Neurotransmitters

DNA Methylation Pathway

In my post last week I briefly talked about the methylation pathway, also called the MTHFR cycle and how disruptions in this pathway may appear on an Organic Acid Test (OAT).  Today, I will go more in-depth into this pathway. Since most practitioners have at least some knowledge of this its function, I’ve decided to focus on the more important polymorphisms (SNPs) common to these genes and on the treatments that work the best for these mutations.  Patients should talk to their healthcare practitioner before starting any treatment. 

The important role of methylation is gaining in popularity among functional medicine groups these days because mutations are quite common and lead to many different chronic conditions. Practitioners interested in treating the root cause of illness are especially interested in learning about this pathway because nucleotide synthesis, neurotransmitter function, detoxification, and numerous other processes are greatly improved once these mutations have been compensated for, leading to much better patient outcomes.

If you’re not already familiar, the methylation pathway is a process by which carbons are added onto folic acid from amino acids and redistributed onto other compounds throughout the body.  This process is responsible for the formation of methionine, S-Adenosyl methionine (SAM), and thymidylate monophosphate (dTMP).  Mutations in this pathway usually lead to the reduction of methionine which leads to the absence of S-adenosyl methionine (SAM). This compound facilitates virtually every methylation reaction in the body. These reactions include the promotion of several neurologically important agents, histamine breakdown, CoQ10 synthesis, and tissue-specific gene expression. The accumulation of homocysteine, which is caused by mutations in this pathway, has been directly linked to oxidative stress which influences multiple factors of disease.      

When we designed the GPL-SNP1000 test, we knew that most other genetic tests were only reporting about 35 SNPs of the common methylation pathway enzymes. When we did our literature research, we found 105 different methylation SNPs that could potentially cause health conditions and included all of these to provide a more useful tool for practitioners.

MTHFR

Methylenetetrahydrofolate reductase (MTHFR) is an enzyme that converts 5,10-methylenetetrahydrofolate to 5,methyltetrahydrofolate, which is the active form of folate.  Mutations in this gene cause the accumulation of homocysteine and a lack of available folate for cellular functions. Both of these factors have been linked to oxidative stress, vascular disease (including cardiovascular), neural tube defects, neurological disorders (including schizophrenia and bipolar disorder), cancer, preeclampsia, hypotonia, and seizures.  Common mutations are rs1801133 (C677T), rs1801131 (A1298C), and rs2274976 (G1793A).  The C677T polymorphism is present in about 39% of caucasians as heterozygotes and 17% as homozygotes.  Table 1 provides data on how much activity your MTHFR enzyme would possess with different combinations of the C677T and the A1298C.

TABLE 1

TABLE 1

Patients with polymorphisms in MTHFR may consider supplementing with methyl-B12 (also called methylcobalamin) and methyl-folate.  We recommended starting at a very low doses and building up.

MTR

Methionine synthase (MTR) is also known as 5-methyltetrahydrofolate-homocysteine methyltransferase.  This enzyme facilitates the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine using cobalamin (B12) and MTRR enzyme as a catalyst. The end products of this reaction are the amino acid methionine and the vitamin tetrahydrofolate.  Mutations in this gene lead to a lack of methionine and the accumulation of homocysteine in the body (hyperhomocysteinemia).  The pathological consequence of the gene mutation depends on how profoundly these methylation pathways are affected and the degree of homocysteine accumulation in the body.  The most common polymorphism is rs1805087 (A2756G), which most genetic tests do analyze.  However, we decided to look at seven different SNPs including the rs121913581 (R52Q) polymorphism.  This is a rare polymorphism; however it could dramatically affect the activity of patients with MTR polymorphisms, who should also consider methyl-B12, as well as S-adenosyl methionine (SAM) supplementation.  ).

MTRR

Methionine synthase reductase (MTRR) is also known as 5-methyltetrahydrofolate-homocysteine methyltransferase reductase.   MTRR is important for the methylation of cobalamin and subsequent activation of methionine synthase (MTR).  Mutations in this gene lead to a lack of methionine and the accumulation of homocysteine in the body (hyperhomocysteinemia). Some common mutations in this pathway are RS1801394 and RS10380.  Patients who are heterozygous for MTHFR mutations and concomitant mutations to MTRR have a greater loss of function and increased levels of homocysteine. Patients with MTRR polymorphisms should consider methyl-B12 and SAMe supplementation. 

AHCY

Adenosylhomocysteinase (AHCY) is also known as S-adenosylhomocysteine hydrolase.  AHCY is an enzyme involved in the degradation of the amino acid methionine.  AHCY converts the methionine substrate S-adenosylhomocysteine (SAH) to adenosine and homocysteine. This reaction is an important part of the regulation of methyl groups which are added to DNA, RNA, proteins, and lipids (fats).  Methyl groups help regulate what parts of the genome are active and control protein activity.  Mutations to the AHCY gene can cause methionine to accumulate in the blood, which is called hypermethioninemia (MET).  Two common mutations are Trp112X which causes tryptophan to be replaced with a premature stop signal and Tyr143Cys.  MET  can manifest in neurological problems, delays in motor skills, muscle weakness, and liver problems.  Patients with MET should consult with a dietician to avoid the amino acid methionine.

