Background/Purpose: Viral infections and major histocompatibility complex class II (MHC II) are both implicated in the genesis of systemic lupus erythematosus (SLE), but a mechanistic understanding of how these factors promote autoimmunity is lacking. One phenomenon observed for MHC class I-restricted self-peptides – but which remains largely unexplored for MHC II – is the ability of viruses to alter processing and presentation of endogenous self-antigens. We investigated the impact of infection with influenza, a virus associated with autoantibody formation in healthy individuals and disease flares in SLE patients, on the repertoire of self-peptides presented by MHC II.

Methods: A murine antigen presenting cell (APC) line expressing C57Bl/6-derived I-Ab, BALB/c-derived I-Ed, and class II transactivator-driven antigen processing and presentation components was either infected with the mouse-adapted H1N1 influenza strain PR8 or mock-infected in vitro. MHC II:peptide complexes were immunoprecipitated, and peptides were fractionated by reversed-phase high-performance liquid chromatography, analyzed by nano-ultra-performance liquid chromatography-tandem mass spectrometry, and identified from a database containing the influenza and mouse proteomes.

Results: An average of 9,895 peptides were identified among influenza-infected APCs per experimental replicate. Self-peptides comprised >95% of the MHC II immunopeptidome in influenza-infected cells, concordant with published observations from other intracellular pathogens. Among these self-peptides, 24-40% were unique to infected, rather than uninfected, cells. Functional annotation clustering revealed significant enrichment of ribosomal proteins and ribonucleoproteins (RNPs) among peptides unique to infected cells. Multiple unique epitopes were identified from ribosomal P0, a known target of anti-ribosomal P antibodies in SLE patients. We also identified peptides derived from histones, other nuclear DNA-binding proteins, and complement proteins including C3, an autoantibody target in at least one-third of SLE patients. Peptides derived from complement C3 were separately identified in published MHC II immunopeptidome data from H1N1 influenza-infected human cells.

Conclusion: Active influenza infection in vitro substantially alters the MHC II self-immunopeptidome and is associated with presentation of SLE autoantigens. These data suggest that influenza manipulates non-classical endogenous antigen processing pathways within APCs to expose new self-epitopes capable of activating autoreactive CD4+ T cells in SLE. Future studies will investigate intracellular processing of these peptides and their presentation in murine models of SLE to elucidate the mechanistic role of viral infection in promoting autoimmunity.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/influenza-virus-infection-alters-the-mhc-class-ii-self-immunopeptidome-to-present-lupus-associated-autoantigens/