SNP

New Marker Additions to GPL-SNP1000 DNA Sequencing Profile

BY: MATTHEW PRATT-HYATT, PHD

The number one goal for The Great Plains Laboratory is to provide the best quality results to our clients.  Our GPL-SNP1000 DNA Sequencing Profile has proven to be a great tool in helping provide personalized healthcare to our clients.  The nine pathways we analyze include: methylation, mental health, oxalate metabolism, drug and environmental metabolism/detoxification, gluten sensitivity, cholesterol metabolism, autism risk genes, and transporter gene.  These are crucial biological pathways, which are at the root of many chronic health conditions.  We are now announcing the addition of nine new markers to our already incredibly comprehensive genetic test:

Dopamine Beta Hydroxylase (DBH)
This is an enzyme that catalyzes the oxidation hydroxylation of dopamine to norepinephrine.  DBH can be inhibited by phenolic compounds including those produced by Clostridium species as well as certain organophosphate herbicides and pesticides.  There are two SNPs that can cause decreased activity of DBH.  These are rs2007153 and rs2283123.  These polymorphisms can lead to an increase in dopamine levels and a deficiency in norepinephrine.  Mental health disorders can result because of the imbalance of dopamine and norepinephrine.  Common symptoms can include depression and anxiety.

Paroxonase 1 (PON1)
This is an important enzyme in the metabolism and elimination of many organophosphorus insecticides (PMID: 13032041) and is located mainly in the liver.  PON1 is important in the reduction of atherosclerosis because of its involvement in the protection of high and low density lipoproteins from oxidation.  Individuals with polymorphisms to PON1 are more susceptible to heart disease (PMID: 8675673).  There are two known polymorphisms that can decrease the activity of PON1 and make the individual more susceptible to pesticide exposure, which are Q192R (rs662) and L55M (rs854560).

Hemochromatosis Protein (HFE)
The hemochromatosis gene HFE (high iron) codes for the HFE protein.   This protein is important for regulating the uptake of circulating iron.  This is done by regulating the interaction between transferrin receptor with transferrin.  SNPs to this gene can cause hemochromatosis, a disorder in which the body loads excess iron, which is autosomal recessive.  This means the patient normally needs two bad copies of the gene in order to exhibit symptoms.  There are three SNPs that can lead to hemochromatosis, rs1800562, rs1800730, and rs1799945.  Patients that are homozygous positive for this SNP should have their iron level measured. 

Vitamin K Epoxide Reductase Complex Subunit 1(VKORC1)
This is an enzyme that is necessary for the reduction of vitamin K 2,3-epoxide to its active form, which is important for clotting.  This enzyme is the primary target for the drug warfarin (Coumadin).  The three SNPs that are associated with warfarin sensitivity are rs9923231 (VKORC1*2), rs9934438, and rs8050894.  These polymorphisms can be used in conjuncture with the genotype of Cyp2C9 in order to accurately dose warfarin.

Tryptophan Hydroxylase 2 (TPH2)
This enzyme catalyzes the first and rate-limiting step in the biosynthesis of serotonin. Mutations to this enzyme have been associated with numerous psychiatric diseases including depression, OCD, bipolar disorder, and suicidal behavior.

Major Histocompatibility Complex DQA1 and DQA8
Patients with SNPs to HLA DQA1 and DQA8 have a higher risk of celiac disease.   The HLA-DQA1 and DQA8 are human leukocyte antigen serotype (also called major histocompatibility complex II). The role of this peptide is to present proteins on the surface of cells for identification purposes. This particular serotype presents proteins belonging to a foreign invader on the cells the macrophages, B cells, and dendritic cells in order to activate the helper T cells of the immune system. Proper presentation is critical for immune system activation against pathogens and may possibly be a mediator of autoimmunity.

UDP Glucosyltransferase 1A1 and 1A8 (UGT1A1 and UGT1A8)
These enzymes are important members of the glucuronidation phase II detoxification pathway.  These enzymes catalyze the addition of a glycosyl group from a nucleotide sugar to a small hydrophobic molecule.  The addition of glycosyl groups results in these molecules becoming more water-soluble and easier to excrete. Some of the target molecules for these enzymes include bilirubin, drugs, hormones, and steroids.

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.