BHMT

Betaine-homocysteine methyltransferase (BHMT) and BHMT2 are the only enzymes that can metabolize betaine.  This reaction is considered the alternate or short route for methylation.  BHMT uses zinc as a co-factor to catalyze the transfer of a methyl group from betaine to homocysteine.  There are several mutations in the human population that decrease the activity of this enzyme.  BHMT mutations can result in fatty liver and hepatocellular (liver) carcinomas.  BHMT mutations in mothers increase the risk of Down syndrome for their children.  Patients with BHMT polymorphisms are recommended to take betaine and zinc.

CBS

Cystathione beta-synthase (CBS) is a pyridoxal-5’-phosphate (vitamin B6) dependent enzyme that converts L-serine and L-homocysteine into L-cystathionine.   L-cystathionine is later converted into the amino acid cysteine.  Mutations to the CBS gene are the most common cause of hereditary hyperhomocysteinemia.   The adverse effects of homocysteine accumulation in the body are related to the substitution of homocysteine for methionine in protein synthesis. The resulting complications include an increase in immune response, increase in cell death, and protein damage. The degree of homocysteinemia is relative to the mutation.  Hyperhomocysteinemia has been linked to multiple mutations to the CBS gene.  The most common of these are the Ile278Thr and the Gly307Ser, which cause homocysteine to build up in the blood.  Complications of hyperhomocysteinemia include mental retardation, seizures, and vascular disease. One of the most common causes of death for patients with homocystinuria (CBS deficiency) is heart attack.   Patients with CBS polymorphisms are recommended to take glutathione and B6.  There are reports that the CBS polymorphisms A360A (rs1801181) and N212N (rs2298758) can lead to an increase in CBS activity.  Some claim that these mutations lead to a buildup of ammonia and decrease in glutathione. Since ammonia is a very unstable compound that must be measured STAT for accurate results, the better marker for increased ammonia is orotic acid which is very stable and accumulates when excessive amines are filtered through the urea cycle. I recommend that patients with this mutation do an Organic Acid test (OAT) and look at marker 60 (orotic acid) for ammonia and markers 58-59 (Pyroglutamic and 2-hydroxybutyric acid) for glutathione synthesis and cysteine accumulation respectively.

SHMT1

Serine hydroxymethyltransferase (SHMT1) is important for linked reactions.  The first is the conversion of tetrahydrofolate to 5,10-methylenetetrahydrofolate.  The second is the conversion of L-serine to glycine.  It also has a role in mediating the synthesis of dTMP and SAM. It preferentially selects for dTMP biosynthesis which is the precursor to the nucleic acid thiamine. Mutations in this enzyme may cause elevations in uracil which can build up when dTMP synthesis in impaired.  Uracil is marker 40 in the OAT.  

SUOX

Sulfite oxidase (SUOX) is an enzyme that is located in the mitochondria of cells.  The enzyme oxidizes sulfite to sulfate.  The physiological damage that occurs as a result of enzyme deficiency may be due to the accumulation of toxic levels of sulfite, from the absence of sulfate, or both. Sulfite is a reactive product of cysteine metabolism found in high concentrations in the brain. Its toxicity is exacerbated by glutathione depletion. Sulfate plays an important role in detoxification and deactivation of toxic compounds. Sulfate deficiency has been linked to autism, Parkinson’s disease, and Alzheimer’s disease.  Individuals with SUOX genetic mutations may benefit from a reduction in dietary methionine and cysteine.

VDR

Vitamin D receptor (VDR) is a nuclear hormone receptor for vitamin D3.  Vitamin D3 interacts with this receptor to influence multiple biological activities by regulating gene transcription.  Vitamin D3 is associated with maintenance of calcium distribution. More recently, it has been implicated in inflammatory processes, vascular integrity, and collagen formation. Mutations in VDR have been linked to metabolic syndrome.  Individuals with VDR mutations have greater propensity for insulin insensitivity, higher triglycerides, and lower HDL levels.  Vitamin D receptor mutations can also lead to vitamin-D-dependent rickets type 2.  Patients with VDR polymorphisms are recommended to take 1000 units/day for children or 5000 units/day for adults. 

I hope this information is helpful.  I know many of these pathways can be very intimidating, but hopefully we can work together to produce useful treatment plans for everyone.  Next week I plan on talking about the mental health genes MAO and COMT.

Email gplblog@gpl4u.com if you have any questions about this blog post.

Genetic Testing and Organic Acids Testing: A Dynamic Duo of Diagnostics

Today I have two words for you:  Personalized medicine.  What does this phrase mean to you?  When I think of personalized medicine I think of treatments that are custom designed for each individual patient, and I believe this is the ultimate goal for all of us in the field of functional medicine.  To make this happen, we will have to work together as a team - the healthcare practitioner, the lab, and the patient.  If we do so effectively, the result should be better health and improved lives of our patients.  The only way to get there is to design a treatment plan that addresses the underlying cause(s) of our patient’s ailments and not try to just suppress the symptoms. 

