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Posted: Mon Nov 22, 2004 9:19 am
by BioDocFL
Lurker(s),
I just did notice your questions. As a quick response, I am thinking of the DNA damage with regards to fragile sites, as I discussed in the polyamines topic. The DNA may have damage that is hidden away in heterochromatin (silenced gene regions). Later, if something stimulates the cell to open up that region, the hidden damage could then be a problem. Neighboring single strand breaks could add up to a double strand break with the result that the chromosome is fragmented. With regards to X inactivation, the X inactivation process does not extend across to other chromosomes or fragments so there could be loss of the epigenetic control (silencing/activation control) of the genes that would otherwise be kept inactive. Then there could actually be extra copies of genes active, giving overexpression. That is the example I keep refering to with regards to loss of epigenetic control but there could be other chromosomes with damage. (Always have to add a caveat about variations with regards to MS theories.)
The genes of particular interest to me (and which appear to be involved in cancer also) are polyamine genes. Particularly spermine synthase and spermidine/spermine N1-acetyltransferase on the X chromosome at Xp22.1. There is also a pseudogene of S-adenosylmethionine decarboxylase at Xq28 which is believed to have some functionality. You could read the polyamine thread to see how I propose they could be a problem. They are not necessarily a problem immediately but they can be a problem when the cell is stressed since that can provide the precursors they need.
DNA replication would spread the damage, daughter cells inheriting uneven amounts of chromatin and/or inheriting chromatin that has lost some epigenetic control. But this could occur early in life as the brain develops, say in a young child, as cells are still dividing and differentiating. Cells are differentiating but some stop at an intermediate step such as glia cells. These partially differentiated cells are poised to continue differentiating when needed to replace other cells that have been lost, but in the meantime they are quiescent. In carrying out further differentiation, there could be opening of heterochromatin. And some of the differentiated cells may have inherited damaged chromatin early on but it was not a problem until the cell was provoked into a stress response. Then the loss of control can lead to overexpression of some genes, such as the polyamine genes. I am trying to figure out, if the hypothesis is correct, when the damage could occur in MS, in what cell types, and how much would it spread. Every cell does not necessarily get damaged DNA so the problem doesn't occur in an MS patient every time there is a stress (bacterial or viral infection for example). It is when one of those few cells with damage has to step in and do its job that it shirks its duty and fizzles out, maybe causing local damage to other cells leading to a lesion.
This is all hypothesis on my part so keep that in mind. (Always have to add disclaimers with regards to MS theories.) And, I am continually trying to refine the hypothesis. But it does bring up questions of what therapies could be applied. That is why I am in cancer research so I can study polyamine enzymes. We are developing inhibitors of polyamine enzymes. Polyamines appear to play a part in cancers too but with different paths, different cell types, and consequences. Think of the cells in cancer (ex. breast cells) as being poised for ongoing replication whereas the cells involved in MS are more poised for apoptosis when things go wrong.
So one therapy could be polyamine inhibitors, perhaps for milder cases of MS. Robin also brought up the idea that metalloproteases could be involved in some of the damage so they could be targeted. Another therapy, stem cells, could be a future therapy for more severe cases whereby replacement cells can be differentiated in tissue culture and added to the brain to replace cells that have been lost. Difficulties that would need to be overcome are: the signals needed to differentiate the stem cell into the proper brain cell (probably tweak it towards being a glia cell); delivery to the site where it is needed; suppression of rejection; and developing the new connections to involve the cells properly. To each of these I would say there is progress being made. Researchers at the University of Florida are able to grow nerve cells in culture now which was a major difficulty just a few years ago. They are able to establish working connections between cells. Delivery is something I want to learn more about because these cells appear to have some mobility, i.e. they could work their way to where there is a need for them, rather than having to place each cell in its final position. Perhaps combining stem cell administration with physical and mental exercise therapy will draw the cells to where they are needed and help them form the needed connections. This suggests that you could even add more cells than were ever there to begin with. I could use that! Also, xenotransplantation is coming along (using cells from one species for transplanting into another species.) A lot of progress is being made in pig to primate (such as baboons) xenotransplantations in overcoming the rejection problems, particularly with regards to cardiac repair. So the possibility might arise in the future to: develop cells in tissue culture into the proper type, transplant the cells into the CNS, suppress rejection, coax the cells into position, and then exercise the region to form new connections with the new cells. And, as you can see, it is not just MS projects that will give us techniques and knowledge but projects on cancer, heart repair, immunosuppression, cytokines and growth factors, and basic neurology, even what I do: computer software development and virtual screening to find new drugs.
Hope that helps. Wesley
OddDuck: Now I have to read up on p53. I swear, I have to wear my sneakers everytime I sign on to the computer to try to keep up with you!

