High-throughput characterization of MHC I-associated peptides presented by B lymphoblastoid cells (100.11)

Abstract

Abstract Sensing of the MHC I-peptide (MHC I-p) repertoire allows elimination of infected or transformed cells. High-throughput strategies used to study MHC I-p include i) the use of secreted forms of MHC I transfected into model cell lines, or ii) chemical or metabolic labeling of MHC I, which is limited to certain MHCs and to cell culture model systems. Here, we used a quantitative proteomics approach to characterize and compare for the first time the MHC I-p repertoire associated to unlabeled HLA-A,B molecules of untransfected B lymphoblastoid cells (B-LCLs). Peptides were obtained from B-LCLs from 3 subjects by mild acid elution, fractionated by liquid chromatography and analyzed by nanoLC-MS/MS on a LTQ-Orbitrap mass spectrometer. We have identified more than 1000 unique 8-11mers associated to 10 HLA-A,B alleles: HLA-A*0101,0201,0205,0301,2902; B*0801,1501,4403,5001,5701. We found MHC-dependent differences in the predicted binding affinity of identified peptides. We used bioinformatic tools to identify the genes source of peptides and to characterize and compare the proteins encoding the MHC I-p repertoire. Peptides were encoded by genes located in all chromosomes and the mitochondria, and were significantly enriched for genes located in chromosomes 17 and 6. Our analysis revealed an enrichment of genes implicated in cell cycle, transcription and protein synthesis, as well as in immune and viral infection-related pathways, reflecting a B cell-specific signature.