Okay, the ovarian cancer grant application stuff I was doing is done for now so I can get back to explaining my hypothesis again because there is still a lot to discuss. In my last big post, last Sunday, I got into nucleosomes and DNA supercoiling stress. Pretty complicated stuff but I felt it was necessary to go into that in order to explain my ideas about the chromosome fragmenting that I think may be involved in autoimmune diseases. Arron put some pictures up for me. I'll try to get some more up soon. What I was trying to point out is the packaging of DNA to keep it organized, compact, and protected. However, the DNA is not very well protected, even when packaged in nucleosomes.
I should probably reiterate the hypothesis again before I start up. Remember, it is just hypothesis and so you should keep in mind that it may be wrong in some areas once we get more research done to prove or disprove points. It is kind of a best guess on my part based on what we know at present.
DNA damage occurs and does not get repaired in a timely manner. This can lead to chromosome breaks so that there can be fragmentation of chromosomes. There can then be reactivation of previously sequestered genes and possibly uneven distribution of chromatin to daughter cells when the parent cell with the damage divides. As a consequence, there can be loss of epigenetic control leading to expression and overexpression of previously sequestered genes. The example I used most was the inactive X chromosome because it has some interesting genes on it, but it could be the active X or other chromosomes (autosomes) that suffer the fragmentation. The particular genes on the inactive X that I cited were polyamine genes: spermine synthase and spermidine/spermine N1-acetyltransferase. Overexpression of these genes is not immediately a problem since their substrate, primarily spermidine, is usually bound to DNA, RNA, or lipids. It is when there is a stress on the cell that there is newly synthesized, unbound polyamines and decarboxylated S-adenosylmethionine (needed for polyamine synthesis). Increased synthesis of polyamines can begin to have many detrimental effects on the cell and there can be an imbalance in the spermidine/spermine ratio. Spermine can interfere with ion channels such as calcium channels and it can alter the blood-brain barrier. An increase in spermine at the expense of spermidine could reduce the spermidine needed in myelin formation and translation efficiency. There can be induction of apoptosis in some cells and disruption of chromatin in other cells leading to expression of previously sequestered genes, such as endogenous reverse transcriptases. There can also be creation of autoantigens, in some cases perhaps due to polyamines in abundance binding to otherwise normal endogenous material, altering the epitopes on them. The work I do is in drug discovery to find inhibitors of polyamine enzymes, but I am in cancer research because I feel the study of polyamines is further along with regards to cancer and the research environment is more open to new ideas. There should be carryover to autoimmune diseases if we find good drugs and the hypothesis is right on polyamine involvement in autoimmune diseases.
I did that all in one breathe. I need to explain about the DNA damage, fragmentation, and the reverse transcriptases and some of the possible autoantigens that could occur.
So the DNA is in nucleosomes primarily; one nucleosome every 200 base pairs on average in humans. The nucleosomes compact the DNA lengthwise about 7x. The nucleosomes can then stack on top of each other so that the beads on a string appearance of nucleosomes can be stacked into somewhat irregular helical stacks giving further compaction. These stacks of nucleosomes may have roughly 300 nucleosomes in them which are attached to a nuclear matrix. There is a lot of supercoiling stress stored in there so they are anchored about every 300 nucleosomes to lock in the stress. If one of these stacks suffers a break in the strands, that stack will puff out as the strands are no longer constrained and the stretch goes into the beads on a string appearance giving it accessibility to DNA repair enzymes. That is what should happen in theory but it would depend on how tight the stacking is, the added hold by ions in the local environment, and the extent of the DNA damage. Since DNA repair occurs more readily in open chromatin stretches, the efficiency of repair will correlate to the accessibility. Supposedly there are checkpoints to halt cell cycle progression but these are mainly around S phase when the DNA is replicated. Once the cell has committed to mitosis, there may not be sufficient means and time to repair DNA damage deep in heterochromatin, especially the inactive X with its peripheral location.
Although histones and DNA are in the chromatin in equal amounts mass to mass (gram to gram), the histones do not provide adequate protection to damaging agents, even deep in the chromatin. Heavy metal ions and mutagens can work their way into the chromatin and cause DNA damage. The histones themselves provide no protection to the DNA from UV light, particularly UVB light. The bases in DNA are referred to as aromatic structures because their big flat structure of double bonded carbons and nitrogens not only have electrons shared between two atoms in each bond, but there are additional electrons circulating the length of the structure. The length of the base structure is such that it can resonate, or absorb UVB light (photons) and get excited electrons. These can then react with neighboring bases causing crosslinking or perhaps causing the base itself to break away from the ribose ring, giving what is called an abasic site. There are approximately 10,000 abasic sites formed per cell per day but they are usually repaired. Repair requires access to the strand and strand separation. The correct base can be ligated in to correspond to the base in the other strand. The base stacking in that area is lost until it is repaired so there is some local instability. Another type of damage is strand breaks in the phosphate backbone. This can then release the local supercoiling stress and lead to disruption of neighboring nucleosomes. These sites also need to be repaired promptly, but should be manageable in a healthy cell.
