Sue 's case and the Yasko genetic variations profile

[Guest guest]

Hi, all.

As you know, I have been encouraging PWCs who have low glutathione

to have their genetic variations characterized by getting Amy

Yasko's panel from http://www.testing4health.com.

People have asked whether this panel is accurate, and also whether

it is worthwhile, particularly in view of the cost, which was

formerly $350 plus shipping for the smaller panel, and is now $750

plus shipping for the panel that is offered. These are important

questions, and when they were asked, I didn't have any experience to

use in answering them.

With Sue 's permission, I want to address these questions in

the light of her recent experience in getting the smaller Yasko

panel that was offered until recently.

The bottom line is first that the results of her gene variations

panel correspond well with other information we had about her case

ahead of time, and I think this is evidence for the accuracy of the

panel, and second that the panel gave particular guidance about what

supplements to take, and I think that is evidence that it was

worthwhile. Sue can of course comment herself on whether she agrees

with this.

Of course, this is only one case, and it remains to be seen whether

the supplements help Sue, but this is at least a progress report on

use of the panel, and hopefully will be useful to others who are

trying to decide whether to order it.

In order to supply some background, I will first reproduce my

original hypothesis for Sue's case back in mid-January, before she

had the Yasko test run. This was based on information she supplied

about her history and symptoms, and an interpretation of results of

other types of tests she had run in the past. (I will leave it to

Sue to comment, if she wishes, on how well she believes this

hypothesis fits, based on what she now knows of her case.) I also

gave some suggestions for treatment at that time. (I think Sue

tried some of them, at least for a while, but she also ran into

problems with some of them, and learned some new things in the

process. She did order the Yasko panel, as I suggested, and also

joined Yasko's internet group, called http://www.autismanwer.com.

Over the course of time, she adopted treatments recommended there.

I'll leave it to her to comment on these things if she wants to.)

Then I will present the results of the Yasko panel, which Sue shared

with me last week, and give some interpretive comments.

Then I will discuss how the Yasko panel results jibe with what we

already thought, based on the information that was available, and I

will also comment on the guidance Sue received about treatment from

these panel results.

So, here's the hypothesis and interpretation of some of her earlier

test results:

" Genetic Predisposition

" I believe that you were born with certain genetic single nucleotide

polymorphisms (SNPs), and that these made you vulnerable to

developing your illness when the appropriate environmental and other

factors came into play.

" There is evidence for some of these SNPs in the results of your

DetoxiGenomic profile. They include polymorphisms in two of the

Phase I cytochrome P450 enzymes, CYP1B1 and CYP3A4. You also have a

heterozygous SNP in your mitochondrial superoxide dismutase enzyme

(SOD2 A16V), and you have two homozygous SNPs in your N-

acetyltransferase-2 enzyme (NAT2 I114T-slow metabolizer and NAT2

K268R-fast metabolizer). Of these, I think the most important is

the SNP in CYP3A4, because this is the most abundant cytochrome P450

enzyme in the human liver, and is the dominant enzyme for performing

Phase I detox on many drugs as well as the steroid hormones. CYP1B1

is not very abundant in the human liver, so its lack is not very

serious. It's not clear what the net effect of the two NAT2 SNPs

would be, since one produces slower metabolism with this enzyme, and

the other produces faster. The SNP in SOD2 causes faster conversion

of mitochondrial superoxide to hydrogen peroxide. This would

normally not be a problem, but in your case your glutathione is low

and your glutathione peroxidase enzyme has low activity (see below),

so the result would probably be higher oxidative stress because of

the conversion of hydrogen peroxide to hydroxyl radical, as also

discussed below.

" In addition, though we do not currently have direct evidence of

this, I believe that you also have one or more SNPs in enzymes that

are associated with your methylation cycle. Among the pieces of

evidence for this are that you have low glutathione, a history of

sensitivity to foods and supplements containing sulfur, and a

positive response to the DAN! (Defeat Autism Now!) treatments for

unblocking the methylation cycle. To be more specific about the

particular SNPs that might be present, it would be necessary to do a

profile of the genes involved, such as with the Economy Basic SNP

Panel III offered by http://www.testing4health.com.

