How heavily does the project depend on obtaining correct target epitopes from Heckerman's protein Gibbs free energy simulation?
Is there a chance that HIV won't be controlled even if we can induce the immune system to be capable of targeting some of the peptide sequences that controllers often target? (i.e., might there be something else at work in controllers?)
Right now the project is only relying epitopes derived from actual controller targets. Our hypothesis is that if we go after the epitopes that HIV controllers preferentially target that we will get an immune response with memory in humans just as we have so far in our animal studies. The only way to test this is to execute on our clinical trial in humans. The current experiment we are aiming to perform is a good middle ground since we will be immunizing human blood against HIV in a controlled environment and then testing that immunity.
Does this make it less likely that targeting specific epitopes is all there is to the picture? (I'm happy to assume that we'll get an immune response with memory in humans -- the question is, how confident should we be that that response will control HIV?)
The article is describing one of the many explanations that has been brought forward to explain why controllers do what they do. If you are looking for a common denominator across controllers broadly, the selective epitope targeting explanation seems to make the most sense to us and does not appear to be constrained by anything but the individual's HLA type which essentially determines what epitopes a particular individual's immune system can "see."
Is there a chance that HIV won't be controlled even if we can induce the immune system to be capable of targeting some of the peptide sequences that controllers often target? (i.e., might there be something else at work in controllers?)
Thanks for working on an important project!