Monday, August 24, 2009

This is going to be fairly immature for a first post...

Medically speaking, you can always trust your shit. Shit won't lie to you. Shit is as shit does and shit don't hide. Your shit can tell volumes about your nutritional habits, your stress level, your digestive efficiency, your intestinal bacteria, and your cholesterol. Listen to your shit. Your shit can warn you about cancer.

Fecal DNA Methylation Detects Gastric And Colorectal Cancers

ScienceDaily (2009-08-23) -- A preliminary evaluation of methylation of two gene promoters in fecal DNA showed promise as a noninvasive method to detect colorectal and gastric cancers, according to a new study.
To start at the beginning, what is your DNA, whole intact genes, doing in your poo? Think of the last time you took a good hard dump. Didn't exactly feel like hugs and kisses, did it? The colon is one of several high wear regions of the body, where repeated stress and trauma tears cells off daily in the thousands and hundreds of thousands. Like the mighty Colorado through the Grand Canyon, every bowel movement scraps a little off your colon and anus as it passes. However, the reason your ass doesn't resemble a multi-miles deep hole in the desert is that regions such as the colon generate new cells at a much higher rate than the body at average. This is precisely what makes it a high risk site for cancer -- being the result of accumulated mutations, oncogenesis, the appearance of a tumor, is a function of how many generations of turn-over your cells have experienced. The more cells you make and discard, the more chances you have to develop a tumor. Your colon is like the guy who sits around the gas all day playing scratch tickets on his credit card; eventually, he's going to hit a winner.

The notion to screen feces for symptoms of lesion/tumor development has been around for quite some time now, in the constant search for an alternate to sliding a camera up someone's butt. Previously, the greatest hope lay with sampling for tumor-related bleeding patterns, but this had the problem that cancer is not the only possible cause of gastrointestinal bleeding. What Takeshi Nagasaka, Okayama University, choose to explore (along with his associates at Baylor University, Kyoto University, and the Radiation Effects Research Foundation of Hiroshima, Japan) was the specific ways in which tumorous cells caught in a bowel movement could be made to expose themselves directly. One exploitable fact known about gastro-intestinal tumors is the number of gene promoter regions in a tumor deactivated by hypermethylation.

Okay, what?

One thing to understand about DNA is that our genes aren't just floating around in our cells, loose and crazy, twenty-four seven. If this was the case, not only would they take up far more space than our cells have to spare, they would be constant targets for RNA transcription factors and/or gene promoters(part of the mechanism that takes the info in our genes and turns it living-breathing us). Without some kind of block, expression proteins would activate any and every gene they came across, within thermodynamic reason. And as bad as it was, I hope the Doom movie has at least taught everybody that having all your genes on all the time is a pretty bad thing. Among the numerous (and it sometimes seems innumerable) strategies our cells have to regulate DNA expression is methylation. Every cell has genes it will never want to express, maybe because it doesn't need that many copies of the gene or the gene was useful during development but is now irrelevant or because it's simply not that kind of cell. To switch the gene off forever, a methyl group -- just a carbon with three attendant hydrogens -- is attached to one of the cysteines in the DNA (the 'C' in the ATGC code). This extra carbon makes the DNA too unwieldy to smoothly dock with any of the proteins that would otherwise make the gene work. The DNA has been defaced. None of its playmates will come around to see it.

Under normal circumstances, methylation will reach some set level (depending on tissue type) and stay that way for the rest of the tissue's useful lifetime. Extra ('hyper') methylation means more genes are being turned off this way than are supposed to. And conveniently, there are a number of regulatory, safe-guard genes that must, by hook or by crook, be done away with before a cell can go out of control and become a tumor. (Named, appropriately, tumor suppressor genes -- their counter-parts are oncogenes, genes who go into overdrive during cancer.) Two such genes are RASSF2 and SFRP2 -- actually gene promoters, they encode proteins that serve as part of the architecture for the transcription of other genes, effectively acting as switches in the great genetic circuit board. When these two genes, along with several others like them, are methylated, the switch is glued in the off position, making it impossible for several police genes upstream to appear when they need. A very effective choke point.

Given that RASSF2 and SFRP2 are sequenced genes ("Thank you, Human Genome Project!"), analysis can be (relatively) quick and (relatively) painless. They key technique here is polymerase chain reaction -- an efficient, economical method for creating copies upon copies of a specific gene. (Any biochemistry grad student curses the name of PCR for being mercurial and unreliable, but the truth is, we'd wither and die without it.) The DNA, now extracted from feces, is treated with sodium bicarbonate. This bit of chemistry removes a nitrogen group from normal cysteines, but can't touch methylated cysteines due to interference from the extra carbon. The normal cysteines are transformed into uracil -- a nucleotide that for all intents and purposes reads like a thymine during DNA replication. For example, the sequence CCTGA becomes UUTGA, then all future copies of it are written as TTTGA. PCR creates these copies, only leaving in cysteines where methylation (in cancer) had occurred.

The end products of PCR are digested with HbaI restriction enzyme, a protein which cuts DNA at an exact pattern in the chain -- a pattern which includes, of all things, cysteines. This means modified copies of RASSF2 and SFRP2 extracted from normal cells won't get cut, but umodified copies from tumors can be. The DNA can then be inserted into a separating gel, tagged with a fluorescent dye, and photographed under UV light -- appearing as either one glowing blob or two. What you have, after a couple days worth of lab work, is a quick visual diagnosis of your patient, with even greater sensitivity than the good ol' asscam.

For illustration, data from Dr. Nagasaka's paper.

Obviously, there's still work to do be done before this method makes its way into your friendly neighborhood clinic, but if this isn't a scientific step in the right direction, I don't know what is.

For further information, please see 'Analysis of Fecal DNA Methylation to Detect Gastrointestinal Neoplasia', Takeshi Nagasaka et al., Journal of the National Cancer Institute, Vol. 101, Issue 18, p. 1244.

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