study of the role of a protein in a lesion - (Apr/26/2012 )
How shall I begin studying the role of a new and promising biomarker in a specific type of cancer development..
How shall I construct a research plan when little is known about this new protein... (Just a few papers in Pubmed about this protein....)
This protein has 2 well conserved domains, so I started studying the role of these domains generally....
At the moment I am trying to understand as much as I can that specific type of cancer....
some straightforward ideas like determining its expression pattern (upregulated in cancer?), examining its function by overexpression or knockdown.
regarding the domains, you can make some deletion mutants to see their respective functions.
since there are already published literature you should have some clue.
Can you give more details about the domains? What are the domains known to do in general in other proteins?
You can try to purify the protein with a GST tag and do pull down experiments to see binding partners using mass spectrometry (there are labs that can do it for you as a collaboration)
If you have a cell line for that particular cancer type, you could do viability assays (MTT/XTT) for the WT vs knock-down and compare the affect on apoptosis/survival of the cell line. In the end, cancer research is reduced to finding what to twist in the cancer cells to make them die. Especially if this protein is upregulated in the tumor.
my first thoughts about study anything like this would be to ask what tools you have:
siRNA/ KO animals
Small molecules inhibitors
Quite often these are not available in new targets, my next thoughts would be on what is common to other systems so look at common signalling systems and work backwards. I agree with the above comments in the expression in pathology and physiology I would add to this by (given your example is cancer) look for mutations and then asses function etc.
A bit of basic advice is know the literature including meeting abstracts patents etc think out side of pubmed!