Posted: Mon Nov 22, 2004 9:20 am
by OddDuck
Well, I spoke too soon.

Something was bothering me about MMP9 (and the "inflammation" focus for the most part), so I continued on. The connection is definitely there, allright, but here is a problem with focusing completely on MMP9: It doesn't appear to apply to inflammatory (RRMS) and non-inflammatory (progressive) MS both:
Mult Scler. 2004 Aug;10(4):376-80. Related Articles, Links

Decreased MMP-9 production in primary progressive multiple sclerosis patients.

Sastre-Garriga J, Comabella M, Brieva L, Rovira A, Tintore M, Montalban X.

Unitat de Neuroimmunologia Clinica, Hospital Vail d'Hebron, Barcelona, Espanya. jsastre@hg.vhebron.es

BACKGROUND: An increase in MMP-9 levels has been found in relapsing-remitting (RR) multiple sclerosis (MS) showing correlation with magnetic resonance (MR) parameters mainly during relapses. However, data regarding primary progressive (PP) MS is scarce. OBJECTIVES: To determine both the pro and active forms of MMP-9 in PPMS and transitional progressive (TP) MS, RRMS and healthy controls (HC), and to assess the relationship between MMP-9 levels and clinical and radiological variables in PP/TPMS. METHODS: 73 patients with PP/TPMS, 50 RRMS and 43 HC were studied. Levels of pro and active forms of MMP-9 in serum were measured with ELISA. EDSS and MSFC scores were recorded and T2- and T1-weighted MR scans were obtained at the time of blood sampling and one and two years later for PP/TP MS cases. RESULTS: MMP-9 levels were 202.27 ng/ml for PP/TPMS, 242.20 ng/ml for RRMS and 274.49 ng/ml for HC. MMP-9 levels were significantly lower in PP/TPMS compared to RRMS (P= 0.026) and HC (P= 0.001). No significant correlations were found between MMP-9 levels and clinical scores or radiological parameters. CONCLUSIONS: These results point to different regulatory mechanisms of MMP-9 production and/or activity between PP/TPMS and RRMS.

PMID: 15327032 [PubMed - in process]
hmmmmmmmmmm...........Are we dealing with distinct separate types of diseases that are currently simply lumped under one umbrella? That being called "MS"?

Do the progressive patterns of MS have a distinctly separate pathogenesis of their own? Or something is mutating that skews MS into progressive? hmmmmmmmmmm.............

Deb

P.S. Still........something like desipramine (in combination therapy with other "specifically" targeted medications) is still a pretty good option right now, mainly because it DOES also appear on paper to apply to progressive types of MS.

I don't know.........right now, even though I agree MMP9 is involved, I haven't reached any type of conclusion on it yet. :?

