Agents for Change: The 10th Invest in ME International ME Conference, 2015 - Part 1
The 10th Invest in ME International ME Conference (IIMEC10) was held, as usual, in the Lecture Theatre at 1 Birdcage Walk in Westminster on May 29th, 2015.
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Combinations of single nucleotide polymorphisms in neuroendocrine effector and receptor genes in CFS

Discussion in 'Genetic Testing and SNPs' started by Beyond, Oct 18, 2013.

  1. Beyond

    Beyond Juice Me Up, Scotty!!!

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    Thanks nandixon, upon reading these reports and others I realised some researchers are suggesting high serotonin in CFS. I don´t now if I personally I have high serotonin, but 5-HTP made me get bad depersonalization so I have the serotonin pathways messed up for sure.

    I am also homozigous AA for the other rs of TPH2 that you provided. And homozigous AA for all the TAAGA rs´s. How is your HTR2A rs6311? That one is an upregulation.

    Moreover, I have some clear degree of OCD and it has been long suspected that is related with abnormal serotonin metabolism. Actually all the meds that help OCD raise serotonin levels and mine was lowish last time tested. 141 ng/ml, range being 100 -283.

    It seems that 5-HT genes and pathways influence HPA axis a lot. Not to mention the HPA genes themselves. Genetic research is very exciting!

    http://onlinelibrary.wiley.com/doi/10.1111/j.1601-183X.2010.00564.x/full http://www.nature.com/mp/journal/v11/n10/full/4001870a.html
    http://www.sciencedirect.com/science/article/pii/S0306453097000024
    http://www.sciencedirect.com/science/article/pii/S0165032797001018

    Furthermore, my multiple GAD1 mutations are consistent with the EXTREMELY low GABA result of these 2011 urine tests.
     
  2. nandixon

    nandixon Senior Member

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    I'm CC for rs6311, so homozygous for the most common allele.
     
  3. Beyond

    Beyond Juice Me Up, Scotty!!!

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    Adding more evidence about the genes in the spotlight for CFS:

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765429/

     
  4. Beyond

    Beyond Juice Me Up, Scotty!!!

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    Going to try Icariin. Remember, at least three studies show it reverses negative changes in HPA axis function following prolonged stress in the mouse model of depression. What chronic "depression" does is decrease glucorticoid sensivity, this is interesting for CFS because similar problems arise in studies, including the genetic ones I posted in this thread long ago. Traditionally horny goat weed the herb icariin is from, is used as an aphrodisiac, now, aphrodisiacs apparently tend to have strong neuro-endocrine effects which I am willing to explore.:D

    I also want to try Curcumin and other natural compounds that manipulate positively a defective brain like Kavalactones (this is huge for many people in these forums as research suggest), will update about it when done.
     
  5. drob31

    drob31 Senior Member

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    I just came across this: NR3C1 as well, and I listed in my notes as being related to my adrenal fatigue! I have 2 hetero mutations on this gene!
     
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  6. nandixon

    nandixon Senior Member

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    Here are the 28 SNPs from the full text of the article @Beyond gave in the first post of this thread: 28 SNPs.png
     
  7. nandixon

    nandixon Senior Member

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    @Beyond
    I've excerpted the quote above from your original post on a different thread. (http://forums.phoenixrising.me/index.php?threads/thread-for-sleep-aids.34813/#post-543366)

    I'm very curious to find out what effect the Bacopa has for you...?

    Since you previously mentioned that, like me, you're also homozygous (AA) for rs7305115, which may be the most potent gain of function (upregulation) SNP on the tryptophan hydroxylase 2 (TPH2) gene, it seems the odds are greatest that we are overall upregulated with respect to THP2 (depending on how many loss of function SNPs we also have).

    Being upregulated with respect to THP2 means more brain serotonin is likely being made, and perhaps too much if, e.g., other genetic factors are also present.

    I made a recent post about a theory about this (that probably only applies to a small percentage of ME/CFS people), in which this upregulation could be a problem (again this is just a theory I'm hoping to test out):
    http://forums.phoenixrising.me/inde...rtion-have-in-common.34799/page-4#post-544218

    Bacopa monnieri (Brahmi) is an upregulator of THP2, which you had noted yourself earlier in this thread. [See also, Bacopa monniera leaf extract up-regulates tryptophan hydroxylase (TPH2) and serotonin transporter (SERT) expression: implications in memory formation (http://www.ncbi.nlm.nih.gov/pubmed/21129470/ )]

    So it seems that Bacopa might possibly be bad for us with respect to THP2, i.e., cause more fatigue. (Although it might be good for sleep.)

    On the other hand, it also upregulates the serotonin transporter SERT gene (SLC6A4), which might be helpful. So that might offset things with respect to THP2.

    Anyway, if you wouldn't mind, please let me know what effects Bacopa has for you when you find out. Thanks!
     
