Abstract. There is now extensive evidence that synthetic peptides corresponding to linear sequences of MHC molecules are effective immunoregulators, targeting the immune response at many different sites. It has been previously shown that peptides derived from a highly conserved region of MHC class II inhibit proliferation to autoantigen and to both the direct and indirect pathways of allorecognition. This study demonstrates that inhibition of lymphocyte proliferation by nonpolymorphic MHC class II peptides, specifically HLA-DQA1, is sequence-specific and that the inhibitory effect is mediated through the induction of apoptosis in antigen-presenting cells via a caspase-independent mechanism. In addition, T lymphocytes stimulated in the presence of HLA-DQA1 are rendered hyporesponsive to subsequent stimuli. Immunomodulation by HLA-DQA1 is effective in vivo because it prevents both the priming and the effector function of primed allogeneic T cells in a murine DTH model. These observations have important implications for the development of a novel therapy for immune-mediated diseases.The adaptive immune response is dependent on the TCR recognition of a peptide ligand complexed with a MHC molecule on the surface of an antigen-presenting cell. This peptide, and the resultant three-dimensional structure formed by it and the MHC molecule, interacts with the TCR triggering a series of signaling events resulting in T cell activation (1). Critical residues within the peptide form the contact points with the TCR, and variation at one of these sites alone is sufficient to disrupt the interaction or change the T cell response qualitatively, resulting in differential cytokine production, antagonism, or anergy (2). There are now several reports of altered peptide ligands that induce partial activation in vitro, resulting in altered responses to autoantigens and allergens (3,4). In addition, the immunoregulatory effects of altered TCR ligands has been demonstrated in vivo, as exemplified by the prevention of experimental autoimmune encephalomyelitis (5). Such studies require that the specific antigen that elicits the immune response be identified. The pivotal role of peptides in allorecognition has highlighted them as a potential strategy for altering the alloimmune response (6,7). Difficulty in identifying the critical allopeptides recognized by alloreactive T cell clones for each given donor-recipient combination make the use of altered peptide ligands potentially less clinically applicable in transplantation (8).APC are continually presenting antigens on the cell surface that represent molecules within their environment, including self molecules. Indeed, it has been demonstrated that a large percentage of peptides bound to MHC on resting APC are derived from MHC molecules themselves (9). The presence of these MHC-bound peptides derived from conserved regions of the MHC raises questions as to their role in the immune process. One may postulate that they function to stabilize the heterodimer for presentation on the cell surface...