EDIT: Ok.....Robin.........get this one....here are our Netherland guys again. (Plus, you know me.........I'm not basing my thoughts totally on these couple of abstracts alone.) We need to submit our findings to the Netherlands, I'm telling ya! They are doing the research WE are doing!
The Expression Profile Of Matrix MetalloProteinases (MMPs) And Their Inhibitors (TIMPs) In Lesions And Normal-Appearing White Matter Of Multiple Sclerosis

Raija L. P. Lindberg, Corline J. A. De Groot, Lisette Montagne, Peter Freitag, Paul van der Valk, Ludwig Kappos and David Leppert
Brain, Vol. 124, No. 9, 1743-1753, September 2001
University Hospitals, Departments of Research and Neurology, Basel, Switzerland and; University Hospital Vrije Universiteit, MS Centre for Research and Care, Division of NeuroPathology, Department of Pathology, The Netherlands
--------------------------------------------------------------------------------
PMID# 11522577
Abstract

In Multiple Sclerosis, Matrix MetalloProteinases (MMPs) are effectors of crucial pathogenetic steps, such as Blood-Brain Barrier breakdown, invasion of Brain Parenchyma by Immune Cells and DeMyelination.

However, only limited data are available on the types of MMPs induced in the course of Multiple Sclerosis, and on the role of their endogenous antagonists, the Tissue Inhibitors of MetalloProteinases (TIMPs).

We quantified the transcriptional expression of six MMPs and the four TIMPs in lesions and in Normal-Appearing White Matter (NAWM) from post-mortem Multiple Sclerosis Brain tissue by real-time polymerase chain reaction, and compared levels with those in Brain tissue from six control patients without Neurological Disease.

The mRNA expression of MMP-7 and -9, but not of other MetalloProteinases [MMP-2 and -3, and Tumour Necrosis Factor-alpha (TNF-)-converting-enzyme] was equally upregulated throughout all stages of lesion formation with active inflammation, and in most of matched NAWM tissue.

The transcription of Cytokines TNF-/ß and InterLeukin-2 (IL-2), known modulators of MMPs, was upregulated only in distinct stages of lesion formation, while their receptors were not induced at all.

Which suggests that additional signalling molecules participate in the sustained upregulation of MMP-7 and -9 in Multiple Sclerosis. None of the TIMPs showed a significant induction over baseline expression of controls.

We hypothesize that an imbalance between MMP and TIMP expression may cause a persistent ProteoLytic overactivity in Multiple Sclerosis, that may be a factor for continuous tissue destruction, and hence for Secondary disease progression.
I don't know.....MMP9 is definitely involved, but I am leaning toward thinking it's not an "instigator" per se. :?:

SECOND EDIT: Ok........I'll shut up now for a while. :roll: :P

THIRD EDIT: Ok....I fibbed. So, basically, this IS telling us something or verifies something, I should say. RRMS (and associated inflammation) migrates into SPMS. Progressive MS appears to start as "progressive" right from the start - similar pathogenesis as it pertains to axonal damage, but..............hmmmmmmmmmm.

Posted: Mon Nov 22, 2004 9:48 am
by raven
MMP-9 levels were 202.27 ng/ml for PP/TPMS, 242.20 ng/ml for RRMS and 274.49 ng/ml for HC
If I read these numbers correctly they are stating that the serum levels of MMP-9 are lower in PPMS than in RRMS, they also show that the serum levels of both are lower than those of healthy controls.

I don't know how serum levels would equate to parenchymal levels. There are many extracts that state that MMP-9 is up-regulated in both PPMS and RRMS. Without examining the full article I can't comment further on this extract.

Robin.

p.s. Deb, I'm not sure how I feel about constantly freaking someone out! :lol:

EDIT: I've just seen your latest edit Deb. I'm not suggesting that MMP-9 is the antagonist within MS. Just that it has a very important role to play within the pathogenesis and possibly forms an important theraputic target. Actually as far as a theraputic target goes I can list a few compounds known to regulate TIMP-1/MMP-9 ratio, minocycline, beta-interferon, statins, circumin, alpha lipoic acid etc.. ring any bells? :wink:

Posted: Mon Nov 22, 2004 9:53 am
by OddDuck
Well, freaking me out could be a "good" thing (I lead a boring life..... :lol: ) Hey, maybe you and I are like the Cat and simply are one in the same. ROFL

Ok......if you will note, the subsequent abstract I posted helped to clarify what I was finding. I realize the first one was overly mathematical.