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  8. Valentijn

    Valentijn Activity Level: 3

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    Is there research supporting the claim that it's a "potent" upregulation? It's very common to be AA and it's not a missense mutations - these sorts of SNPs usually have pretty tiny impacts, if any.
     
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  9. nandixon

    nandixon Senior Member

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    (@Valentijn Yes of course. I was actually writing the following footnote when you posted, and I give a link to the source at the end. That SNP actually gives up to a 2.5 fold increase in mRNA expression.)

    An additional footnote:
    Note that rs7305115 is not one of the 28 SNPs in the table a few posts higher up.

    The actual SNPs are probably not critical, because this gene has very few SNPs that actually modify the functioning of the enzyme produced.

    Rather, most of the SNPs change how much enzyme is made (I'm still researching this). Rs7305115 has the largest effect, I think, with respect to making more of the enzyme.

    So in general, AA (~17% frequency) people are going to make more TPH2 enzyme than GG (~35% freq) people. (See: http://www.ncbi.nlm.nih.gov/pubmed/17453063/)
     
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  10. Beyond

    Beyond Juice Me Up, Scotty!!!

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    It is clear there are specific SNP´s or genetics that determine neurotransmission and other neurological factors, and that greatly influences chronic disease. If ANY of the SNP´s I originally brought to the table have any significance that I don´t know, honestly.

    @nandixon Will do don´t worry. I am taking a highly potent 50% bacosides extract double dose since not long, need more time, but so far it is not sedating at all and likely energizing if anything. I am starting to feel some effects in regards to verbal competence.

    YES it does cause more fatigue in some people in longecity/reddit which confirms your hypothesis, but my special interest in bacopa is how it favourably influences neurogenesis and neuroplasticity. I want to heal my brain!

    Another thing that could be helpful for these "adrenal fatigue" genetics would be curcumin, so thats something else to try.
     
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  11. nandixon

    nandixon Senior Member

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    @Beyond
    Okay, great! I'm hoping to find the Acorus tatarinowii ("Shi Chang Pu") that I mentioned on the thread where I gave the TPH2 upregulation theory.

    So I'll possibly be doing the opposite experiment that you are, with respect to TPH2 anyway:

    Bacopa monnieri = upregulation

    Acorus tatarinowii = downregulation

    Here's an interesting reference for Acorus as an anti-fatigue agent (in rats) where it prevents exercise-induced serotonin:

    The effects of Acorus tatarinowii Schott on 5-HT concentrations, TPH2 and 5-HT1B expression in the dorsal raphe of exercised rats
    http://www.ncbi.nlm.nih.gov/pubmed/25456438/

    (BTW, curcumin causes me additional fatigue.)
     
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  12. Valentijn

    Valentijn Activity Level: 3

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    Actually they're just saying that the "A" allele shows up more often than the "G" allele in the mRNA of corpses who are heterozygous. This doesn't necessarily indicate any overall increase in TPH2, just the ratio of the two expressed versions in heterozygotes.

    Also, it was a range of ratios (1.05-2.5), with an average of 1.74, not 2.5. While one patient did have 2.5, the rest were necessarily lower, and it's important to reflect that accurately.

    The graph at http://www.nature.com/mp/journal/v12/n5/fig_tab/4001923f5.html#figure-title actually does compare AA to GG+GA and indicates that while AA does result in more mRNA expression on average, the GG+GA range is wider than the AA range on both ends, and there's a pretty big cluster of the GG+GA samples in the same area where all the AA results are - hence it would seem that there is a factor other than those alleles which is likely having a big impact.

    As mentioned above, the SNP does not result in a mutation, despite being in a coding region (exon) of the gene. Which would raise the question as to how "A" might be overexpressed in mRNA compared to "G". They looked at how the DNA expresses itself when injected into hamster cells, and there weren't any significant differences between rates of "A" and "G" appearing in mRNA, nor in rates of degradation, which potentially could have indicated that there was more A in the mRNA because it took a bit longer to break down.

    Eventually they theorize that the "A" allele creates a nicer splicing site which results in that exon being included more often than when there is a "G" allele. And that might not have any effect on the TPH2 enzyme, if having the proteins from exon 7 added to it isn't having any impact on the enzymes ability to function as required, and at the normal rate.

    And finally I'd point out that they refer to the "A" allele as representing a gain of function over the ancestral version, and they suggest that this mutation has persevered and become more prevalent because it might offer some reproductive benefit. Hence they really don't offer any suggestion that it might result in any counter-productive effects.

    Anyhow, pretty interesting research, but no definitive indication that the "A" allele affects the actual functioning of the the gene's product, especially in any negative manner. I also wouldn't pay much attention in general to any research correlating SNPs with personality traits or psychological disorders - that stuff usually has tiny effect sizes, too-high p-values, and a lot of contradictory findings.
     
