CD8+ T Cell Cross-Reactivity Profiles and HIV-1 Immune Escape towards an HLA-B35-Restricted

Antigen cross-reactivity is an inbuilt feature of the T cell compartment. However, little is known about the flexibility of T cell recognition in the context of genetically variable pathogens such as HIV-1. In this study, we used a combinatorial library containing 24 billion octamer peptides to characterize the cross-reactivity profiles of CD8+ T cells specific for the immunodominant HIV-1 subtype B Nef epitope VY8 (VPLRPMTY) presented by HLA-B*35:01. In conjunction, we examined naturally occurring antigenic variationswithin the VY8 epitope. Sequence analysis of plasma viral RNA isolated from336 HIV-1-infected individuals revealed variability at position (P) 3 and P8 of VY8; Phe at P8, but not Val at P3, was identified as an HLA-B*35:01-associated polymorphism. VY8-specific T cells generated from several different HIV-1-infected patients showedunique andclonotype-dependentcross-reactivity footprints.Nonetheless, all T cells recognizedboth the indexLeuandmutantVal atP3 equallywell. In contrast, competitive titration assays revealed that theTyr to Phe substitution at P8 reducedT cell recognitionby 50–130 fold despite intact peptide binding to HLA-B*35:01. These findings explain the preferential selection of Phe at the C