We are pleased to announce that Dr. Amanda Dudek, PhD, Assistant Professor in the Department of Microbiology and Immunology, has been awarded a research grant for her project titled: “Proteomic and gene expression alterations facilitate HIV-1 evasion of NK cell recognition using HLA-E in CD4+ T cells.” This NIH award is sponsored by the University of California, San Francisco/NIH HARC: HIV Accessory and Regulatory Complex – Collaborative Development Award - NIH NIAID Parent U54 AI170792.

PROJECT ABSTRACT: Successful HIV control relies on the presentation of viral peptides on major histocompatibility complex (MHC) class I proteins, enabling cytotoxic immune cells to recognize and destroy infected cells. However, HIV efficiently evades immune surveillance through accessory proteins like Nef, which modulate MHC surface expression. This study aims to elucidate mechanisms of HIV immune evasion using proteomics and single cell RNA sequencing (scRNA-seq) in primary human CD4+ T cells and natural killer (NK) cells isolated from healthy peripheral blood donors. We will employ global protein abundance, phospho- and ubiquitin-modified proteomic analyses, and immunoprecipitation-mass spectrometry (IP-MS) to characterize how primary HIV-1 Nef variants from patient isolates alter host cellular pathways, focusing on MHC modulation and immune evasion. Comparative analysis with the lab-adapted NL4-3 strain will reveal unique Nef-mediated interactions and post-translational modifications critical for immune escape. Single-cell RNA sequencing will provide high-resolution insights into transcriptional changes in infected CD4+ T cells and co-cultured NK cells, identifying genes and pathways involved in immune recognition, activation, and cytotoxic response. Aim 1 will quantify NK cell escape by primary Nef variants using proteomic profiling and functional co-culture assays. Aim 2 will leverage various proteomic techniques to characterize NK cell receptor expression and downstream signaling during co-culture with HIV-infected T cells, highlighting genetic and functional variability across donors. Aim 3 will incorporate single-cell long read RNA sequencing to identify unique transcriptional changes occurring in response to HIV-1 infection in CD4+ T cells and various NK cell subsets. These integrated approaches will deepen our understanding of HIV-host interactions, revealing novel targets for therapeutic intervention and informing personalized strategies for HIV vaccine and immune-based therapies.