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T cells compare non-self antigens to HLA (human leukocyte antigens) molecules with proteins the system already knows are its own. Your T-cells don't react to your HLA because of tolerance but are not tolerant to the HLA proteins of someone else. Thus, when there is a non-self system in your body (i.e.: after a transplant), your T-cells will begin a cell-mediated immune response against it, considering them foreign.

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