The subsequent one is pathological.

Read on, my man........Read on! :wink: (Or is that "Go West"........)

Deb

EDIT: You know......I BETTER slow down now, and allow the "men" to catch up. hehehe.............. I'm JUST kidding! :lol:

Posted: Mon Nov 22, 2004 9:55 am
by OddDuck
....ring any bells?
You KNOW it does! :lol:

How about "simvastatin" (as only ONE example).........hehehe......

Deb

EDIT: What's that taunt........"my gray matter is bigger than your gray matter?" :lol:

Posted: Mon Nov 22, 2004 10:11 am
by raven
"my gray matter is bigger than your gray matter?"
oooooh, let's compare MRI's :lol:

Posted: Mon Nov 22, 2004 2:48 pm
by OddDuck
I'll just second Deb's comment that our 'discussion' on cognition vs intellect was a side issue, albeit a very important one and probably deserving of it's own thread. Of all the effects of MS cognitive decline is the one that scares me most!
Robin (and all), I'm starting a new thread on the above if you care to review and contribute!! :D

Deb

EDIT: Not indicating that this thread is by any means exhausted!!!

FWIW

Posted: Sat Nov 27, 2004 7:34 pm
by feesher
My wife, who is a dx RRMS, and her sister, who is in the middle of a maybe-dx of RRMS, both tested for hogh iron levels by their OB's when pregnant. It's odd that most pregnant women are low in iron. Oh, and they are of Norwegian descent.

Iron-ic (da dum dum) (sorry, but had to do it)

Posted: Sun Nov 28, 2004 11:55 am
by BioDocFL
Feesher,
'ironic', great pun but I ferrous that many people will miss the humor (or is it: I ferric that many people will miss the humor? Chemistry nerd joke.)

We can go way out there theorizing about heavy metal involvement with MS. I think many people have pondered a connection between the distance from the equator where someone grew up, sunlight exposure, and the incidence of MS. Something about sunlight helping with the production of vitamin D, which then aids in maintaining sufficient calcium levels. Calcium (+2 charge) at normal levels would help neutralize some of the DNA negative charge (from the phosphates in the DNA) so that the DNA is not as stiff and can function and be maintained properly with regards to packaging, replication, transcription, and repair. Proper calcium levels could help mask the heavy metal ions and perhaps modulate their flow into and out of cells and the creation of free radicals from unmasked heavy metal ions. Someone growing up in a northern region may not get enough sunlight exposure on a regular basis to establish the production of vitamin D and the right levels of calcium. Probably a lot of holes, vagueness, and loose ends in that theory.
Okay, that's a theory. Maybe it's good, maybe it's a bit flimsy. But now let's go way out on a limb. The northern regions were covered by glaciers during the Ice Age. The glaciers pushed their way southward, such as to Wisconsin in North America and probably much of Scandanavia. As the glaciers moved, they scraped the earth off and pushed it along, carving out many lakes. Just look at Minnesota with all its lakes, for example. This could remove the upper levels of earth and expose deeper levels that are richer in heavy metals. Water flowing from the receding glaciers as the Ice Age ended could leave higher levels of heavy metals in the lakes and surrounding areas. Then, as humans moved back into the areas, they were exposed to these higher levels of heavy metals. Of course earlier humans were simply concerned about living to 30 or 40 years old without succumbing to all the diseases and threats around: malaria, small pox, tuberculosis, gangrene, typhus, cholera, food poisoning, starvation, hypothermia, etc. But now that we live longer, some other threats emerge and we can put names to them: cancer, MS, lupus, etc.
I would imagine that water is tested on a regular basis in any public water supply, but perhaps there are some occasions or situations where extra amounts of heavy metals could get into a local water supply or local food supply. Most of this might be eliminated from the body but the CNS presents a different, difficult situation in removing the excess ions. Perhaps there have been studies on heavy metals and MS but my feeling is that the heavy metal ions may have come and gone, generated free radicals that caused DNA damage in quiescent cells. Later the heavy metal ion levels returned to normal when the person moved to another region or better water standards and supplies were available but the damage had been done. When those damaged cells were stimulated later in life to differentiate and serve, the DNA damage then led to loss of some epigenetic control. The free radicals could have reacted with the DNA causing single strand breaks in the phosphate backbones. Several neighboring single strand breaks in both DNA strands could lead to a double strand break and fragmenting of a chromosome. These sections of genes with DNA strand breaks could not retain supercoiling stress and could not be packaged up tightly into heterochromatin so it would be accessible to transcription, even if the genes were supposed to be silent, they are now closer to a state for expression, they are more accessible for histone acetylation, DNA demethylation and for gene expression. Also, the DNA damage might interfere with the establishment and maintenance of epigenetic silencing markers such as DNA and histone methylation and histone deacetylation. Then there could be overexpression of some genes that should be tightly controlled. And, as I have said before, it might be that the consequences could have the greatest chance of appearing when the cell is stressed.

