Folate And Methylation - (Mar/31/2005 )
Kia hey hey ora Nick,
Sometimes this happens - u find the new questions before discussing the old one. I'we studied what does mechanics say about embryo development and was lucky to find interesting ideas. They were published 2002 and I'll present the main ideas from:
How is an Embryo Formed?
An Overview of the Research Carried Out In Dr. Brodland's Lab
www.civil.uwaterloo.ca/brodland
G.W. Brodland
...However, it is clear that the answer will require a highly multidisciplinaryapproach, drawing on input from biochemistry, micro-morphology, mechanics, and other fields.
... embryonic tissues must undergo precise, self-driven changes of shape [1] (Fig 1). It is generally accepted that the cytoskeleton and other sub-cellular structural components drive these movements. ...However, no morphogenetic process has been investigated with sufficient rigor that its medical outcomes canbe predicted. This is tragic because, every year, nearly half a million babies enter the world with a serious birth defect such as.... a neural tube defect due to a tissue malformation. ....
....constructed and controlled by complex sequences of biochemical events that are ultimatelyregulated by the genes. Fig. 2. A schematic illustration of an epithelium hints at the complex geometry of its structural components and the plethora of biochemical factors present. These interact together, under genetic control, to produce mechanical forces with the potential to reshape the tissue. The changes of shape that occur in any particular tissue depend also on its mechanical and biochemical interactions with adjacent tissues. In order to investigate morphogenetic movements, our research team has followed two main approaches. The first of these uses a unique Robotic Microscope System (Fig. 3) to collect images from different viewing angles over the surface of a live embryo and original software to make three-dimensional reconstructions (Fig. 4) of it [2].
The second approach we use attempts to answer this fundamental question using finite element software that we wrote to model cells and tissues.
In the course of this work, [6-10] we made the unexpecteddiscovery that the Differential Adhesion Hypothesis, which had been almost universally acceptedfor forty years, was mechanically untenable. This led to a new theory based on differential interfacial tensions to explain cell sorting and a family of related phenomena.
Our software made possible an unbiased test of any of the 50 hypotheses that had been offered in the literature to explain this critical developmental process. Our calculations showedthat only one theory - contraction of apical microfilaments coupled, with axial elongation of theembryo - could produce the requisite changes of shape. The simulations also revealed aninteresting interaction between the current shape of the embryo and the effect of a fixed set of forces. As the geometry of the embryo changed, a single fixed set of driving forces was able to produce ridges at the edges of the neural plate, followed by narrowing of the plate and, finally, rolling up of the
From a philosophical perspective, the elegance of embryo design is impressive. Onemorphogenetic movement sets up the geometry for the next, with each following so smoothly that it may be difficult to define a point of transition. Often, as in neurulation, the means by which asequence of movements is driven is deceptively simple. Since many hundreds of precisemorphogenetic movements are required to produce a normal embryo, one has to wonder that embryos, including human ones, are ever normal.
Our software made possible an unbiased test of any of the 50 hypotheses that had been offered in the literature to explain this critical developmental process. Our calculations showedthat only one theory - contraction of apical microfilaments coupled, with axial elongation of theembryo - could produce the requisite changes of shape. The simulations also revealed aninteresting interaction between the current shape of the embryo and the effect of a fixed set of forces. As the geometry of the embryo changed, a single fixed set of driving forces was able to produce ridges at the edges of the neural plate, followed by narrowing of the plate and, finally, rolling up of the plate.
To conclude: 50 hypothesys had been offered. Which is true? We concentrated on epigenetic change. Treatment results using folate showed that this sometimes works. How? Some epigenmechanic process? Histone state is interesting of course. But is this intermediate chain or side effect?
Is calcitonine gene methylation involved? I can't answer even- is this question of great importance or not. I think some strong brain group must discuss those 50 hypothesys again and try to predict necessary experiments and they results. But histone methylation state is interesting anyway brcause this is not only NTD problem.
Kestutis Urba
hi kestitus,
more food for thought, that is great, I was wondering what the 50 hypothesis were that the group tested.
your mechanical models do sound plausible. I have always thought that cell movement was due to growth towards a chemical gradient or something along those lines and this could have been adapted for neural tube closure,
there are some very interesting animations on that website. Do you know if one of the hypothesis was a chemigenesis towards a gradient??
