Genomics, Epigenetics, Chemistry Flashcards
inborn error of amino acid metabolism
The inborn error of amino acid metabolism classic homocystinuria
an elevated blood level of homocysteine may be an
independent risk factor for CVD.
A defect in the vitamin B6–
requiring enzyme cystathionine beta-synthase prevents the conversion of homocysteine to cystathionine. Homocysteine
accumulates, appears to promote atherogenesis, and forms the
dipeptide homocystine, which leads to abnormal collagen
crosslinking and osteoporosis. Nutrition therapy is multipronged,
depending on the specific genetic defect. Some individuals
have an enzyme defect that requires a high concentration
of the vitamin B6 cofactor for activity. Others are not
responsive to B6 and need a combination of folate, vitamin B12,
choline, and betaine to convert homocysteine to methionine.
Others must limit their methionine intake. At least three forms
of homocystinuria exist, each requiring a different nutritional
approach. The ability to use genetic analysis to distinguish these
similar disorders has been a useful technological advance (see
Chapters 7, 32, and 33).
The consequences of genetic variation
MTHFR
Specific variants of this gene can influence
the body’s ability to supply the active form of the B vitamin
folate. Enzymatic impairment also results in insufficient conversion
of homocysteine to S-adenosylmethionine, a critical
methyl donor to numerous metabolic reactions,
A common variation in the MTHFR gene
is the:
677C.T gene variant, which involves substitution of
thymine (T) for cytosine (C) at nucleotide position 677 within
the coding region of the MTHFR gene. The resultant enzyme
has reduced activity, which leads to decreased production of
active folate and accumulation of homocysteine. Elevated homocysteine
levels often can be lowered through supplementation
with one or more of the B vitamins, folate, B2, B6, and B12,
and key mineral cofactors.
Among the genes known to be of particular importance
to the inflammatory response are the proinflammatory cytokine genes called:
IL1, which encodes the interleukin-1b cytokine
(also known as IL-1F2), IL6 (encoding the interleukin-6
cytokine), and TNF (produces the tumor necrosis factor
cytokine). Variants in each of these genes have been discovered
that increase the susceptibility of humans to be in a
proinflammatory state, which in turn increases the risk of
developing one or more chronic disorders.
These genes are a part of the phase I and phase II detoxification system, respectively,
found in the liver and the gut.
cytochrome P450 isozymes
(CYPs), glutathione S-transferases (GSTs), and superoxide
dismutases (SOD1, SOD2, SOD3).
These are part of the phase I and phase II detoxification system, respectively,
found in the liver and the gut. The SOD genes code
for proteins that dismantle the reactive oxygen species superoxide.
Glutathione
Glutathione (GSH) is a tripeptide that is formed from glutamate, cysteine and glycine
Our major, endogenous antioxidant
May account for half of cysteine requirements in the body
Helps stabilize RBC membranes
GSH reduces peroxides (H2O2) formed during O2 transport into H2O
Liver phase II detoxification uses glutathione to conjugate and excrete toxins/drugs by making them more water soluble
Amino acid transport across cell membranes
Part of some leukotriene structures
Cofactor for enzymes
Participates in rearrangement of protein disulfide bonds
CBS
Cystathionine Beta Synthase
Cofactor: Vitamin B6 (pyridoxal-5-phosphate)
Function: Converts homocysteine to cystathionine (Blocked by lead)
Product: Hydrogen sulfide (H2S) and cystathionine
Upregulated variants: CBS C699T (rs234705 C>T); controversial—always check for elevated ammonia and taurine
Downregulated variants: CBS A360A/C1080T (rs1801181 C>T), C1039+530T, rs28924891/G1330A (risk allele A), rs5742905 or T833C (risk allele C)—typically increases homocysteine.
Important for the production of glutathione, taurine and sulfate.
CBS Upregulation
CBS C699T
In basic chemistry, you have a substrate (starting material) and enzyme catalyst (something that makes the reaction go) and this then creates a product.
In upregulations, you will literally go faster through the reaction, using up your substrate and catalyst (and cofactors) and having more product.
In this case, you will have more cystathionine, low homocysteine and low levels of vitamin B6.
The next enzyme in the pathway, CGL becomes “overwhelmed” by this excesss and dumps ammonia and literally “skips” over the glutathione enzyme GCL in favor of CDO.
Review of SNP Effects on Homocysteine
MTR/MTRR: Likely Increased BHMT: Likely no effect CBS C699T: Likely decreased CBS A360A: Likely increased MTHFR C677T: Likely increased MTHFR A1298C: Likely no effect
Review of SNP clinical ramfications
MTR/MTRR: Decreased folate and B12 status; macrocytic anemia
BHMT: Likely no effect; possibly increased need for zinc and trimethylglycine
CBS C699T: Sulfur intolerance, decreased B6 status, increased cystathionine, and decreased glutathione and Bh4 with increased levels of ammonia and glutamate.
CBS A360A: Decreased B6, cystathionine and glutathione
MTHFR C677T: Decreased folate, increased risk for CVD and miscarriage
MTHFR A1298C: Decreased folate, depression
One carb metabolism requires these vitamins as cofactors
B2, B3, B6 and B12
Does NOT require folate. it metabolizes folate. Folate is a substrate not a cofactor.