" Etiology

" I believe that the root cause of your illness was a combination of

environmental and other factors, each of which tends to deplete

glutathione. I suggest that these included exposure to toxins

(pesticides, solvents, and mercury from amalgam removal), infections

(viral and intracellular bacterial), at least one tick bite, and

other stressors.

" Pathogenesis

" I believe that the combination of factors described above

interacted with your detox-related SNPs to cause your glutathione to

become sufficiently depleted so as to produce a state of oxidative

stress. I believe that this oxidative stress, together with your

putative methylation-related SNPs, caused a partial blockade in

your methylation cycle, and that this in turn further depleted your

glutathione status, producing a vicious circle that has continued to

keep you ill for 18 years.

" This had a very large number of effects, and it is difficult even

to identify all of them. First, it decreased the levels of several

sulfur-containing substances that have important functions in the

body: S-adenosylmethionine, cysteine, glutathione, taurine and

sulfate. Since S-adenosylmethionine is the main methylator in the

body, your ability to perform methylation reactions was decreased.

This decreased your production of creatine, carnitine, and

melatonin, as well as impacting a number of other important

reactions.

" The decrease in cysteine would have impacted the synthesis of many

enzymes as well as decreasing the production of glutathione.

" The lowering of glutathione would have produced a permanent state

of oxidative stress, allowing reactive oxygen species to damage

lipid, protein and DNA molecules in your cells. It would also have

suppressed your cell-mediated immunity, and would have given rise to

reactivation of latent viral and intracellular bacterial

infections. Furthermore, it would have allowed partial blockades to

form in the mitochondria of your cells, particularly your skeletal

muscle cells, and they would have had to shift more toward anaerobic

metabolism to supply needed ATP. Lower glutathione would also have

allowed the buildup of toxins which it normally removes from the

body, one of which is mercury.

" The lowering of taurine would have had a number of effects, some of

them neurological in nature.

" The lowering of sulfate would have inhibited the detox of several

other toxins, as well as affecting the cartilage in the joints in a

deleterious way.

" The block in the methylation cycle would have propagated to the

folate metabolism, which in turn would have propagated to the

biopterin cycle, which in turn would have impacted the urea cycle.

All of this would have produced an avalanche of effects, including a

decrease in serotonin and dopamine production and difficulty in

dealing with ammonia.

" Intestinal problems would have arisen from the low serotonin,

because serotonin is involved in promoting peristalsis, and from the

low glutathione, because glutathione is important for protecting the

gut. Poor peristalsis would have led to dysbiosis. Dysbiosis would

have led to lowered absorption of nutrients from the gut. This in

turn would have decreased the status of minerals such as magnesium

and selenium. Low magnesium would have inhibited reactions involved

with energy utilization as well as possibly producing heart

arrythmias, mitral valve prolapse, muscle twitching and migraines.

Low selenium would have inhibited the enzyme glutathione peroxidase

and the enzyme that converts T4 to T3.

" The state of oxidative stress would probably deplete other

antioxidants, including coenzyme Q-10.

" The heart muscle cells would probably have a lower rate of ATP

production because of the decreased levels of magnesium, carnitine

and coenzyme Q-10, and this would in turn cause a depletion of D-

ribose. The effect of this would be diastolic cardiomyopathy and

reduced cardiac output, resulting in lower blood pressure.

" Neurological effects would also follow from the buildup of toxins

and probably also infections.

" Infections would have increased because of the lack of effective

cell mediated immunity.

" Interpretation of Lab Test Results

" 1. Detoxification Profile (Comprehensive)--collected Nov. 28, 2005

" The Phase I caffeine clearance rate was above the normal range. I

believe that the reason for this is that you have an SNP in CYP3A4.

There is overlap in the substrates that can be detoxed by the

different CYP enzymes, and the lack of normal CYP3A4 has caused

upregulation of the other CYP enzymes to compensate. Caffeine is

detoxed primarily by CYP1A2, and also by CYP2E1 (Klaassen, p. 179).

Since you have normal versions of these enzymes, caffeine is

processed rapidly.

