Presentation description

Host-pathogen interactions are driven by ongoing evolutionary arms races, where rapid adaptations on both sides lead to dynamic genomic changes. Viruses employ gene accordions, transient gene copy number expansions that accumulate adaptive mutations followed by contraction, to adapt against host immune defense. Whether gene accordions arise in host genomes and facilitate the evolution of immune defense mechanisms is less understood. Interestingly, mammalian genomes harbor amplicons, gene expansions within large (>10kb) segmental duplications that have high copy number variation within and between species, similar to viral gene accordions. I hypothesize that amplicons can act as potential host gene accordions in facilitating the evolution of host antiviral immune response. To address the necessity of amplicon gene families in host antiviral defense, I conducted shRNA-mediated knockdown experiments of candidate amplicon gene families (GOLGA8 and TBC1D3) with potential links to HIV-1 retroviral replication in a human cell line (HEK293T). To achieve cell lines with stable knockdown of amplicon gene expression, I cloned plasmid constructs with shRNA transgenes targeting TBC1D3 and GOLGA8 ampliconic genes. I then used CRISPR-Cas9 to target transgene integration to the AAVS1 safe harbor locus for long-term, stable transgene expression. Downstream validation of transgene integration was conducted using DNA genotyping at the AAVS1 locus and transgene expression via PR-qPCR to detect changes in relative TBC1D3 and GOLGA8 mRNA transcript level. After confirming knock-down of TBC1D3 and GOLGA8, we will transfect cells with an attenuated HIV-1 plasmid and expect increased HIV-1 replication relative to wild-type controls. Future experiments will over-express TBC1D3 and GOLGA8 to address their sufficiency to reduce viral replication. Thus, amplicons could hint at a novel mechanism of host immune adaptation to viruses in the on-going host-pathogen co-evolutionary conflict.