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  13. nandixon

    nandixon Senior Member

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    It's not clear to me whether you're understanding several important concepts. I'll try to explain a few things, if only for other people.

    First of all, geneticists have a very confusing lingo where when the word "allele" is used, that can refer to either a particular single nucleotide (SNP) on a gene strand, or to a continuous sequence of any number of nucleotides that also includes that SNP. The same name is used in both cases (e.g., "A-allele"). For purposes of this article, we're mostly talking about the latter. It'll be clearer later below.

    Second, it's critical to understand that SNPs within the coding region of the gene for an enzyme can potentially not only affect the functioning of the resultant enzyme that's made, but also affect the quantity of mRNA that is expressed and thus the amount of enzyme that's actually made. For purposes of this article, we're only interested in the latter.

    So for example, in the Abstract, where the word "functional" is used, they're not referring to SNPs that have an impact on how well the enzyme functions, rather they're referring to SNPs that affect expression, and therefore how much enzyme is produced. The quantity of enzyme made can be as important, or more important, than how well the enzyme functions.

    This particular gene, TPH2, is especially different than others you may have looked at, like MTR, CBS, MTHFR, etc. With this gene, the authors are not interested in SNPs that affect the function of the resulting enzyme (like, e.g., MTHFR C677T), because there are very few of those on this gene. Rather, they're interested in SNPs that affect expression of mRNA, and therefore how much enzyme is produced. There are lots of those on this gene:
    Now here are some additional comments within what you wrote to explain some things:

    This isn't the most important issue, but from this, and what you write later, it appears you might be thinking that the term "expression" is referring to expression of the SNP by itself, when actually it's referring to expression of a multi-nucleotide allele that the SNP is included on, and from which the amount of mRNA it produces provides a means, using allelic expression imbalance (AEI), for determining the relative amounts of enzyme that each SNP/allele is likely to cause to be yielded upon transcription.

    Finding the expression ratio of the two different alleles (again, not the SNPs alone) is essentially the entire purpose for doing the AEI assay. It's not a flaw. It gives a way of determining which allele variant is likely to produce more (or less) enzyme. Additionally, note that AEI has been found to have a very high accuracy, precision and sensitivity.

    I did say "up to 2.5 fold."

    That's not exactly the correct conclusion to be drawn. The correct observation is that there are many SNPs on this particular gene that effect expression (and consequently how much enzyme is produced), and so naturally you might expect to see that type of pattern.

    The researchers weren't interested in looking for mutations that might affect the functioning of the enzyme. Rather they were looking for SNPs that can affect how much enzyme is produced. This is a major focus of research now because many genes in the brain have SNPs that are more likely to affect the quantity of the enzyme produced as opposed to the functioning of the enzyme.

    Again, they're not looking for a potential impact on the function. They're looking to see if more, or less, enzyme is likely to be produced from one allele versus the other:

    The potential counter-productive effect is readily apparent once you understand that "gain of function" is referring, not to a gain of function in the enzyme, but rather a gain of function of mRNA expression and therefore a greater quantity of enzyme being produced.

    The enzyme, tryptophan hydroxylase 2, performs the first and key step in the production of serotonin. Having too much serotonin (= e.g., fatigue) can be just as bad as not having enough (= e.g., depression).

    It should be clear now that they were not interested in looking for that.

    I wouldn't be so dismissive. Seemingly contradictory findings may be the result of a complex interaction between multiple SNPs on the same and different genes, including SNPs that affect function and others that effect quantity of enzyme (as in this study). As we understand those interactions useful trends can emerge.

    Anyway, I think that the bottom line here is that, until proven otherwise (i.e., unless it's shown, e.g., that rs7305115 is not in linkage disequilibrium with another SNP that is the true "functional" SNP), that given two otherwise genetically (and epigenetically) and environmentally identical human beings, this study has demonstrated that an individual who is homozygous AA will have a greater capacity to produce serotonin than an individual who is GG. And this might conceivably, in combination with other SNPs or factors, potentially contribute to tipping the balance to a pathogenic state.

    Lastly, I've had a thought that you might possibly need to revisit your analysis of Yasko's CBS C699T. I've never looked at that SNP, but if there's research showing that the homozygous state Yasko claims is bad results in an increased amount of mRNA/enzyme, it's obvious the potential could exist for it to appear good with respect to lowering homocysteine on the one hand, but bad for sending too much material down the transsulfuration pathway on the other.
     
  14. Valentijn

    Valentijn Activity Level: 3

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    I agree with what you've said about what they were looking for, and what they found, but I still think you're drawing conclusions which aren't warranted.

    But in the meantime, we get a pretty small likely effect size for the AA group versus the others, and a whole lot of "maybe". And some good questions for researchers to follow up on. Until that happens, this is very preliminary, and any conclusions are going to involve a lot of conjecture.