" Both your plasma cysteine and plasma sulfate were low. This

suggests that the rate of movement of sulfur-based metabolites

through your transsulfuration pathway is slower than normal. This

could be due to a problem in the transsulfuration pathway itself, or

a block higher up in the methylation cycle. For other reasons,

given above, I suspect the methylation cycle, but both are dealt

with by the DAN! treatments.

" Your Phase II glutathione conjugation came out low. This suggests

a problem either with glutathione depletion or a problem with the

glutathione transferase enzymes. Because your DetoxiGenomic profile

showed normal glutathione transferases, I suspect low glutathione,

and this is consistent with low flow through the transsulfuration

pathway and a block in the methylation cycle.

" The two abnormal Phase I/Phase II ratios reflect these problems.

The high plasma cysteine to sulfate ratio suggests a block in the

sulfoxidation pathway, which may be correctable by high molybdenum

intake.

" The high normal catechol means that there is mild oxidative stress

going on, due to elevation in hydroxyl radicals. The high normal

lipid peroxides is consistent with this. This is also consistent

with the low reduced glutathione and the low activity of glutathione

peroxidase, since they are the basis of the antioxidant enzyme

system. The glutathione is likely low because of low flow through

the transsulfuration pathway and that in turn is likely due to a

block in the methylation cycle. The low glutathione peroxidase

activity is probably due to selenium depletion, as shown elsewhere

in the test results.

" 2. Amino Acids (plasma)--date received 12-12-05

" The low histidine may suggest a problem with folate metabolism.

The low isoleucine, together with low normal leucine and lysine

suggest that amino acids are being burned for fuel. The low

tryptophan may mean that the tryptophan in the diet is not being

absorbed normally, but is being broken down by bacteria in the gut

to form indican, which shows up high (see below). The low

tryptophan may result in low production of serotonin and melatonin.

The former is supported by your low 5-hydroxyindoleacetate (below).

The latter is consistent with sleep problems and the benefit of

taking cherry juice, which you reported. The low tyrosine in the

presence of a relatively normal level of phenylalanine suggests a

slow conversion of the latter to the former. This can be produced

by low iron, but your iron level had been restored by mid-November,

so I think it is more likely that this is due to low

tetrahydrobiopterin, which is consistent with a problem propagating

from the methylation cycle block through the folate metabolism to

the biopterin metabolism. Low tyrosine would have lowered your

production of the catecholamines, including dopamine, and this shows

up as low homovanillate (below). The low asparagine probably

results from low magnesium (see below).

" Your methionine level was low normal. This could be due to low

intake of methionine or a block in the methylation cycle. Your

homocysteine level was normal. This does not rule out a problem in

the methylation cycle. Your taurine level was high, and this likely

resulted from the fact that you started supplementing taurine in mid-

November.

" 3. Minerals (red blood cells)--date received 12-12-05

" Your essential minerals were all on the low side of normal, with

magnesium, manganese and selenium being particularly low. The

overall low mineral status suggests that your absorption of minerals

from your digestive tract is below normal. This could result from a

lack of stomach acid or from dysbiosis, or both. Low magnesium is

very common in CFS, and is probably due to more than one factor,

including low absorption, low transport into cells, and elevated

wasting in the urine. It affects your ability to make use of

energy, and it is also probably responsible for the muscle twitching

and perhaps also some of the muscle pain. The low selenium may be

partly due to elevated mercury, since these two elements form

tightly bound complexes. The low selenium is probably responsible

for the low activity of your glutathione peroxidase, as discussed

above, and also for your need to take T3, since a selenoenzyme

normally converts T4 to T3.

" You had elevated aluminum in your red blood cells. This would be

consistent with low glutathione, as discussed above. Red blood cell

testing does not reflect total body burden of the heavy metals, such

as mercury, but only shows recent exposure. Therefore, the low

values for mercury and the other heavy metals does not rule out

significant body burdens of them.

" 4. Fat-soluble antioxidants--date received 12-12-05

" These appeared to be in the normal ranges. However, note below

that there is other evidence that suggests low coenzyme Q-10.

" 5. Lipid peroxides--date received 12-12-05

" These came out normal, but note that they were high normal in the

detox profile (above).

