About tissue-specific and epigenetics - (Feb/06/2009 )
Hi dear all, I am writing a review about epigenetics and some new diseases. But I still don't know one point. We know epigenetics statue has tissue-specific. PBMC only secret some inflammation cytokines such as IL, TNF and so on. But I found some paper (such as 11B-HSD2 DNA methylation in hpertension) mentioned some gene' s epigenetics statue in PBMC reflect the global epigenetics statue. Can we say most genes in PMBC such as AT1, angiotension ( genes not secreted by PBMC ) could also reflect the global epigenetics statue? Is there any report or evidence about it?Your help will help me in my review. And if we want to dectect some gene's epigenetics statue in some disease such as hypertension, while we can not get the corresponding tissue. can we also detect PBMC? 
I don't think the PBMC epigenetic status relects the global picture. What is the global epigenetic status, every tissue/cell type has its own epigenetics which determine what they are.
As for tissue specific DNA methylation, only a few studies have shown this, a very controversial idea.
pcrman on Feb 6 2009, 07:45 PM said:
As for tissue specific DNA methylation, only a few studies have shown this, a very controversial idea.
Yes, Most research on tumor show us the tissue-specific characterise of epigenetics . But if some disease we can not get the specific tissue sample, how can we do? Thanks a lot!
ips008 on Feb 7 2009, 04:16 AM said:
pcrman on Feb 6 2009, 07:45 PM said:
As for tissue specific DNA methylation, only a few studies have shown this, a very controversial idea.
Yes, Most research on tumor show us the tissue-specific characterise of epigenetics . But if some disease we can not get the specific tissue sample, how can we do? Thanks a lot!
Hi everybody,
about the hypertension HSD11B2 paper: check the primers against the human genome. You will find that the forward primers misses several G's that are in the GENBANK sequence they used, but are not in the human genome --> genbank accession is sloppy sequencing! Since MSP completely depends on good and accurate primers, their results are most likely bullshit: I measured it with BS-sequencing and indeed in humans the sequence is unmethylated....bullshit article with bullshit results.
About tissue specificity: check the newest article of the Feinberg group about CpG island shores. Furthermore, people should note that the tissue specificity in epigenetic patterns is real, but all studies to date have focussed on finding differences. I did some work in rats and found very very nice and high similarities for promoter DNA methylation patterns for several genes, between fat, liver and muscle (R2=0.98). So, people dont say things nobody ever bothered to test: if For instance the average methylation might differ between tissues, but the actual pattern (so variation from CpG to CpG) might still be identical (again from my rat experiment). So lets measure and not infer....
greetings and salutations fellow epigenetics people
ips008 on Feb 7 2009, 04:16 AM said:
pcrman on Feb 6 2009, 07:45 PM said:
As for tissue specific DNA methylation, only a few studies have shown this, a very controversial idea.
Yes, Most research on tumor show us the tissue-specific characterise of epigenetics . But if some disease we can not get the specific tissue sample, how can we do? Thanks a lot!
DNA methylation might be different between tissues (and blood and the "relevant" tissue), if you are lucky the tissue of interest is embryonologically of the same lineage.
Furthermore, even if the average level is different, the variation (so difference in methylation between adjacent CpG sites) might be similar --> thus there is a correlation between tissues. Even if this correlation is not perfect one can increase the population size to increase power and still pick up relevant information in blood about other tissues.
Hmmm, I have given you advice twice now....maybe I should be in the acknowledgements now