OT: I have a few ideas for threads we could start if anyone is interested:
1. As an MSer, especially if you use a cane, crutches, or wheelchair, how do you or would you react
to someone (stranger or friend) who comes up and asks if you have MS, (or muscular dystrophy, or some other disabling disorder)? Are you offended, angry, embarassed, nonchalant, thankful for their interest or what? I've never been nosey towards anyone or asked but nowadays I seem to notice the people in wheelchairs or using a cane and am curious. I assume they would be offended but I don't know and would never ask.
2. We don't seem to get much or any input into these forum topics from MS researchers or so-called MS experts. I am wondering why. I tend to approach everything with attempted logic so I have been trying to put myself in their shoes and trying to guess why. Perhaps: 1) they have great breakthrough secrets they don't want to expose, 2) they consider our discussions too trivial, 3) they don't feel confident in their own knowledge, 4) they don't have enough time, 5) they don't have enough interest or incentive, 6) they don't know of the forums. We could address this last one with some directed emails to notify them of ThisIsMS.com.
Wesley

Posted: Fri Jan 07, 2005 8:22 am
by OddDuck
Wesley,
We could address this last one with some directed emails to notify them of ThisIsMS.com.
I do that all the time! :wink:

Deb

Posted: Fri Jan 07, 2005 10:19 am
by SarahLonglands
We don't seem to get much or any input into these forum topics from MS researchers or so-called MS experts. I am wondering why
Wesley, I would hazard a guess that it is lack of time: after working hard all day, you probably want and need to turn your mind off and think of something else completely.

I am a professional painter, so can do the odd post while having a coffee break, but David sometimes does not even get the time to have a proper lunch break. :(
.

Posted: Fri Jan 07, 2005 5:05 pm
by BioDocFL
Anecdote,

Yes, time is always pressing.

However, I am in research and I know how some researchers are, including myself. We get obsessed with curiosity. We can not leave a problem alone and are continuely preoccupied about it.

Of course each researcher is off in their own little world trying to figure out their particular area of interest. Perhaps there are not enough of them preoccupied with MS and related disorders. We need to enlist more. I have a meeting on Monday with a really big fish. I am hoping to get him interested in my overly complicated hypothesis about MS.

One thing I think might dissuade researchers from following forums very much is that so much of the discussion is in regards to therapies and standard protocols for determining the disorders. Routine stuff for MDs, not interesting for basic scientists unless it is a drug that they helped develop.

I, for one, am always looking for a forum that is heavy into discussions on the causes (MS, lupus, RA, cancer). I tried recently to get started in another MS forum but it was just a very negative environment and the attention span was extremely short. That's when I decided I wasn't going to waste my time. This forum has really helped me with my thinking though.

