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Where in the body are self antigens important? In terms of central tolerance and autoimmunity, but also in terms of T cell activation?

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Could you clarify a bit? What do you mean by important? Most problematic? Most relevant? I assume the body you refer to is the human one? –  terdon Dec 19 '13 at 11:33
This was a question in a PhD defense so I can only add my own interpretation. It's in the mouse and by important I mean anything really, relevant for proper development, where defects may lead to autoimmunity, and/or poor activation...I'm not entirely sure. –  DunjaM Dec 19 '13 at 17:26

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There can be many responses. They are important by alloimmunity (so by transfusion, transplantation, etc...), by recognizing pathogens, cancer, virus, etc... By T cell activation, the regulator T cells recognize these antigens as self, and prevent the autoimmune reaction.

I guess they were thinking on MHC1 and MHC2. MHC1 shows the inside of the cells, so e.g. by viral infection or cancer non-self oligopeptides (from degraded proteins) bind to MHC1. These non-self antigens are recognized by CD8+ T cells, which destroy the affected cells. MHC2 is used by APCs to present possible pathogens to CD4+ T cells in a similar way.

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