About the Author
Beth Ellen DiLuglio, MS, RDN, CCN, LDN is a Certified Clinical Nutritionist and Registered Dietitian with a 20 year history of certification in nutrition support. Beth earned a Master of Science degree in Human Nutrition from Columbia University in New York City. She earned her Bachelor’s in Biology/Psychology and developed a course of independent studies in Nutrition at Wheaton College in Norton, Massachusetts. Beth also completed “Applying Functional Medicine in Clinical Practice” through the Institute for Functional Medicine (IFM) and continues to train in the areas of Functional Laboratory Assessment and Functional Clinical Nutrition.
Introduction
Advances in genetic research confirm that we may be as different on the inside as we are on the outside. Genetic makeup is clearly reflected in outward appearance but genetic differences on the inside are not so obvious. Genes control production of the very elements that drive our biochemical machinery such as cofactors, enzymes, and other proteins. These elements are involved in metabolic activities from tissue building and repair to energy generation and detoxification. In turn genetic variations, particularly single nucleotide polymorphisms (SNPs), generate variations in enzyme activity, metabolic competence, and even nutrient requirements. SNPs and their expressions are believed to help explain susceptibility of certain individuals to specific diseases.[i]
SNPs significantly influence detoxification/biotransformation (ability to breakdown and eliminate endogenous hormones and exogenous toxins); individual response to certain drugs and medications; and even disease risk. Ongoing research reveals associations between SNPs and complex diseases including heart disease, diabetes, and cancer, and vascular disorders such as abdominal aortic aneurysm.[ii] [iii] [iv] [v] [vi] [vii] Additional factors such as consumption of alcohol may have a synergistic effect with certain SNPs, considerably increasing cancer risk, especially of the esophagus, stomach, and liver.[viii]
Background and rationale
Understanding SNPs and their consequences is essential to understanding both health and disease. SNPs that affect methylation (one-carbon transfer) have particularly wide-reaching effects. Adequate methylation is critical for DNA function and gene regulation; detoxification/biotransformation; homocysteine and amino acid metabolism; and glutathione synthesis. Altered methylation can ultimately affect DNA stability and gene expression.[ix] [x]
Folate plays a pivotal role in these reactions and hence is required by almost all tissues in the body including the brain.[xi] Therefore genetic variations in folate metabolism and one-carbon methylation reactions have a profound influence on disease risk. They are associated with elevated homocysteine levels, impaired methylation processes, and limited detoxification capacity. These factors can contribute to accelerated aging, chronic disease (e.g. cancer, cardiovascular disease, and neurodegenerative disorders), impaired gene regulation, poor drug clearance, and impaired neurotransmitter metabolism.
SNPs in the the methylenetetrahydrofolate reductase (MTHFR) gene and its role in methylation and homocysteine metabolism have been extensively researched. However, while knowing your patient’s MTHFR status is important it may not reflect the entire clinical picture. Research reveals that a number of genes, beyond MTHFR, influence not only methylation cycles but downstream byproducts and gene function.[xii] Such genes include 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR), 5-methyltetrahydrofolate-homocysteine methyltransferase reductase (MTRR), catechol-O-methyltransferase (COMT), and AHCY (S-adenosylhomocysteine hydrolase). These genes play a major role in a patient’s methylation and detoxification capacity, neurotransmitter competence, and homocysteine metabolism.[xiii] [xiv] [xv] [xvi] [xvii] Measurement and monitoring of homocysteine levels are of equal importance as serum homocysteine can serve as a biomarker used to assess methylation.
Advanced Genetic Testing
Advanced genetic testing for SNPs allows a practitioner to take into account a patient’s unique genetic makeup when developing a care plan. Identifying SNPs and monitoring associated biomarkers lays the foundation for “personalized lifestyle medicine.” This focused approach enhances not only the practitioner’s ability to see the clinical picture clearly but enhances patient care and outcomes.[xviii] [xix] [xx] [xxi]
MTHFR testing strictly evaluates folate metabolism. Additional testing for SNPs in other genes that influence methylation potential and metabolic function provides a more comprehensive approach and may reflect a new set of “best practices.” Practitioners are acknowledging that testing for only MTHFR is no longer enough.
While knowing your patient’s MTHFR gene function is vital, it’s not enough to understand the whole clinical picture. MTR, MTRR, COMT, and AHCY are additional genes that play a major role in understanding patient methylation/detoxification capability. Knowing about the functioning of these genes can enable healthcare providers to address important chronic medical conditions. Methylation is also monitored using homocysteine levels. MTHFR only evaluates folic acid metabolism. Genetic variations in a variety of SNPs can influence methylation potential and this is why testing for only MTHFR is no longer enough.
