The success of a blood stem cell transplant relies upon the interactions of markers on the surface of all body cells, including the immune cells of both the patient and the donor. Normally, all cells within the patient's body coexist peacefully in a state known as self-tolerance because all bear the same "self" marker proteins. These proteins are also called antigens because, should they be introduced into a new environment, they are capable of stimulating a powerful immune reaction. This is what occurs when a blood stem cell preparation with "non-self" antigens is transplanted into a patient whose "self" antigens are very different.

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