The reason I say that histones/nucleosomes don't provide protection to DNA from UVB light is because the histones are notoriously void of aromatic amino acids in their structure. This would be phenylalanine, tyrosine, and tryptophan. These are bulky amino acids so 'evolution' probably eliminated them as too bulky for the tight packaging needed in the histone to make a tightly compacted nucleosome core. So the histones do not absorb UVB to protect the DNA and, depending how tightly packaged the heterochromatin is, may even hinder prompt repair.
Here is the interesting thing. As if the cell knows it has damage and needs to do repair work, polyamine synthesis is invoked by UVB light in a stress response, particularly ornithine decarboxylase, the first of the polyamine synthesis genes. This then provides the precursor putrescine for the rest of the polyamine synthesis. The polyamines induced by the UVB stimulation can then stabilize the chromatin by either helping to hold nucleosomes together in internucleosomal links that might be possible in closely packed heterochromatin, or the polyamines may help open the nucleosomes in a stack by stealing any available supercoiling stress and twisting the nucleosomes apart momentarily enough to start unstacking the stack to make it more accessible. Who knows what goes on at that tiny of a level. It probably depends locally on the DNA sequence, extent of packaging and modifications, ionic milieu, supercoiling stress, and the extent of damage.
Now think, if this is a normal process where some sunlight exposure on a daily basis temporarily induces polyamine synthesis in skin fibroblasts, those polyamines then raise the person's entire levels of polyamines and help each cell seek out any hidden, unrepaired DNA damage it might have. Without a regular up tick in polyamine levels as a youth, perhaps there could be an accumulation of unrepaired damage hidden away.
One thing about DNA damage, particularly with regards to fragile sites, DNA damage is often found to be clustered 80% of the time. This means that if there are a number of DNA sites being damaged, 80% of them will be within a few helical turns of the DNA strands from each other, even within a few base pairs from each other. If they are in opposite strands, the only thing holding them together might be a few hydrogen bonds, which isn't much strength. If the strands come apart giving a double strand break, it is very difficult for the cell to recover at that site and religate the strands. This then could be the chromosome fragmentation that leads to the problems I've described. Even if the cell reacts quickly to a damage site, repairing one site may put strain into neighboring sites hindering their repair. We should also consider that some sites may not be easily accessed even if the stack of nucleosomes tries to unravel. There may be crosslinking of proteins, another type of chromatin damage, that keeps some of the chromatin clumped up and interferes with repair. In a time consuming process the chromatin is ribosylated, putting large trees of ribose groups around the site of damage. This can help lock in the chromatin so the disorder does not spread and the ribose trees can help compete histones off the DNA to give more accessibility. I don't know all the details about DNA repair. It's been quite a while since I have studied it, but it is several different cumbersome processes, some of which are stop-loss type processes. One autoantigen mentioned a lot in lupus is the Ku antigen. I believe one function attributed to this is to bind to double strand ends of DNA, as if it plays a part in stabilizing DNA damage.
So what I am saying is that DNA damage can be difficult to repair, particularly when it is accumulating without sufficient regular flexing/breathing/scanning of the chromatin that might be provided by daily stimulation systemically of polyamine synthesis and circulation. If there is an accumulation of unrepaired DNA damage, it may pass the point where it can be repaired properly and then a surge in polyamines may simply expedite the consequences of double strand breaks. What I am having trouble imagining is the time frame in which all this might occur, if it is at the root of MS development. Is this something that only occurs over many years accumulating unrepaired DNA damage and then shows up as an adult, or is it something that can occur in a matter of days in an adult? How long has DNA damage been hidden and has it spread to daughter cells and through how many generations of daughter cells?
Lupus bouts can be instigated by UVB light so that is known. Lupus, of course, is known for its light-sensitivity. But, since I am not an MSer and am somewhat new to studying it, I would like to know what you folks know about the light sensitivity in MS. I have heard through the forums that some people are greatly fatigued by sunlight while others say it makes them feel better. Can anybody explain that? That is why I am wondering about how quickly DNA damage could accumulate in an MSer and then show up as a bout, if in fact my idea of UVB light exposure and MS is valid. Is it insufficient exposure overtime (years) as a child or is it individual exposures (days) as an adult? MS really is a puzzler.
I'll try to get into the reverse transcriptases later this weekend.