DNA Differences Observed Between Blood and Organs 85
Scrameustache writes "Researcher working on a rare type of aortic abnormality found that the DNA from diseased tissue did not match the DNA from the blood of the same patients So far it's unclear whether these differences in the blood and aortic tissue are the consequence of RNA editing, which changes the messenger RNA but not the gene, or DNA editing, which involves differences in the gene itself. Based on the evidence so far, the researchers believe the differences resulted from developmental rather than somatic DNA alterations. 'Traditionally when we have looked for genetic risk factors for, say, heart disease, we have assumed that the blood will tell us what's happening in the tissue,' lead author Bruce Gottlieb said in a statement. 'It now seems this is simply not the case.'"
Re:complexity (Score:3, Informative)
Re:How... (Score:3, Informative)
title misleading (again) (Score:5, Informative)
The researchers did NOT say, definitively, that the patients DNA varied between blood and aorta.
What they said was that the SEQUENCING showed a difference. The sequencer used cannot distinguish between messenger RNA and DNA differences.
While it is possible that micro-environment, such as being blood vs. being aorta could result in changes to DNA, it is far more likely to result in tweaks to messenger RNA.
Since they found the same SNPs in aortic tissue from the organ bank, it could just be a common adaptation for that tissue.
Re:good old days (Score:4, Informative)
Re:Chimera (Score:5, Informative)
http://en.wikipedia.org/wiki/Chimera_(genetics) [wikipedia.org]
The name comes from the mythical chimera, but is actually an organism (humans can possibly have this) with two or more distinct types of DNA in it's body. For example, if a human had one set of DNA in their kidneys and a different set in their liver.
Re:title misleading (again) (Score:1, Informative)
I'm sorry, but you're wrong. Sequencers can and do distinguish between mRNA and DNA, because you have to use reverse transcription to sequence RNA at all. Without using the RT step, you're still only going to amplify gene (from TFA: BAK1), because you're still using a Taq DNA polymerase, not a reverse transcriptase, which would be necessary to amplify from RNA. As far as a "common adaptation for the tissue", you're speculating about tissue adapting over the course of an organism's life which - although interesting - seems unlikely because the cells that divide are not the same as the cells that are subject to "selection" due to the division of myoblasts into myocytes (muscle cells). It is also unclear what that selection would be.
It's cDNA, _c_DNA! (Score:1, Informative)
The summary made no sense until I RTFA and found out that they sequenced cDNA, not genomic DNA. The "c" is important, people. It's like the "m" in "vim" or the "ba" in "bash" - if you omit it it's not too far wrong, but in certain contexts it makes a world of difference.
cDNA is a lab-made copy of RNA. That's what the RNA editing versus DNA editing confusion is about. Genomic DNA gets copied to RNA, and then it's further processed. The researchers isolated that processed RNA, and made a cDNA copy of it. This is NOT the conventional way DNA gets sequenced. 99% of the time if you talk about sequencing someone's genes, you're talking about sequencing the genomic DNA directly, without the intermediate RNA step.
Re:How... (Score:4, Informative)
You'll note that even in this study they didn't sequence any DNA; they just looked at the expressed mRNA.
I couldn't quite figure that out from TFA. It sounded like they sequenced the DNA and cDNA, but then they talk about mRNA.
http://www.genomeweb.com/sequencing/snps-non-cancerous-tissue-may-differ-those-blood-study-finds [genomeweb.com] http://74.125.93.132/search?q=cache:0S55-4qOoysJ:www.genomeweb.com/sequencing/snps-non-cancerous-tissue-may-differ-those-blood-study-finds+SNPs+in+Non-Cancerous+Tissue+May+Differ+From+Those+In+Blood,+Study+Finds&cd=2&hl=en&ct=clnk&gl=us [74.125.93.132] Sneaky cache to avoid login
On the other hand, when the team sequenced BAK1 cDNA from healthy aortic tissue obtained from a Quebec transplant service, they found the same three SNPs as in the aortic tissue from the AAA cases. The researchers verified their findings by sequencing both strands of DNA and repeating the sequencing several times.
So far, Schweitzer said it's unclear whether these BAK1 differences in the blood and aortic tissue are the consequence of RNA editing, which changes the messenger RNA but not the gene, or DNA editing, which involves differences in the gene itself.
Original article (Score:2, Informative)
Re:title misleading (again) (Score:4, Informative)
If you read TFA (not the news piece, the actual one), then you will see that they sequenced cDNA, which means that they have the RNA sequence, but NOT the DNA sequence, and therefore cannot tell whether the changes occurred at the DNA or RNA level (such changes occurring at the RNA is old news). The GP did not quite express this clearly, but is correct in spirit.
What I cannot fathom, is why they did not simply sequence the DNA of their gene of interest (really just the area around the mutation(s)) for a few patients. This would be really straightforward (can be done in a week), and i woud have thought any reasonable peer reviewer would request it. Overall, there is not enough evidence to support the hype in the news piece, as far as I'm concerned, which explains why it's not published in a high-end journal.