HLA-DR immunopeptidomics on cells from bronchoalveolar lavage in early rheumatoid arthritis

<bold>Background:</bold> Rheumatoid arthritis (RA) is an autoimmune disease characterized by the presence of anti-citrullinated protein antibodies. HLA-DR shared epitope (SE) is the strongest genetic risk factor. Evidence suggests that loss of self-tolerance is triggered in the lung, however to our knowledge the HLA-DR antigen landscape of the RA lung has not been studied. <bold>Aims and objectives:</bold> To characterize the HLA-DR immunopeptidome of the bronchoalveolar lumen in early-stage RA patients and controls taking into consideration the HLA-DR type, and to link the findings to known and potential novel autoantigens in RA. <bold>Methods:</bold> HLA-DR antigens were isolated from immune cells obtained by bronchoalveolar lavage from early-stage RA patients (n=9) and age-matched controls (n=10). Peptides were measured by nano-flow liquid chromatography coupled to an Orbitrap mass spectrometer collecting tandem mass spectra in data dependent acquisition mode. <bold>Results:</bold> Significantly more peptides were predicted to bind to HLA-DR SE in individuals expressing one SE in combination with one non-SE allele compared to individuals expressing two distinct SE alleles or two non-SE alleles. Furthermore, native peptides of known citrullinated autoantigens were detected: E.g. Ten α-enolase peptides sharing the core sequence FRAAVPSGA, which is predicted to bind to HLA-DRB1*01:01. <bold>Conclusions:</bold> Potentially increased antigen presentation by HLA-DR SE receptors compared to non-SE alleles might be a contributing factor for the SE allele risk to develop autoimmunity. Furthermore, allele specific presentation patterns of the native peptides of known autoantigens will contribute to a better understanding of RA pathogenesis.