Publication Date


Document Type

Doctoral Dissertation

Academic Program

Interdisciplinary Graduate Program



First Thesis Advisor

Lawrence J. Stern, Ph.D.


CD8-Positive T-Lymphocytes, Receptors, Antigen, T-Cell, Receptors, Pattern Recognition, Cross Reactions


Intracellular pathogens are recognized by a specialized subset of lymphocytes known as CD8+ T cells. Pathogen recognition by CD8+ T cells occurs through binding of T cell receptors (TCR) to processed antigens in complex with major histocompatibility complex (MHC) class I proteins. TCR engagement of antigens in complex with MHC class I typically lead to cytotoxic CD8+ T cell responses, which result in pathogen clearance. Due to the large number of foreign antigens that might be encountered by any given host a diverse repertoire of TCRs must be available for immune recognition. The main source of TCR diversity is generated by somatic recombination of the TCR genes. However, it has been suggested that selection eliminates so many recombined TCR sequences, that a high degree of TCR cross-reactivity must occur for the immune system to be able to recognize a large set of foreign pathogens. The work presented in this thesis was directed towards the understanding of the molecular mechanisms of CD8+ T cell recognition and cross-reactivity.

Chapter I of this thesis gives an overview of the immune system, with a focus on CD8+ T cells.

Chapter II of this thesis describes the development of novel bi-specific MHC heterodimers that are specific towards cross-reactive CD8+ T cells. Classically, MHC tetramers have been used for phenotypic characterization of antigen-specific T cells. However, identification of cross-reactive T cells requires the simultaneous use of two MHC tetramers, which was found to result in MHC tetramer cross-competition. For this reason, we generated bi-specific MHC heterodimers, which would not be affected by the affinity between the component peptide-MHC complexes for TCR. We generated T cell lines, which cross-react with antigens from lymphocytic choriomeningitis virus (LCMV) and vaccinia virus (VV), to test our bi-specific MHC heterodimers. We show that the heterobifunctional cross-linking utilized to generate bi-specific MHC heterodimers does not affect specific binding onto cross-reactive CD8+ T cells.

Chapter III describes a mechanism for a cross-reactive CD8+ T cell response between the disparate antigens, lymphocytic choriomeningitis virus (LCMV)-GP34 (AVYNFATM) and vaccinia virus (VV)-A11R (AIVNYANL), which share the three underlined residues. The recognition determinants for LCMV-GP34 and VV-A11R were compared by an alanine/lysine scanning approach for both epitopes. Functional analysis of the mutated peptides clearly indicates that the shared P4N residue between LCMV-GP34 and VV-A11R is an important TCR contact for the recognition of both epitopes. In addition, we determined the crystal structures of both Kb-VV-A11R and Kb-LCMV-GP34. Structural analysis revealed that the two complexes are nearly identical structural mimics, which was unexpected due to the primary sequence disparity. Together with the functional studies, our results highlight that structural similarities between different peptide-MHC complexes can mediate cross-reactive T cell responses.

Chapter IV of this thesis includes additional discussion, overall conclusions and future directions.

Chapter V includes the protocols and the gene constructs that were used in this work. Also included in Chapter V are results from two unrelated incomplete projects which have yielded significant findings.



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