T and B cells recognize splicing-derived neutrophil neoantigens in lupus

Proteome diversity is generated through alternative mRNA splicing¹. In tumours, mis-spliced transcripts that contain intronic sequences, skipped exons or noncanonical donor/acceptor splice junctions resulting in frameshifts are often translated into neoantigens that drive anti-tumour immunity^2,3. Here we report that neutrophils from patients with systemic lupus erythematosus (SLE), unlike neutrophils from healthy donors or patients with rheumatoid arthritis, contain many aberrantly spliced gene transcripts, the translation of which was predicted to result in novel amino acid sequences that are absent in normal splice variants or any other proteins. Twenty-one peptides derived from these novel amino acid sequences were detected by mass spectrometry on class I major histocompatibility complex molecules in patient samples. Co-culture of T cells from patients with overlapping sets of 15-mer peptides from the novel sequences resulted in the expansion of CD4⁺ and CD8⁺ T cells that were rapidly reactivated to secrete interferon-γ. T cell antigen receptor sequencing and re-expression transferred neoantigen reactivity to a reporter T cell. Serum from patients with SLE also contained IgG autoantibodies that recognized epitopes within the novel amino acid sequences. Our findings demonstrate that dysregulated mRNA splicing in SLE neutrophils generates neoantigens that have caused T and B cell activation, clonal expansion, IgG class-switch and autoimmunity.