PhD Lecture by Sheila Tuyet Tang, CBS

Genome - and HLA-Wide Scanning and Validation of Cytotoxic CD8+ T Cell Responses in Bacterial and Viral Pathogens

Friday February 27, 2009 at 13:00
CBS, DTU, Lyngby, Building 208, Auditorium 062
Assessment Committee:    Associate professor Rasmus Wernersson, DTU (Chairman)
MD, DMSc Thomas Benfield, Hvidovre Hospital
MD, PhD David M. Lewinsohn, Portland VA Medical Center
Chair of defense:Associate professor Thomas Blicher, DTU
Supervisor:Professor Ole Lund, DTU

T cells play a major role in the recognition and subsequent elimination of intracellular pathogens and cancers. Both CD4+ and CD8+ T cells play a well-documented role in the clearance of infectious diseases through cell-mediated immunity. In particular, pathogen specific CD8+ T cell epitope responses have received great attention during recent years. There is a mounting interest in designing therapeutic or prophylactic potentials epitope-based vaccines capable of inducing or enhancing virus or bacteria specific CD8+ T cell responses. The studies in this thesis describe the identification of novel T cell epitopes for vaccine and diagnostic purposes, for Mycobacterium tuberculosis (Mtb), Mycobacterium leprae (M. leprae), influenza and poxvirus. We have used bioinformatics approaches to scan entire genomes for potential epitopes. Some pathogenic proteins, such as secreted, immunomodulatory proteins or conserved proteins shared between highly variable virus strains, e.g. influenza A, may be targeted more frequently by the immune system than others. We therefore applied different selection schemes to select a subset of proteins prior to the epitope prediction. In the work presented we have demonstrated that a previous developed method for epitope prediction, which integrated proteasomal cleavage, TAP transport efficiency and MHC class I binding, is successful in identifying binders to MHC class I molecules. Furthermore, experimental validations, such as binding assays, T cell assays and other functional assays, have verified that a subset of these epitopes is cable of eliciting CD8+ T cell responses. Herein we have identified 80, 13 and 8 putative CD8+ T cell epitopes for Mtb, Influenza and poxvirus, respectively. For Mtb this is a considerable increase from the 80 CD8+ T cell epitopes previously described in the Immune Epitope Database and Analysis Resource (IEDB). In addition to the epitope discovery for vaccine purposes, this thesis also describes two on-going studies aiming at identifiying synthetic peptide antigens for immunodiagnosis. For these studies we have used a novel comparative genomic approach to identify species-specific epitopes for diagnosis of Mtb and M. leprae from whole genome sequences. The overall goal is to include these unique epitopes for Mtb and M. leprae in a T cell-based assay similar to the current existing IFN- ? T cell assay but without the problem with cross-reactivity to antigens from other closely related mycobacteria. Currently some of these epitopes for both MHC class I and II have been synthesized and are currently being tested for T cell responses in leprosy infected individuals. More experimental work is underway to elucidate the role of our novel T cell epitopes in order to examine their role in protective immune response. A detailed understanding of the epitopes recognized by the immune system may provide aid in vaccine and diagnostic development, as well as greater knowledge of the functional role of T cells gained from these studies.

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