DHFR
Dihydrofolate Reductase (DHFR)
rs7387 (T>A), rs1643649 (T>C), rs1643659 (T>C), rs1677693 (G>A,T), rs1650697 (A>G,T)
Cofactor NADPH
Codes the enzyme dihydrofolate reductase used in conversion of dihydrofolate into tetrahydrofolate
Dihydrofolate is reduced to tetrahydrofolate and NADPH is oxidized to NADP+
Is the precursor to both one carbon metabolism AND neurotransmitter synthesis where it is used to produce tetrahydrobiopterin (BH4).
More DHFR
Causes difficulty in conversion of synthetic folic acid into the active form of folate
Fortification with folic acid is a problem as it requires two DHFR steps for conversion as compared to only one required with natural folate
DHFR is the target for anticancer and antibiotic therapies such as methotrexate and trimethoprim (folate is required by rapidly dividing cancer cells to make thymine therefore inhibition of DHFR can limit growth and proliferation of cancer cells)
“Leucovorin does not require reduction by DHFR to participate in reactions in which folates are used as a source of 1-carbon moieties. Moreover, leucovorin is rapidly converted to other reduced folates, thereby restoring the pool of reduced folates.” (Chuang V.T.G. and Suno, M., 2012 p. 1350)
Consider dosing folinic acid (calcium folinate) rather than L-methylfolate
Leucovorin is prescription folinic acid.
MTHFR
Methylene Tetrahydrofolate Reductase
Key Variants: C677T (rs1801133 C>T) and A1298C (rs1801131 A>C)
C677T heterozygous=40% loss of function
C677T homozygous=75% loss of function
A1298C heterozygous=20% loss of function
A1298C homozygous=40% loss of function
Compound heterozygous=40%loss of function
Cofactor(s): Riboflavin, NADH, and ATP
Approximately 45% of the population has 1 copy of MTHFR C677T (Esp. Mexican, Italian, and Chinese).
Consequences of MTHFR
C677T variant will increase homocysteine, A1298C will not.
Increases risk for neural tube defects, miscarriage, dementia, mood disorders, peripheral artery disease, colon cancer, and acute leukemia.
Common in those with ADHD, autism, depression, Alzheimer’s disease, Parkinson’s disease, coronary artery disease and those with detoxification challenges
MTR/MTRR
Methionine Synthase
Methionine Synthase Reductase
Accounts for half of homocysteine catabolism.
Recycles homocysteine back to methionine.
Regulates and recycles cellular cobalamin levels
Methionine Synthase (MTR)
MTR is vitamin B12 dependent
rs1805087 (A>G)
Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to produce methionine and tetrahydrofolate
Maintains adequate intracellular methionine required for production of S-adenosyl methionine (SAM)
Responsible for maintaining sufficient intracellular folate pools and regulating homocysteine levels
Methionine Synthase Reductase (MTRR)
rs1801394 (A>G), rs1802059 (G>A), rs162036 (A>G)
Responsible for maintaining sufficient levels of methyl B12 required for homocysteine remethylation to methionine.
MTRR A66G polymorphism increases homocysteine levels and may also contribute to dyslipidemia in men (Zhi et al., 2016). This is particularly true in combination with the MTHFR C677T polymorphism.
One Carbon to Methylation Pathway
Starts with dietary folate (dihydrofolate—DHF)
Converts to tetrahydrofolate—THF via DHFR (the useable form of folate in the body—No, it is not methylated folate!).
Which then converts to 5,10-methylene THF, the substrate (starting substance) for our celebrity SNP, MTHFR.
Which then creates a methyl donor to be handed off to methionine synthase to participate in methylation.
And the folate is now back in the THF form to do it all over again!
The methyl donor then moves through to methionine and ultimately lands at homocysteine.
Validation Marker: Formiminoglutamate (FIGLU)
FIGLU is an intermediate in the deamination of the amino acid histidine and requires folate as a cofactor for formiminotransferase, the enzyme that converts FIGLU to glutamic acid.
Folate accepts the formimino group from FIGLU creating N5-forminio THF.
FIGLU excretion increases when there is a folate deficiency, particularly when a histidine oral load is given.
In this way, a decrease of the amino acid histidine is also a marker for folate deficiency.
Remember, DHFR is the regulatory enzyme for folate metabolism.
FIGLU specifically measures
THF levels or cellular availability of folate metabolism.
A cellular vitamin B12 deficiency will cause an elevation of the organic acid
methylmalonic acid (MMA)
When MMA is elevated, homocysteine is also typically elevated.
What is the function of Methylation?
Gene regulation Biotransformation Neurotransmitter synthesis Hormone catabolism (estrogen) Build immune cells such as T cells and NK cells DNA and histone synthesis Energy production Creation of myelin sheath on nerve cells Build and maintain cell membranes (phosphatidylcholine)
Glutathione
Glutathione (GSH) is a tripeptide that is formed from glutamate, cysteine and glycine
Our major, endogenous antioxidant
May account for half of cysteine requirements in the body
Helps stabilize RBC membranes
GSH reduces peroxides (H2O2) formed during O2 transport into H2O
Liver phase II detoxification uses glutathione to conjugate and excrete toxins/drugs by making them more water soluble
Amino acid transport across cell membranes
Part of some leukotriene structures
Cofactor for enzymes
Participates in rearrangement of protein disulfide bonds
