Tuning DO:DM ratios modulates MHC class II immunopeptidomes

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 register positioning on 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.

RIPPA: Identification of MHC‐II Binding Peptides from Antigen Using a Yeast Display‐Based Approach

“…In the last few decades, two experimental approaches have been deployed to determine binding peptides for specific MHC‐II alleles (summarized in Liu, Jiang, & Mellins, 2021). One approach focuses on eluting peptides from a particular MHC‐II protein and sequencing them by mass spectrometry (MS; e.g., Olsson, Jiang, Adler, Mellins, & Elias, 2021). The other approach quantifies binding (i.e., affinity, relative binding capacity) of a set of peptides to an MHC‐II protein using in vitro peptide binding assays (e.g., Jiang et al., 2015).…”