin).
Several biochemical steps are needed to convert the folates in food or folic acid in supplements into the active form used by the body to lower homocysteine. First, the polyglutamates (food form) must be converted into simpler monoglutamates. Even the simpler folic acid (supplement form) must be converted into dihydrofolic acid, as must monoglutamates. Next, dihydrofolic acid must be converted into tetrahydrofolic acid, which in turn, must be converted into the active body form, 5-methyl-tetrahydrofolic acid.
We have seen a fair amount of research about identifying SNP variations in the population, but what I especially liked about your recent PNAS paper was that you and your group actually went a step further and looked at the relative effectiveness of the enzymes produced by the various SNPs. Instead of just saying that some genes are disadvantaged genes in that they produce enzymes that are less efficient, you actually produced the enzymes and measured their relative efficiencies. What did your study of MTHFR variants demonstrate?
Marini: I think there are several conclusions. First, low-frequency genetic variants (allele frequencies <1% in the population) may have a significant metabolic impact and, therefore, these should be considered in looking for genetic determinants of disease. Second, while many of the changes we noted negatively affected enzyme function, some did not. Thus, not all variation is equal and this is why functionation studies are so important (as you point out). In fact, this is one of the greatest challenges in human genetics: understanding which genetic changes are the most meaningful. The third point, and probably most important, is that most of the functionally impaired enzyme variants could be improved by elevating intracellular folate levels. The implication is that for MTHFR and other folate utilizing enzymes (possibly all vitamin utilizing enzymes), supplementation may compensate for genetic defects.
Passwater: Well, that certainly is good news! Even though we can’t change our genes, your research implies that if we have a disadvantaged MTHFR gene and we have high homocysteine levels in our blood, we can take supplemental folic acid or Metafolin and test to see if our homocysteine levels return to normal.
Would it be beneficial if people knew if they had certain SNP such as an inefficient MTHFR variant? Is there a practical use for this information? Can a person do something about having a disadvantaged gene?
Marini: Quite possibly. In addition to the lower frequency variants of MTHFR that may be unique to individuals, we already knew of one common variant of MTHFR (an alanine-to-valine change at position 222) that is clinically significant. This particular allele is very common with a frequency of 30% in the global population. The valine enzyme has about 50% activity of the common alanine version due to an enzyme stability defect, but this can be remedied with elevated folate. Clinically, homozygotes of the valine variant with inadequate folate intake show elevated levels of the metabolite homocysteine, which may be a risk factor for diseases such as cardiovascular disease or neural tube defects. In these individuals, homocysteine levels can be corrected with folate supplementation. Thus, there may be a practical use in being aware of any folate-correctable mutation that will lead to homocysteine accumulation.
Passwater: Did your research demonstrate that nutrient supplementation actually compensated for the SNP variant, at least to some beneficial degree?
Marini: In one sense. We focused on enzyme function and found that elevated levels of folate boosted the activity of some mutant enzymes. In some cases, we were even able to restore full function. However, we did not look at the metabolic consequences of these variants in individuals or what outcomes of folate supplementation may yield.
Passwater: That certainly gives scientists a strong foundation to study the benefits of supplemental vitamins in the segment of the population afflicted with disadvantaged genes. Dr. Bruce Ames has spoken to our readers in this column before about fine tuning metabolism with nutrient supplementation. Does your research suggest that it can become practical to uncover unsuspected disadvantaged genes and then scientifically fine-tune them?
Marini: Yes, in theory. However, I need to emphasize that uncovering enzyme variants in the population and determining their effect on enzyme function is much easier than trying to understand the impact of that enzyme variant on the metabolic status of an individual. For example, a defective enzyme may be relatively insignificant metabolically if that step is not rate-limiting or excess substrate in the cell can still drive the reaction efficiently. On the other hand, mildly impaired enzymes may have a significant impact when combined with other variants. It’s difficult to extrapolate the behavior of a single enzyme in an assay to changes in an individual.
Passwater: Does your study suggest that there may be more MTHFR variants than previously understood? Does this imply that there may be many more SNPs that involve nutritional pathways than previously thought?
Marini: Probably. I think that extrapolation of our findings for MTHFR combined with what other researchers are uncovering in other sequencing studies is really pointing to the significance of low-frequency variation, not only in nutritional pathways, but throughout the entire genome.
Passwater: If the population has so many different genetic variants, would this suggest that that the optimal diet or nutrient intake may have variation from person to person?
Marini: Yes. Although that is not to say that there will be as many optimal diets as people—individuals with different genotypes may share the same optimal intakes. However, I do truly believe that genomic information will, at some point, be critical in determining how to tailor one’s diet. And if low-frequency or individual-level variation contributes significantly to metabolism, it will only be uncovered by re-sequencing the entire genome. This goal of sequencing an entire individual genome inexpensively and routinely is a main driver in developing newer-generation DNA-sequencing technology.
Passwater: What is the next variant that you will be examining and where do you see your research leading you?
Marini: I think we need to examine more closely the true clinical utility of vitamin-remedial alleles in diagnosing and treating disease. We are currently collaborating with scientists from the Children’s Hospital Oakland Research Institute to study the etiologies of neural tube defects (NTDs). The epidemiology indicates that NTDs are folate-preventable and there is a genetic component that has been difficult to unravel. We are starting a study similar to what we did for MTHFR (a lot of sequencing and functionation) but looking at several folate enzymes in cases and controls. Studies like this in which we can correlate enzymatic function with clinical phenotype will be essential for moving this concept forward.
Passwater: Dr. Marini, our readers thank you for your brilliant research and reviewing it with us. We look forward to seeing the fruits borne from the research of the entire Berkeley group. WF
1. N.J. Marini et al., “The Prevalence of Folate-Remedial MTHFR Enzyme Variants in Humans,” PNAS 105 (29), 8055–8060 (June 10, 2008)
2. Science Daily, “Good News in our DNA: Defects You Can Fix with Vitamins and Minerals,” http://www.sciencedaily.com/releases/2008/06/080602214135.htm, (June 3, 2008)
3. J. Ruflin, J. Foreword. Nutritional Genomics.
4. R. Passwater, “Tuning Up Metabolism: Vitamins, Minerals and Key Biochemicals Can Aid in Cancer Prevention and Help Delay Signs of Aging: An interview with Bruce N. Ames, Ph.D. Part 1: Mutations, Genetic Diseases, and Slowing Aging,” WholeFoods Magazine, 25 (11), 60–62 (2002).
5. R. Passwater, “Tuning Up Metabolism: An Interview with Dr. Bruce N. Ames. Part 2: Treating Many Genetic Diseases with Megavitamins,” WholeFoods Magazine, 25 (13), 42–45 (2002).
© 2008 Whole Foods Magazine and Richard A. Passwater, Ph.D.
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