Homocysteine
Homocysteine is an amino acid that is a part of methylation cycles yet at elevated levels it can become toxic to cells, damage blood vessels, promote oxidation, elicit an autoimmune response, increase risk of atherosclerosis, and contribute to dementia, depression, and neural tube defects.[xxii] [xxiii] [xxiv] [xxv] [xxvi] [xxvii] [xxviii] [xxix] [xxx] [xxxi] [xxxii] [xxxiii]
Though homocysteine is generated from methionine, it must be continuously recycled back to methionine (or on to cystathionine) in order to avoid accumulation. A number of genes play an active role in the overall processing of homocysteine and associated SNPs can disrupt that process and lead to toxic Hcy levels.[xxxiv] [xxxv] [xxxvi] [xxxvii] [xxxviii] [xxxix] [xl] Methionine/homocysteine balance is important for optimal health; the primary purpose of such balance is to ensure proper methylation by donating methyl groups for:
- DNA methylation (gene regulation)
- Regulation of neurotransmitters (e.g. epinephrine, norepinephrine, and dopamine)
- Detoxification of catecholamines from the environment
- Drug clearance (phase II liver detoxification)
- Homocysteine is also a precursor in the biosynthesis of L-cysteine for glutathione; glutathione is important for the detoxification of electrophilic compounds (metals).
Elevated serum homocysteine (Hcy) is a widely accepted marker for methionine/homocysteine imbalance, which is a genetically controlled process. Elevated homocysteine levels can lead to accelerated aging, cardiovascular disease and neurodegenerative disorders among others.[xli] [xlii] [xliii]
Single Nucleotide Polymorphisms
Methylenetetrahydrofolate reductase (MTHFR) is an enzyme that regulates folate metabolism in the body. Specifically MTHFR converts 5,10-methylenetetrahydrofolate into 5-methyltetrahydrofolate (5-MTHF), the active form of folate. 5-MTHF then plays a key role in the single carbon transfer (i.e. methylation) reactions involved in the synthesis of nucleotides for DNA and RNA production; manufacture of S-adenosylmethionine (SAM-e); methylation of DNA, proteins, neurotransmitters, and phospholipids; and remethylation of homocysteine to methionine.[xlvi] [xlvii] MTHFR is especially critical in converting synthetic folic acid (which lacks coenzyme activity) to active 5-MTHF.[xlviii]
A SNP in the MTHFR gene (also known as methylenetetrahydrofolate reductase (NAD(P)H)) can ultimately jeopardize the methionine/homocysteine cycle leading to toxic levels of Hcy. Ultimately MTHFR SNPs can cause hyperhomocysteinemia (especially if folate levels are low); affect neurological, behavioral, and vascular health; contribute to birth defects, miscarriage, and preeclampsia; modulate cancer risk; and increase chronic disease risk.[xlix] [l] [li] [lii] [liii] [liv] [lv]
If a patient has acquired MTHFR SNPs from both parents (homozygous positive), she/he likely has significantly reduced MTHFR activity and a marked deficiency of 5-MTHF. If the patient received the SNP from only one parent (heterozygous positive) she/he may have suboptimal MTHFR function. At present the two most researched and understood MTHFR SNPs are 677C>T (C667T also called rs1801133) and 1298A>C (A1298C also called rs1801131). Testing these SNPs can help assess how well homocysteine can be cleared from the blood.[lvi] [lvii] [lviii] [lix] The final expression and influence of these variants can be affected by nutritional status, environment, genotype, and race/ethnicity.
Supplementation: When MTHFR SNPs are present, supplementation with 5-MTHF is recommended. Prolonged exposure to folate may be preferred to high doses that can be rapidly excreted.[lx] [lxi] Patient tolerance to supplementation should be monitored and nutrient administration individualized accordingly. It is equally important to promote intake of folate from food sources. Healthful folate sources include dark leafy greens, spinach, asparagus, legumes (e.g. lentils, chick peas, lima beans, black beans, kidney beans, pinto beans, green peas), Brussels sprouts, avocadoes, and broccoli.[lxii] [lxiii] [lxiv]
MTR[lxv] [lxvi]
5-methyltetrahydrofolate-homocysteine methyltransferase is the gene that codes for (i.e. provides instructions for) the methionine synthase enzyme (also known as cobalamin-dependent methionine synthase). Methionine synthase (MS) facilitates regeneration of methionine, an amino acid critical to protein synthesis in the body. During the process 5-MTHF serves as a methyl donor and vitamin B12 as the methyl transfer compound. In a first reaction, MS attaches the methyl group from 5-MTHF to cobalamin, forming a MS-methylcobalamin complex. The MS-methylcobalamin complex then transfers this methyl group to homocysteine, thus converting it into methionine.
During this process, cobalamin becomes oxidized over time and has to be reduced again to maintain proper function. During this step methionine synthase reductase (encoded by the MTRR gene) utilizes S-adenosylmethionine (SAM-e) as a methyl donor to regenerate methylcobalamin.[lxvii] Ultimately methionine synthase is crucial to amino acid metabolism; maintaining safe levels of homocysteine; and maintaining adequate cellular levels of methionine and SAM-e. SAM-e in turn is an essential methyl donor during DNA/RNA metabolism and neurotransmitter synthesis.
The MTR gene mutations C3518T and A2756G affect function of the enzyme even in the heterozygous form. They are associated with higher homocysteine levels and may lead to hypomethylation.
