Genome scale identification of HIV Dependency factors across multiple HIV-1 strains

Abstract

In this thesis, I developed a method called HIV-CRISPR screening at genome-wide scale, and then at a smaller, targeted scale, to uncover novel genes that may act as HIV-1 dependency factors. By using a screening technique which assesses enrichment or depletion of guide based on HIV-1 release from infected cells, I was able to assess the role of host factors across the entire life cycle of HIV in a T lymphocyte cell line. Host dependency factors for HIV-1 were uncovered across multiple strains, from different clades and with different co-receptor tropisms. Nearly all of the host dependency factors were validated in subsequent follow-up studies and there was a direct relationship between the scoring of a dependency factor in the screen and its effect on HIV replication in validation studies. Work from this thesis thus identifies at least several dozen novel HIV dependency factors across multiple pathways.