" 6. 8-hydroxy-2-deoxyguanosine--date received 12-12-05

" This was elevated, indicating oxidative damage to DNA. This is

consistent with a state of oxidative stress as a result of low

glutathione function, as discussed above.

" 7. Fatty Acids--date received 12-12-05

" The low dihomogamma linolenic acid in the presence of normal

linoleic acid suggests that the delta-6 desaturase reaction is

slow. This may result from low magnesium or zinc, as discussed

above. The consequence of this is low production of the series 1

prostaglandins, which are anti-inflammatory. So this could result

in more inflammation. Docosadienoic acid is low, but it doesn't have

important functions.

" 8. Urinary organic acids--date received 12-12-05

" The high ethylmalonate suggests poor metabolism of fatty acids,

which could result from low vitamin B2 or low carnitine. Since the

beta-hydroxyisovalerate was normal, B2 is probably not deficient,

and that suggests that carnitine deficiency is responsible. Since

carnitine production requires methylation, this is consistent with a

block in the methylation cycle.

" The high lactate indicates a high level of anaerobic metabolism,

which is consistent with mitochondrial dysfunction, which could be

secondary to glutathione depletion. It also explains the burning

pain in the muscles.

" The simultaneous high values for succinate, fumarate and malate

indicate either a deficiency in coenzyme Q-10 or an inhibition of

cytochrome oxidase. It is difficult to decide which is

responsible. Coenzyme Q-10 tested normal (above), but its

precursor, hydroxymethylglutarate, was elevated, suggesting a

possible block in production of Co Q-10. On the other hand, it is

known that cytochrome oxidase can be blocked by superoxide or

peroxynitrite, which rise under conditions of oxidative stress,

which is present, as discussed above

" Methylmalonate was elevated, indicating vitamin B12 deficiency. I

don't recall for sure when you started supplementing with methyl-

B12, but I think it was slightly before this test. If you had been

taking it for some time, this would suggest that the B12 absorption

might not have been up to normal. This is possible, in view of your

gut problems.

" The low homovanillate and low 5-hydroxyindoleacetate indicate low

dopamine and low serotonin, respectively. These are consistent with

the low tyrosine and low tryptophan, and also with a problem in

biopterin metabolism, secondary to a methylation cycle block. These

low neurotransmitters could be responsible for some of your

neurological symptoms.

" The high 8-hydroxy-2-deoxyguanosine indicates oxidative stress, as

already discussed.

" The high orotate could be due to low arginine (but it was not found

to be low), or more ammonia than the urea cycle can deal with, which

may be the case because of the dysbiosis, or low magnesium, which

was found.

" The high indican is produced by bacterial action in the small

intestine, converting tryptophan to indican, as already discussed.

" Suggested Treatments

I realize that you are already carrying out several of the

treatments discussed below, but I will describe them for

completeness.

" 1. Bowel treatment:

" I think that bowel treatment must be one of the first things done,

because the bowel is important both in carrying out toxins and in

bringing in nutrients. Until these are done effectively, healing

cannot take place. I suggest the bowel treatment described by Dr.

Serafina Corsello in her book " The Ageless Woman. " It includes

three separate phases: bowel scrubbing, bowel soothing, and bowel

repopulation. Prior to doing the bowel treatment, I think it is

wise to run a Comprehensive Diagnostic Stool Analysis, including

searching for the extra pathogens, and also a Parasitology stool

analysis. These may reveal particular pathogens that will need to

be countered during the bowel scrubbing phase. For bowel

repopulation, I suggest using Primal Defense.

" 2. General nutrition:

" Once the bowel is functioning properly, it is important to make

sure you are getting enough of the essential vitamins, minerals,

essential fatty acids, and essential amino acids. The vitamins and

minerals can be obtained from a high potency general nutritional

supplement, such as Sparx (http://www.krysalis.net) or something

equivalent. Omega-3 fatty acids can be obtained by taking flax oil

or a clean fish oil such as Nordic Naturals or Eskimo-3. High

quality protein, such as whey protein or egg protein or meat will

supply the essential amino acids.

