The cytolytic arm of the specific immune response is dependent upon the presentation of immunogenic epitopes to cytotoxic T lymphocytes (CTL). It is the role of the major histocompatibility complex (MHC) class I molecules to retrieve such epitopes from the endoplasmic reticulum (ER) and carry them to the cell surface. Once the MHC-epitope group is available, CTL can survey the resultant complex via the T cell receptor (TCR). Under the appropriate conditions, the recognition of a foreign antigen, whether it be derived from an invading pathogen or a mutation in the host cell genome, results in the activation of the CTL signal transduction pathways and, ultimately, the release of the lethal hit to the cells. The crucial first step in this whole cascade is the generation of substrate from which epitopes can be excised. The nature and diversity of substrate directly influences the ability of an antigen presenting cell (APC) to activate a CTL-dependent immune response.
Historically, it has generally been presumed that the native substrate for antigen processing is fully-translated, full-length protein. However, there are sufficient examples in the literature to challenge this assumption. Here we demonstrate that, in addition to conventional translation, variations of the protein production pathway can provide alternative, unappreciated sources of substrate. Using the vaccinina expression system and a well studied viral antigen, we show that this substrate is probably produced at levels undetectable when using standard biochemical techniques, though in sufficient quantities to activate CTL (as assessed in standard chromium release assays). We have identified one particular mechanism as having great potency in the production of substrate from the 5$\sp\prime$ end of the gene, while demonstrating that other proposed variants of translation are unavailable for substrate production from the 3$\sp\prime$ regions of a gene. Furthermore, these cryptically produced epitopes are indeed immunogenic in vivo and therefore may be of important consequence to an array of immune responses, whether these be involved in immune activation or immune desensitization.
