SUMMARYThe HLA association with insulin-dependent diabetes mellitus is highest among individuals heterozygous for DR3 and DR4. To investigate potential mechanisms to account for this association, we performed two-dimensional gel-electrophoretic analysis of HLA molecules from DR3/4 heterozygous patients. These studies demonstrated hybrid molecular dimers corresponding to products of HLA-DQ genes linked to DR3 and DR4, i.e., the DQw2 and DQw3 genes, respectively. Two types of OQ molecules were found: immunoprecipitation by DQw3-specific monoclonal antibody 17.15 identified a DQw3 p-chain associating with a DQw3 a-chain and a DQw3 p-chain associating with a DQw2 a-chain. The identity of a-and p-chains comprising these hybrid molecules was confirmed by HPLC peptide-map analysis. Several characteristic peptide peaks identified both DQw2 and DQw3 a-chains associated with DQw3 p-chains. The formation of such DQa(DQw2)-DqP(DQw3) dimers potentially contributes a direct molecular mechanism for HLA-associated contributions to disease in DR3/DR4 heterozygotes. Diabetes 36:114-17, 1987 T he class II molecules of the human major histocompatibility region (HLA) are strongly associated with several autoimmune diseases (1). Several of these HLA-associated diseases show a dramatically increased relative risk for individuals possessing a particular heterozygous combination of class II antigens [e.g., DR3/4 in insulin-dependent diabetes mellitus (IDDM) (2) and Dw4/ Dw14 in seropositive juvenile rheumatoid arthritis (3) increased disease susceptibility may be related to an altered immune response resulting from the formation of hybrid class II molecules contributed from both haplotypes (3-6). We describe the identification of such hybrid molecules on cells from heterozygous DR3/4 IDDM patients, consisting of dimers containing products of genes from both DR3-and DR4-associated haplotypes.Class II HLA molecules are dimers of a-and p-polypeptide chains encoded by separate genes and function as recognition signals for activation of immune responses. These HLA gene products include both DR and DQ molecules encoded in different but linked genes. DQ a-and p-molecules are polymorphic; i.e., the DQ a-chain linked to one DR gene, such as DR3, is different from the DQ a-chain linked to another, such as DR4, and the same is true for DQ (3-chain. Thus, in a heterozygote, mixed ap-dimers potentially could form between DQ-chains from different haplotypes. Such transcomplementation of DQ a-and p-chains from opposite haplotypes would dramatically broaden the diversity of class II antigens available to participate in the immune response. The DR a-molecules are not polymorphic; i.e., DR a-molecules are invariant among haplotypes, and mixed DR ap-dimers would not result in novel HLA molecules. A DQ ap-dimer composed of transcomplementing chains would be unique to a heterozygous individual and not expressed by either parent. In the mouse, such transcomplementation has been demonstrated structurally, and epitopes newly formed on the resulting hybrid mole...