    People with AA might produce more of the mRNA than some with AG/GG, but some with AG/GG were still out-producing all of those with AA. And that's just in the realm of the mRNA, without even getting to the TPH2 enzyme stage, where more of the AA TPH2 mRNA might not be translating to more (or more functional) TPH2 enzyme. Granted, that's hard to study in either the brains of the living or of the deceased.


    There isn't any regarding CBS C699T in mRNA. Just correlations with a couple diseases. And no research at all regarding her other pet +/+ CBS SNPs. Who knows, maybe people eventually spontaneously combust if they get those ones :rolleyes:

    It seems rather silly to guess that something specific must be happening in the lack of evidence. We could spend an eternity blaming random SNPs for everything under the sun - but it wouldn't be at all productive. I'd rather focus on what the science says and leave it to the researchers to fill in the gaps, instead of guessing and then treating it as truth as seems to happen often with Yasko.

    However I do think the above TPH2 research is rather good and interesting research. But it's far from reaching a conclusion which would be useful for lifestyle adaptions, supplementation, etc.

    And I think the psych-related research might have a lot more potential if researchers in general (not those in the above paper) stop dicking around with weak methodology and a drive to prove their own assumptions. Bias isn't as bad in the genetic studies, since they don't really care which direction their findings go, as long as they get findings. Hence we get a ton of contradictory papers with weak effects and weak p-values, and no real advancement in understanding anything.
     
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  15. Snow Leopard

    Snow Leopard Senior Member

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    A few minutes ago, I wrote a previous comment (now deleted), since I confused this study with another.

    Nevertheless, I strongly agree with the comments that @Valentijn has made.
     
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  16. nandixon

    nandixon Senior Member

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    After researching Acorus, it seems it's probably too dangerous to use. Although it's supposedly a treatment for dementia/Alzheimer's in China, the active components (e.g., β-asarone) are apparently quite toxic even in very small amounts.

    Additionally, this plant apparently tends to grow in wastewater areas contaminated with mercury. So all around probably not a good idea.

    However, I found a much better alternative for a TPH2 inhibitor. It turns out that just last year, it was discovered that quinine is a TPH2 inhibitor, and has other anti-serotinergic effects as well. (This is mostly the reason for its adverse effects among some people taking it for malaria, i.e., people with low tryptophan status.):

    The antimalarial drug quinine interferes with serotonin biosynthesis and action (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3885885/)

    So I'll attempt to try quinine to see if excess serotonin might somehow be associated with my particular version of ME/CFS (which may only pertain to people who have calcitriol levels that are naturally high, and who find vitamin D extremely fatigueing, and thus will be a very small subgroup). It should be a very good test.
     
    Last edited: Jan 13, 2015
  17. nandixon

    nandixon Senior Member

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    @Beyond
    It's going to take me awhile to get some quinine (a TPH2 inhibitor) so I decided to go ahead and try the Bacopa monnieri (upregulates TPH2) as a sort of "negative" experiment.

    I bought the Himalaya brand standardized caplets, which I guess is what you've been trying.

    I was expecting that I would feel worse, based on the excess serotonin theory I have for my own version of ME/CFS (see here) and given that Bacopa can upregulate TPH2.

    But instead I've found, like you, that the Bacopa is actually energizing. I've only taken it two days in a row (1 caplet in the morning) with the same result each time.

    I did some additional research and found that Bacopa is considered to be adaptogenic, including with respect to serotonin, so that would keep my theory alive for the time being.

    Depending on the circumstances, Bacopa can either increase low serotonin levels, or decrease high levels. See, e.g.:
    Effect of Bacopa monniera on stress induced changes in plasma corticosterone and brain monoamines in rats
    http://www.ncbi.nlm.nih.gov/pubmed/17321089/

    Hopefully the Bacopa will keep working. Another adaptogenic herb I tried about a year ago, Rhodiola, was energizing for about a week, stopped working, and then even became fatigueing.

    I'm still planning to try the quinine, and maybe also p-chlorophenylalanine, another tryptophan hydroxylase inhibitor.
     
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  18. Beyond

    Beyond Juice Me Up, Scotty!!!

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    I am taking the AOR extract, although Himalaya are very reputed. Initially I tried Bacopa for sleep and I was dissapointed to see that it seemingly kept me more awake.
     
  19. nandixon

    nandixon Senior Member

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    Just a quick update: The Bacopa only had a beneficial effect those first couple days I mentioned. I then gradually began to feel increasingly worse (= more fatigue) over succeeding days.

    So if my theory for the immediate cause of my fatigue is correct (i.e., excess serotonin), then Bacopa may indeed be up-regulating TPH2, per the previously cited study (Bacopa monniera leaf extract up-regulates tryptophan hydroxylase (TPH2) and serotonin transporter (SERT) expression: implications in memory formation).
     

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