Olsson and Jiang et al. generated stable cell lines with varied HLA-DM (peptide exchange catalyst) and HLA-DO (limits DM activity) levels(DO:DM) and performed detailed mass-spectrometric peptidomic and proteomic analyses to elucidate the impact of DO:DM on MHC-II peptidomic landscapes. (DO:DM)H cells (low DM activity) presented “DM-sensitive” peptides, and a decrease in DO:DM (increasing DM activity) led to increasingly varied peptide subsets with higher predicted affinity (“DM-resistant”). DO knockdown in (DO:DM)H cells resulted in a DO:DM state similar to (DO:DM)M cells, suggesting DO-mediated tuning of DM activity, and resulting DR4-presented peptide repertoires.
Contributed by Shishir Pant
ABSTRACT: Major histocompatibility complex class II (MHC-II) antigen presentation underlies a wide range of immune responses in health and disease. However, how MHC-II antigen presentation is regulated by the peptide-loading catalyst HLA-DM (DM), its associated modulator, HLA-DO (DO), is incompletely understood. This is due largely to technical limitations: model antigen presenting cell (APC) systems that express these MHC-II peptidome regulators at physiologically variable levels have not been described. Likewise, computational prediction tools that account for DO and DM activities are not presently available. To address these gaps, we created a panel of single MHC-II allele, HLA-DR4-expressing APC lines that cover a wide range of DO:DM ratio states. Using a combined immunopeptidomic and proteomic discovery strategy, we measured the effects DO:DM ratios have on peptide presentation by surveying over 10,000 unique DR4-presented peptides. The resulting data provide insight into peptide characteristics that influence their presentation with increasing DO:DM ratios. These include DM-sensitivity, peptide abundance, binding affinity and motif, peptide length and choice of binding register along the source protein. These findings have implications for designing improved HLA-II prediction algorithms and research strategies for dissecting the variety of functions that different APCs serve in the body.
Author Info: (1) Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94025, USA. (2) Department of Pediatrics - Human Gene Therapy, Stanfo
Author Info: (1) Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94025, USA. (2) Department of Pediatrics - Human Gene Therapy, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA. (3) Department of Pediatrics - Human Gene Therapy, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA. (4) Department of Pediatrics - Human Gene Therapy, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: mellins@stanford.edu. (5) Chan Zuckerberg Biohub, Stanford, CA 94025, USA. Electronic address: josh.elias@czbiohub.org.
