MAPPING OF HLA CLASS-I BINDING MOTIFS IN 44 FUSION PROTEINS INVOLVED IN HUMAN CANCERS

Chromosomal translocations coding for abnormal proteins are present in several human cancers, The junctional region of fusion proteins repre sents a potential target for a T cell-mediated antitumor response, T l ymphocytes recognize antigens in the form of short peptides that must bind to HLA molecules, Different HLA specificities can bind different peptides, thus depicting different ''peptide binding motifs,'' It woul d be useful to know whether a certain fusion protein presents, within its fusion region, the binding motif(s) for a certain HLA molecule, Th is information would allow a more focused immunological analysis, Here we present data obtained from the screening of the fusion regions of 44 different fusion proteins for the presence of binding motifs to 34 class I HLA molecules, including all of the most frequently encountere d specificities, A total of 201 independent peptides was identified (r ange, 0-11 peptides/fusion protein), A marked heterogeneity among the 44 different fusion proteins analyzed is evident, For example, the pml /RAR alpha fusion protein present in acute promyelocytic leukemia pres ents no binding motif (BCR 3) at all or to a single HLA molecule (Cw0 301, BCR 1), Alternatively, the fusion proteins BCR/ABL, ALL1/AF-6, EW S/ATF-1, or NPM/ALK exhibit motifs for several common HLA specificitie s, Heterogeneity is also present inside a single translocation (in ALL 1/ENL, for example, different subtypes match motifs with cumulative fr equencies in the population from 108 to 0%), In two cases where the re lative frequency of different fusion protein subtypes was available, a tendency toward an inverse relationship between frequency and the per centage of population covered by the identified binding motifs was obs erved, Peptides with motifs for HLA A0201, A3, and Cw*0702 were also tested for actual binding using a stabilization assay; 13-40% showed s ignificant HLA binding, using this assay, However, fewer fusion protei n-derived peptides bound to HLA A0201 and A3 than non-fusion protein- derived peptides, These data provide the first list of peptides derive d from fusion proteins that may be assessed as potential tumor-specifi c antigens.