Wesley

Posted: Thu Jan 13, 2005 12:02 pm
by OddDuck
Wesley,

How did your meeting go with that "big fish" last Monday?

I'm dying to know!

Deb

Posted: Fri Jan 14, 2005 6:57 pm
by BioDocFL
OddDuck,

I had the meeting on Monday and then have been out of town dealing with aging parent issues. No fun.

The meeting was to go over our collaborative project in cancer drug discovery. We have a few basic molecular structures that I then grew various side chains on and then I did some computer docking into the model of the enzyme we are studying. I created over 3000 variants.

I got alot of good hits. I included a known inhibitor of the enzyme (which is in clinical trials now) and it only ranked 92. The hits I got may or may not be toxic, we need to do actual enzyme kinetics and tissue culture testing to start getting an idea of which are good. I am going to take a few of them and develop more variants with particular side chain groups to try to improve the structures.

This is really exciting work in relation to cancer research. And, as I have said before, I think there could eventually be carry over to autoimmune disorders.

Anyway, one member of our group is a big name in polyamine research so I had a little time to discuss my ideas with him. He seemed very interested. My thoughts on fragmentation of the X chromosome leading to multiple active copies of polyamine genes in the cell, he thought possibly some aberrant replication could be a better explanation because he thought the fragments would be degraded normally. So I suggested the aberrant replication could possibly start at Alu sequences which have been proposed as sites of alternate origins of replication. That could be an interesting possibility because Alu sequences in the genome are 13% of the total but in the free DNA circulating in the blood of lupus patients it makes up 55% of the total (Liu & Steinman, ~1982?). My thought before was that it originated from reverse transcriptase activity but it could be from aberrant replication. What triggers Alu sites to be origins of replication would be something very interesting to study. Anyway, he wasn't familiar with the Alu sites being alternate replication sites.

I also mentioned the Quaking and Jimpy mice which have neurodegeneration and alterred spermidine/spermine ratios (polyamines). I think he had heard of them. He said he wondered if that was a cause or a result of the neurodegeneration. That's an open question which I doubt anyone is working on, but should be.

Anyway, I mentioned to him that I had seen plenty of chromosome fragmentation in tissue culture work I have done before and that MS patients show increased chromosome fragmentation. Of course, is that from DNA breaks or replication of portions of chromosomes? Still an open question.

Overall he seemed interested but didn't appear to have thought too deeply on polyamines with regards to autoimmune diseases. He focuses mainly on cancer as his angle towards funding. I did like seeing the perk up in his eyes when I did mention the X inactivation process though. There are some recent new findings I am mulling over regarding heterogeneity in the histones in different regions of the inactive X (Chadwick & Willard, 2004). I think there is something interesting in the pattern that was seen, particularly around Xp22.1 where the polyamine genes are. I really didn't have much time to discuss my ideas and it is, as usual, frustating not to be able to give an hour long presentation and then get into hours of further discussion with him. Maybe I started a spark, planted a seed, baited a hook, etc.


Anyway, overall I think Monday was one of my better days. These guys are all members of the National Academy of Science and I ( a lowly Research Scientist) was leading most of the meeting talking about my results. The big guy in polyamines I think could get a Nobel prize if he can just get the one big breakthrough on a topic of current interest, like polyamines and transcription control or polyamines and cell signalling or, dare I hope, polyamines and autoimmune disorders, if those ever become areas of current interest. He has the body of work over his career. If I can get a spark going in the mind of someone important, that is the greatest reward for me.

We agreed on some other structures for me to model so, at our next quarterly meeting, maybe I can impress them some more.

Now I need to focus on getting the ovarian cancer grant application done. We got past the preliminary screening with our preproposal so now I have to write the full thing for a mid-Feb deadline. Dealing with stubborn ailing parents certainly takes alot out of a person though. I now have more diseases to study.

Wesley