When I talk to both practitioners and patients, they often ask “Where do we start?” or “What is your most important test?”, and until recently I would have always said that the Organic Acids Test (OAT) is the obvious place to start.  The reason for this is that the OAT provides more information than any other test.  The OAT gives us a metabolic snapshot of multiple pathways in the body, offering insight into possible underlying causes of symptoms, as well as what kind of nutritional support is needed.  However, now the OAT by itself is no longer the obvious choice.  I am now recommending the OAT + GPL-SNP1000 combo because these two tests, one metabolic and one genetic, work so well together.   Today I would like to share some of the markers in each of these tests that work really well in tandem.    The primary pathways where we see overlap between the two tests are methylation, mental health, detoxification, and oxalate metabolism. 

The first pathway that GPL-SNP1000 covers is the DNA methylation pathway, also called the MTHFR pathway.  This pathway is a process by which carbons are added onto folic acid from amino acid and redistributed onto other compounds throughout the body.  This process is responsible for the formation of methionine, S-Adenosyl methionine (SAMe), and thymidylate monophosphate (dTMP).  These compounds are then used in neurotransmitter metabolism, detoxification, nucleotide synthesis, and multiple other processes.  I can’t say enough about how important neurotransmitter metabolism and detoxification of chemicals are to everyone’s health.  We have so many patients for whom the majority of their symptoms result from the upset of these two processes.  Since the methylation pathway is so important we decided to make it a high priority in our new genetic test.   GPL-SNP1000 looks at 105 different methylation SNPs (single-nucleotide polymorphisms).   Next week I plan on going more in-depth on the methylation pathway and how GPL-SNP1000 can be useful.

So what markers in the OAT are important for patients with MTHFR mutations?  The first one we have is vitamin B12.  We evaluate B12 levels by measuring the amount of methylmalonic acid (see Figure 1).  B12 is an important cofactor for many of these methylation enzymes.  The second important marker is pyridoxic acid, which is a form of vitamin B6. I have counted over 50 enzymes that require B6 in the body.  It is an important cofactor in the methylation pathway.  It is directly involved with the function of CBS enzyme and indirectly involved with MTHFR, BHMT, and SHMT.  Another marker involved with the MTHFR pathway is uracil.  Having an elevated uracil level can be indicative of folate pathway malfunction.

The next pathway that is helpful to analyze in both the OAT and GPL-SNP1000 is the mental health pathway, which involves the synthesis and breakdown of neurotransmitters in the brain.  The combination of measuring the neurotransmitter metabolites and knowing if the enzymes involved are functional will help guide us to the best treatment options.  GPL-SNP 1000 covers 14 different mental health genes, which I will cover next week (I’m trying not to make these blog posts too long).  Three of the best markers in the OAT for measuring neurotransmitter metabolism are homovanillic acid (a dopamine metabolite), vanilymandelic acid (epinephrine/norepinephrine), and 5-HIAA (serotonin, marker).  These markers are the metabolites of the neurotransmitters by the enzymes MAOA and COMT (see Figure 2), the genes for which are analyzed in GPL-SNP1000.  Deficiencies in these enzymes due to faulty SNPs  may cause low neurotransmitter levels, which may also be caused by low amounts of precursors, cofactors, or increased inhibitors which is why information from both the OAT and GPL-SNP1000 is so incredibly useful.   

The third pathway that I will briefly touch on today is the detoxification pathway, and specifically for glutathione (GSH).  Detoxification is so important in today’s industrial, polluted, and toxic world.  Every day we are inundated by hundreds of chemicals.  We are exposed to many through the environment and some by choice (like medications).  Our bodies have to process these chemicals in some way.  GPL-SNP1000 looks at dozens of genes that are important for detoxification.  A good marker in the OAT for how well the body is detoxifying is pyroglutamic acid.  Elevated values of pyroglutamic acid are indicative of glutathione deficiency due to excessive toxic exposure or a genetic issue. 

The final pathway I’m going to discuss today is oxalate metabolism.  Oxalates are crystalline molecules that we absorb from our diet (high oxalate foods) or are produced by an infection, like yeast/fungal overgrowth.  These oxalates can accumulate in the body and cause inflammation.  The symptoms of oxalate accumulation include pain, nephrolithiasis, and neurological symptoms. Oxalates are known to cause/create kidney stones.  Children with autism who exhibit eye-poking behavior have been shown to have a build-up of oxalates behind their eyes, causing tremendous pain, and thus the eye-poking.  GPL-SNP1000 covers five different genes involved with the production and elimination of oxalates.  The OAT has three oxalate markers:  glyceric, glycolic, and oxalic acids. (Figure 3)  In addition, low B6 and increased yeast or fungal markers are associated with increased oxalates. 

I think that is all I’ll cover today.  In the future I will cover the methylation pathway and the neurotransmitter pathway a little more in-depth.  If there is another pathway you want me to cover in greater detail, please let me know.  I want to be a part of your healthcare team as we all work together for the better well-being of our patients.

Email gplblog@gpl4u.com if you have any questions about this blog post.