Cryptic MHC-E epitope from influenza elicits a potent cytolytic T cell response

Abstract

Abstract Non-classically-restricted T cells have shown remarkable therapeutic activity in a variety of disease settings; most notably, CD8 T cells restricted to MHC-E (Qa-1 in mice; HLA-E in humans) have proven capable of eliminating a primate lentivirus infection. Here, we used mass spectrometry to identify a Qa-1-restricted 9-mer peptide, named M-SL9, that elicits a strong CD8 T cell response in mice infected with influenza A virus. The M-SL9 specificity accounted for roughly 5–10% of all lung CD8 T cells, approaching the frequency of classically restricted CD8 T cell responses to flu. A broad investigation of the M-SL9-specific T cells showed that they are generally similar in phenotype to classically restricted CD8 T cells, including strong co-expression of type 1-associated cytokines (polyfunctionality) and cytolytic markers; however, M-SL9-specific T cells were unique in that they were anatomically restricted to the lungs and were not present in blood and spleen like other specificities. Intriguingly, the M-SL9 epitope derives from a previously unknown translation product encoded by the +1 alternative reading frame of the matrix 1 (M1) protein-coding sequence. Presentation and immunogenicity of M-SL9 were completely dependent on ribosomal initiation at the second AUG codon of the matrix gene segment. Analysis of potential precursors suggests that M-SL9 is processed from a novel 16-mer peptide that is not required for viral replication in mice. These discoveries imply that unconventional epitopes may drive a large fraction of physiologically relevant T cell responses, and M-SL9 presents a highly tractable system in which to dissect the mechanisms governing MHC-E-restricted T cell responses and their protective effects. Supported by Cancer Research Institute Irvington Fellowship, Roy and Diana Vagelos Molecular Life Sciences Program and College Alumni Society Research Grant from the Univ. of Pennsylvania, and NIH grants R01 AI146101, R01 AI153064, R01 AI046709-18S1, R01 AI046709, R01 AI125524, and R21 AI153978.