Nick
Kia ora Nick,
Oxidative stress is - I've seen something and I'm trying to guess - but my Pubmed search doesn't works now at the end of year unfortunately...
I would like to explain now - why I suppose the study of histone state and NTD of great importance anyway - even if it is only the side effect...The month ago I had the idea about two different discusions - methylation, folate and NTD; methylation, folate, cancer; Now I think it's great we've had not separated discusion, because both topics helped to understand me what experiment could be very usefull for cancer research - folate system is one of the main in cancer studies and this system is at the centre of NTD development research. So, if compare normal ectoderm (fast growing too) cell, preNTD(with low folate, which is supposed to be some cancer risk factor), embryosarcoma cell, and adult sarcoma cell, it is possible to reveal differencies and to find out THE KEY to the malignant growth!!!
I've tried to describe these ideas in:
The hot article in this direction is:
Nuclear cloning of embryonal carcinoma cells.
Blelloch RH, Hochedlinger K, Yamada Y, Brennan C, Kim M, Mintz B, Chin L, Jaenisch R.
Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
BUT THEY DIDN"T USED NTD CELLS to compare.
The ectoderm cells give the begining for neural and brain cells, so the origin of neoromas could be revealed by this experiment too.
The experiment using mesoderm cells ( develops muscles, bones...) is needed too for comparing and better understanding o9f teratomas.
The same ideas are valid for endoderm cells - to reveal the origin of lung tumours...because endoderm gives the beginning for the respiratory system. Of course this is only the scetch, but I hope it's understandable.
The preNTD situation gives very good model for folate system involvement into growth regulation and if to minus these features from embryotumour cells features, the result would be THE KEY!!!
This is why results of Folate and histone methylation/acethylation state together with DNA methylation are of great importance anyway. One more detail - well known marker of cancer - alphafetoprotein depends on corresponding gene methylation too. What about its histones?
I wish You, Nick and Your lab friends in all the world NEW YEAR full of revelations discoveries explorings which solve these problems successfully.
Kestutis Urba
Hi Nick,
Before revealing (by someone) differences in embryo normal, embryo preNTD cells and embryo carcinoma cells ... I would like to ask about the Shh path, which according to
Leonardo Piedomonte, Ian K.Wailes and Howard L.Weiner from NYC
recent perfect article
MEDULLOBLASTOMA:mouse models and novel targeted therapies based on the Sonic hedgehog patway (Neurosurg Focus 19(5):E8, 2005
is essential in developmental patterning the neural tube too
and is involved in medulloblastoma formation (Ptch mutations...).
My question is about the TIME moment:
is it possible that some disturbance of Shh path till neural tube closure leads to embryo NTD
and the same disturbance of this path after neural tube closure leads to medullosblastoma?
Could simmilar time moment of mutation idea have the key role for the genes which can couse both developmental anomalies and cancer - PAX3(2q35), KIT (4q12), I've mentioned above - PTC(Patched) (9q22), RET (10q11), WT1 (11q13) ???
Kestutis Urba
P.S. I'm trying to improve the Cancer research experiment comparing cells in different but simmilar enough growth conditions plan I've proposed in the poster before, but why there is no criticism...
I think this plan is only 25 percent done
Kestitus,
sorry for the delayed reply......trying to absorb your comments and sourcing the papers you are citing.
With Jaenisch's paper, they were performing the experiments as a proof of principle to show that indeed nuclear cloning can be achieved, I have had the previlige to hear Jaenisch speak on two occasions and was inspired by his cause. It would indeed have been interesting to investigate NTD cells in this respect but that would be answering a different question altogether.
as for sonic hedge hog (SHH), as I am not familar with this morphgen, I had to read up on it, but indeed the temporal production of this compound is crucial for brain development and it could well be that folate status affects the temporal expression of SHH.
Indeed reading a review article from Copp et al 2003, Nat Genet., it summarises over 80 genes that when mutated, will lead to NTD and brain malformation, there is no reason why folate depletion either directly or indirectly affects the expression of one of these genes that would lead to NTDs.
more thinking is needed, but it has certainly added another dimension to the hypothesis Kestutis, I thank you.
Nick
Nick,
I'm sorry for too heavy problems I can't solve alone.