Supplementation: MTR SNPs may manifest as a methylcobalamin deficiency.[lxviii] When genetic mutations are present in the MTR gene, supplementation with methylcobalamin (methylated form of vitamin B12) is recommended.
MTRR[lxix] [lxx]
The 5-methyltetrahydrofolate-homocysteine methyltransferase reductase gene codes for methionine synthase reductase (MSR), an enzyme that remethylates cobalamin to methylcobalamin and reduces or “reactivates” oxidized methionine synthase so that conversion of homocysteine to methionine can continue.
SNPs in the MTRR gene may lead to an MSR enzyme that is less effective or ineffective, contributing to megaloblastic anemia as well as elevated levels of homocysteine in blood and urine. A common MTRR SNP known as A66G appears to be specifically associated with neural tube defects, colorectal cancer, cardiovascular disease, and increased risk of Down syndrome.[lxxi] [lxxii] [lxxiii] [lxxiv] The A66G polymorphism. In combination with the MTHFR C677T polymorphism, MTRR genotypes AG/GG influence total plasma homocysteine levels. Additionally, the combination of the genetic polymorphisms in MTRR and MTHFR was linked to an increase in DNA damage as measured by micronucleus frequency (MN).
Supplementation: When genetic mutations are present in the MTRR gene, supplementation with SAM-e is recommended.
COMT[lxxv] [lxxvi]
The catechol-O-methyltransferase (COMT) gene codes for an enzyme of the same name. The enzyme itself is produced in two forms. The long form, membrane-bound catechol-O-methyltransferase (MB-COMT), is synthesized primarily by nerve cells in the brain. Here the COMT enzyme facilitates degradation of catecholamine neurotransmitters (e.g. dopamine, epinephrine, and norepinephrine) by catalyzing the transfer of a methyl group from SAM-e to the catecholamines. The same activity facilitates the breakdown of catechol drugs (e.g. those used in treatment of hypertension, asthma, and Parkinson’s disease). COMT plays an especially important role in maintaining neurotransmitter balance in the prefrontal cortex where personality, behavior, emotion, abstract thinking, and short-term memory are managed.[lxxvii] The shorter form of the COMT enzyme (soluble catechol-O-methyltransferase (S-COMT) helps control hormone levels the blood, liver, kidneys, and other tissues.
Two SNPs, Val108/158Met and Ala52/102Thr, are known to alter COMT methylation capacity.[lxxviii] These two SNPs of the COMT gene are associated in literature with[lxxix] [lxxx] [lxxxi] [lxxxii] [lxxxiii] [lxxxiv] [lxxxv]
- Impaired DNA methylation
- Impaired neurotransmitter metabolism
- Decreased drug metabolism (important in neurodegenerative disorders)
- Decreased detoxification of toxic catecholamines from the environment
- Chronic widespread pain and fibromyalgia
- Involvement in the manifestation of a variety of human disorders, including estrogen-induced cancers, Parkinson’s disease, depression, and hypertension
Supplementation: When genetic mutations are present, supplementation with SAMe is often recommended. Attention should be paid to other medications being taken, including anti-depressants.
AHCY[lxxxvi] [lxxxvii] [lxxxviii]
The adenosylhomocysteinase (AHCY) gene codes for S-adenosylhomocysteine hydrolase, the enzyme that converts S-adenosylhomocysteine (AdoHcy) to adenosine and homocysteine in a reversible hydrolysis reaction that occurs during methioinine metabolism.[lxxxix] This conversion is an integral step in methylation and its related functions including the carrying out of DNA instructions, regulation of protein and lipid metabolism, and neurotransmitter processing.
Initially SAM-e (also known as AdoMet) is converted to AdoHcy after donating its methyl group in a step catalyzed by COMT (see COMT). AdoHcy is then converted by S-adenosylhomocysteine hydrolase back to homocysteine. (Nicotinamide adenine dinucleotide (NADH) serves in this reaction as a co-factor for AHCY.) The ratio or balance between SAM-e and AdoHcy is referred to as methylation potential. Because AdoHcy inhibits methylation, it is crucial that conversion of AdoHcy to homocysteine occur immediately in order to maintain optimal methylation potential.
Several genetic polymorphisms (SNPs) in AHCY are known to alter activity and expression of the S-adenosylhomocysteine hydrolase enzyme, leading to elevated AdoHcy concentrations and impaired methylation potential. Recent studies show association between those mutations and poor methylation potential, severe myopathies, developmental delays, and hypermethioninemia.
Supplementation: When genetic mutations are present, supplementation with NADH (nicotinamide adenine dinucleotide + hydrogen) is often recommended. Supplementation with SAMe may also be recommended.
Summary
There is a growing body of knowledge and awareness with regard to nutrigenomics, nutrigenetics, and functional genetic testing. This research supports the premise in functional medicine that “genes load the gun, but environment pulls the trigger.” The recognition that genes, nutrients, and the environment interact on such a fundamental level is an important component of comprehensive healthcare. In view of this knowledge, hopefully testing for SNPs will become routine and correcting for these variants will become best practice.[xc]
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