UCLA

CD8+ Cytotoxic T-Lymphocytes (CTLs) are critical for control of viremia during Human Immunodeficiency Virus-1 (HIV-1) infection. While CTLs ultimately fail to fully suppress viral replication in most individuals, a small subset of infected persons can effectively control viremia for several decades. Understanding the factors that allow CTLs to mediate this control of viremia can provide a mechanistic basis for the failure of the CTL response in most individuals and help in the development of future HIV-1 vaccines.

Certain Major Histocompatibility-I (MHC-I) types are associated with better containment of viremia, but the mechanisms mediating control have been difficult to elucidate. In this dissertation, I construct HIV-1 libraries with saturation mutagenesis at several commonly targeted epitopes and utilize these libraries to demonstrate that epitopes presented by protective MHC-I types are highly constrained in their fitness landscapes and abilities to escape CTL clones targeting the epitope. I then demonstrate that an epitope presented by a non-protective HLA type has multiple fit variants, allowing for mutational escape from CTL recognition with little or no loss in replicative capacity.

Next, I examine the CTL response induced by the Mrk/Ad5 HIV vaccine to understand how mutational escape may have contributed to the vaccine’s failure. I demonstrate that the vaccine may have generated CTLs that were less efficient at cross recognizing fit epitope variants, and thus allowed for rapid mutational escape from CTL recognition, likely contributing to the failure of this vaccine trial.

In the final chapter of this dissertation, I focus on the HIV-1 Nef protein. Nef downregulates the expression of MHC-I on the surface of infected cells and represents another mechanism through which the virus can escape CTL recognition. I conduct a high throughput screen of an HIV-1 library containing thousands of point mutations throughout nef to identify amino acid residues essential for Nef’s ability to downregulate MHC-I and demonstrate that these residues are highly conserved in circulating virus isolates.

These the results support a mechanism wherein protective MHC-I types elicit superior CTL responses through immunodominance of highly fitness-constrained epitopes and underscore the importance of escape pathways for successful vaccines and immunotherapies based on CTLs.