Well, one more - It was found that Embryo stem cells are unfortunately...cancerous. WHY? and HOW? Now I think that cancer is ...adult development abnormality, but very specific...
Why cancerous? Possibly those Patched gene mutations shows its destructive strenght too... So, philosophically I could conclude only, that these embryo abnormal developments and malignant developments intersections depending on the same genes has the great meaning and revealing of those growth control mechanism will really make tissue repairment much more efective.
Our practical problems are - how folate system and OCU(one carbon unit) metabolism controls genes using methylation and especially specific genes...in NTD and cancer research tasks.
I've studied some other aspects of NTD too and I would like to share and discuss some more facts. It was found that Diabetes mellitus makes risk of NTD five fold greater. It was published that inositol helps in this situation too. Mr. Copp et al 2003 noticed that not folate dependent NTD could be attacked using inositol too. I've asked myself - what mechanisms do this, becouse it was written that metabolism of inositol is unclear?
One possibility is - I remembered from Roche map, that inositol is not "so far" from Serine - Glycine, Folate systems. More it's very close. Studying pathways on exelent www.genome.jp gave some more exact hypothesys: inositolphosphate metabolism (it is - map - presented in PATH separately) is directly connected to Glycerophospholipid metabolism (presented in PATH separately too). So, it's easily to travel on those maps from inositolphospahate to (2.7.8.11 enz) controled reaction (some problems with reversibility appears but some article showed that reversibility exists...)and from cdp-diacyl-glicerol go to phosphotidylcholine (via 2.7.7.41 and 3.1.1.4 enz) and from this point choline (one of ONE CARBON UNITS donors) is reachible... It was published that inositol has the other functions - signaling an so on, but this could work possibly too. To conclude - Folate system is essential for NTD, leading to methylation like possibly Inositol metabolism path via Choline system. Another problem is about Serine concentration in Diabettes mellitus - this seams to be important because of changes in glycolysis...Whats your opinion?
Good luck.
Kestutis Urba
P.S. It's deep night in Vilnius - 2 o'clock. Sculptor Arthuras gave me computer...to finish solutions of some questions I was walking on the streets with them in my head. Oh those inositols, folates... Thanks Arthuras and for my sister Laimute - she's supporter of my research trusting I'm doing something interesting.
Happy birthday to her on January 9!!!
Why cancerous?
Stem cells are both by definition, immortal and pluripotent, which unfortunately are also characteristics of cancer cells.
as you have rightly pointed out kestitus, many pathways would feed into OCU metabolism and serine is no exception.
I wish your sister a happy birthday, how old would she be?
Nick
Thanks Nick,
Theoretical consideration of NTD in lots of possible directions could be helpful for some partial problems, I suppose. Diabetes mellitus influence (significant risk factor) on NTD is empirical fact. Revealing mechanisms why some inheritance could increase NTD possibility in dbmellitus case I would like to evaluate changes in One carbon units metabolism having carier folate. Insulin deficiency changes glycolysis characteristics and changes Serine synthesys branched from glycolysis. Serine is essential input into One Carbon unit - I've noticed this in November 25 post, but I have very little understanding about OCU situation and Serine metabolism in cell affected by dbmellitus. I've read some pages about dbmellitus biochemistry - found facts that gluconeogenesis is more active and so on, but I can only predict that Ser synthesys branched from glycolysis could be less intensive having consequences on Met cycle finally too. Maybe someone having greater experience about dbmellitus biochemistry than we, have information about Ser and OCU....
My prediction was supported by
Poirier, L. A., Brown, A. T., Fink, L. M., Wise, C. K., Randolph, C. J., Delongchamp, R. R. & Fonseca, V. A. (2001) Blood S-adenosylmethionine concentrations and lymphocyte methylenetetrahydrofolate reductase activity in diabetes mellitus and diabetic nephropathy. Metabolism 50:1014-1018 ]
A general defect in DNA methylation in diabetes is suggested by the recent observation that S-adenosylmethionine (SAM), the main physiologic donor of methyl groups, is decreased in erythrocytes of diabetic patients. In addition, decreased erythrocyte concentrations of SAM and other alterations were found to be associated with disease progression
but What about dbmellitus and preNTD situation?