" 3. Supporting the detoxication system:

" Because of the SNPs in your detox system, I think it will be

necessary for you to support it on a continuous basis for the rest

of your life. First, it will be important to minimize your exposure

to toxins to the degree you can in the air you breathe, in the water

you drink, and in the food you eat. I suggest an effective air

purifier in your living space, a water filter that uses activated

carbon, and organic foods to the degree possible. Avoiding exposure

to pesticides, solvents, engine exhaust, perfumes, smoke and other

impurities in the air would be a good idea. Second, I think that

taking a small amount of activated charcoal and some insoluble fiber

orally on a daily basis would also be a good idea, to help in

removing toxins. This may help to compensate for the SNPs in your

detox system.

" 4. Lifting blocks in the methylation cycle:

" This should be done using the treatments developed by the DAN!

project and described in the book by Jon Pangborn and Sydney Baker

entitled " Autism: Effective Biomedical Treatments, " Sept. 2005,

available from http://www.amazon.com or from

http://www.autismresearchinstitute.com.

" 5. Countering oxidative stress:

" While working to lift the methylation cycle blocks and to raise

glutathione, in the meantime the oxidative stress can be countered

by a combination of antioxidants. These should include vitamin C (3

grams per day), vitamin E including gamma tocopherol (800 I.U. per

day), and coenzyme Q10 (360 to 600 mg per day). I think it would

also be a good idea to try OPCs (oligomeric proanthocyanidins) as in

Pycnogenol or grape seed extract, starting low and working up in

dose if tolerated.

" 6. Refilling the sulfur metabolism from the bottom up (most

oxidized species first):

" Start by taking a sulfate, such as glucosamine sulfate. Work up to

1500 mg per day of glucosamine sulfate. Another possibility would

be magnesium sulfate (Epsom salts), up to an equivalent amount of

sulfate. Then add molybdenum, starting at a low dose and working up

to 2,000 micrograms per day, if tolerated. After reaching 2,000

micrograms and continuing it for a few days, add some MSM, starting

low and working up to one gram per day. Then add glutathione in a

liposomal form at 100 mg per day. If all this works satisfactorily,

then try SAMe at 100 mg per day. If this is tolerated, I think it

means that your sulfur metabolism is operational again. If you can

tolerate whey protein, take RenewPro to build up glutathione,

starting low and building to three scoops per day. If you can't

tolerate whey protein, then take glutathione precursor amino acids

(http://www.cfsn.com). Start with a low dosage and work up as

tolerated.

" 7. Supporting the heart muscle metabolism:

" Take magnesium (going up to 600 mg per day), coenzyme Q10 (going up

to 360 to 600 mg per day), L-carnitine (going up to 2 grams per

day), and D-ribose (going up to 5 to 15 grams per day).

" 8. Chelating heavy metals:

" When the glutathione level is up to normal, chelate heavy metals

using DMSA, according to the protocol of the DAN! project

(http://www.autismwebsite.com/ari/dan/heavymetals.pdf).

" 9. Dealing with the remaining pathogens:

" After the above is completed, it would be a good idea to test to

see what infections remain, and then to treat them specifically if

necessary. "

O.K., that was the analysis, test interpretations and suggested

treatments as they stood in mid-January. Now, last week Sue got the

results of the short Yasko panel. This panel includes ten genetic

variations, while the currently offered more expensive panel

includes forty. Sue has gone on to order the other thirty. Here

are the ten in the short panel:

ACE Del 16 +/+

CBS (C699T) -/-

COMT (V158M) -/-

MTHFR (C677T) +/-

MTHFR (A1298C) -/-

MTR (A2756G) -/-

MTRR (A66G) +/-

NOS (D298E) +/-

VDR Bsm/Taq +/-

VDR Fok +/-

(Two pluses indicate that she has both copies of the particular

variation (inherited from both her mother and her father), two

minuses mean no copies, and a plus and minus mean one copy. Two

copies is called homozygous, and one copy is called heterozygous.)

I think that the first ones to look at are those that directly

affect the methylation cycle.

Note that she has one copy of the MTHFR (C677T) genetic variation.

This will hinder her folate cycle in producing 5-methyl folate,

which will make it difficult to convert homocysteine to methionine

via the methionine synthase enzyme.