My question for You Nick is
Are there any wider reviews than exelent article
Am J Med Genet C Semin Med Genet. 2005 May 15;135(1):31-41.
Mouse models of neural tube defects: investigating preventive mechanisms.
Greene ND, Copp AJ.
Could we choose this article (and TABLE 1!!!) to be basic for further discussions?
Kestutis Urba
P.S.
My sister is ful of energy like very young, She's clever teacher and She says
my scientific research must be continued anyway...
........
Indeed reading a review article from Copp et al 2003, Nat Genet., it summarises over 80 genes that when mutated, will lead to NTD and brain malformation, there is no reason why folate depletion either directly or indirectly affects the expression of one of these genes that would lead to NTDs.
more thinking is needed, but it has certainly added another dimension to the hypothesis Kestutis, I thank you.
Nick
Dear Nick,
Thank for support in discussion, sharing information about interesting authors...when making hundreds of advices during the year every day moderating and helping.
It's time to make some conclusions, because amount of information we touched and problems complexity is terrifying even me.
I think, the article (perfect at biological and genetical level):
Greene ND, Copp AJ.
Am J Med Genet C Semin Med Genet. 2005 May 15;135(1):31-41.
Mouse models of neural tube defects: investigating preventive mechanisms.
and TABLE 1 summarises achievments in NTD and folate preventive role research during last decade.
Folate, plus Methionine, Inositol, Arachidonic acid, thymidilate, rhetinoid acid, panthothene, vitamin E were studied by different experimentators, but molecular mechanisms are unclear still now, so problem at the molecular biology level must be considered more deep.
There are two different points of view about possible Folate influence in NTD development:
first- it is well known, that Folate is needed for purine and thymidylate synthesys, so insufficiency of folate directly affects those vital for cell processes, according to Mr. Greene and Mr. Copp article, leading to NTD
in Cart1 mouse , but
WHETHER the effect of folic acid is mediated through prevention of apoptosis in the forebrain mesenchyme has not been reported to date.
in Cited2 mouse
HOWEVER, there is no obvious amelioration of the excessive midbrain apoptosis in folic acid-rescued embryos suggesting either that the increased extent of apoptosis is not the direct cause of NTD in this mutant, that there is a subtle decrease in apoptosis that is sufficient to allow the neural tube to close or that folic acid acts by an alternative mechanism to promote neural tube closure.
in Splotch
to cell death like p53 inhibition mutation effect, ....
CONCLUSION: mechanisms are unclear but cell appoptosis becouse of Folate deficiency is possible reason of NTD
second - it is well known that Folate is One carbon units carier and on this depends SAM concentration in Met cycle and finally DNA methylation effects too, leading to according ....
I would like to present sequence of facts supporting point of view that some DNA and histones methylation disorders could be the reason of NTD (too):
1. Folate system is the carier of One carbon units used for DNA methylation
2. Methionine has possitive efect against NTD (this supports 1.)
3. some DNmethylase disturbances were detected to be important in NTD development
4. possitive results using 5-azacytidine prevent NTD were obtained
5. If Inositol really is metabolised to Choline -Methionine path as I mentioned in post above (experiments with labeled carbon are necessary) then this supports DNA ,ethylation involvment
The problem is HOT ( prof. A .J. Copp group announced project to investigate mechanisms of Folate influence on NTD deeper, 2005 November)
and SHARP - (prof. H.J. Blom - Netherland group announced project to investigate DNA methylation role, 2005-2007)
and What about histones, Nick?
(to be continued)
Kestutis Urba
P.S. I'm very angry because some "friends" don't allow to finish this post, I haven't made some drawings for better understanding and not mentioned the authors exactly supporting 1-5...but it's easily to find them on Pubmed and Google- an hour of reading, but THANKS them for two hours of computer time - we've bought using municipality money...
Thank for support in discussion, sharing information about interesting authors...when making hundreds of advices during the year every day moderating and helping.
..........
and What about histones, Nick?
(to be continued)
Dear Kestitus,
Thank you for making a valuable contribution to everyone here on this board about this topic. I can say for myself, it's certainly been very informative and has stirred my brain cells into action, I don't have that many!
Histone methylation is something that I would like to investigate in the lab. it is certainly a great question that remains to be answered.
I hope you find yourself some more computer time over there in Vilinus!
Nick