Note that this problem is compounded by one copy of the MTRR (A66G)

genetic variation, which hinders the operation of methionine

synthase by making it difficult to recycle methyl B12. Both these

variations will hinder the operation of the methylation cycle.

How does this jibe with earlier information? Well as you saw

earlier, I had projected that there must be a block in her

methylation cycle from the other evidence, and here it is,

confirmed. We didn't know which enzymes were involved, and now we

do. How does this affect treatment? Well, it says that Sue should

take supplemental methyl B12 simultaneously with 5-methyl

tetrahydrofolate (FolaPro). Before, in response to my suggestion to

follow the DAN! protocol until we had more specific information from

the Yasko profile, she tried taking several supplements, including

folinic acid rather than FolaPro, and ran into some difficulties.

Now we know that she should take methyl B12 and FolaPro. Sometimes

trimethylglycine is also recommended to help the conversion of

homocysteine to methionine by a parallel pathway, but I think Sue

has reasons to avoid forms of glycine, and I leave it to her to

comment on that if she wants to.

Another effect of the shortage of 5-methyl folate will be a partial

block of the biopterin cycle. Since, in addition, Sue had elevated

aluminum, which blocks the DHPR enzyme, and she also has one copy of

the NOS (D298E) genetic variation the result of all three of these

together will be a significant shortage of tetrahydrobiopterin,

which will slow the conversion of phenylalanine to tyrosine,

decrease the production of serotonin and dopamine, raise the

production of oxidizing free radicals and inhibit the ability of the

urea cycle to detox ammonia.

How does this jibe with earlier information? Well, there was

evidence from her urine organic acids test that both serotonin and

dopamine were low, and now we have a reason. There was evidence

from her amino acids test that phenylalanine was not being converted

into tyrosine at a normal rate, and this is likely the reason, as I

projected. There was evidence for oxidative stress, and this could

be one contributor. And she knew she had an ammonia issue, because

she could actually smell it. So again, this appears to be right

on. What can be done about this? Well, first, the FolaPro should

help, second, she thinks she found the source of her aluminum

exposure in some nutritional bars she was eating that were wrapped

in aluminum foil, and also she is controlling her protein intake to

limit the ammonia production from breakdown of excess amino acids.

Next, she has both copies of a polymorphism in the angiotensin

converting enzyme (ACE) gene. This homozygous (both copies)

polymorphism causes the concentration of ACE to be twice as high in

the blood as if it weren't present. The result is more rapid

conversion of angiotensin I to angiotensin II, faster inactivation

of bradykinin, and elevation of aldosterone. This has been found to

be associated with a higher risk of heart disease. In the present

context, Amy Yasko reports that in children with autism, this leads

to a higher level of anxiety. I don't know if this is relevant to

adults, such as Sue. Maybe she will comment on this.

Finally, Sue has one copy each of two vitamin D receptor

polymorphisms. Amy Yasko has found that this tends to produce lower

levels of dopamine. This would seem to be another factor explaining

the observed low levels of this neurotransmitter. What can be

done? Well, the measures discussed above will help to raise the

dopamine production.

So, my conclusion from this is that the Yasko panel was valid and

was worthwhile. Sue now has a later metabolic profile that shows

considerable improvement in quite a few parameters as well as some

ongoing detox results. Maybe she will comment on them.

Again, this is only one case, and Sue is still undergoing treatment,

so the final results of all this remain to be seen. But I am very

encouraged that my suggestion a few months ago that many cases of

CFS have in common with many cases of autism that there is chronic

glutathione depletion as a result of a vicious circle involving a

block higher up in the sulfur metabolism appears to be supported so

far. I am very hopeful that Sue will be able to break this vicious

cycle, now that we know where the genetic variations are located.

I want to note that Sue also has some challenges related to some

serious genetic variations in the enzymes of her detox system and

the consequent buildup of toxins, so that is an additional aspect

that she has to address. This points up the importance of getting

the Genovations Detoxi-Genomic profile in addition to the Yasko

profile when there is evidence of major detox problems, as Sue had

from her experience with difficulty in tolerating pharmaceuticals

and steroid hormones.

Rich