Systematic discovery of pro- and anti-HIV host factors in primary human CD4+ T cells

We performed orthogonal genome-wide CRISPR activation (CRISPRa) and CRISPR knockout (CRISPRn) screens in primary human CD4+ T cells to systematically discover pro- and anti-HIV host factors. Candidate hits were validated using secondary pooled screens and arrayed perturbations and were further characterized using assays for HIV infection, T cell activation, and HIV receptor/co-receptor expression.

CRISPRa identified multiple potent antiviral factors including PI16, PPID, SHISA3, and ITM2A. PI16 interacts with host pathways involved in HIV fusion and inhibits viral entry, while PPID (Cyp40) binds HIV capsid and restricts infection by reducing nuclear import of the HIV core. Structural modeling, evolutionary analyses, and targeted mutagenesis identified domains and residues required for PPID-mediated restriction, including non-human primate ortholog substitutions that enhance antiviral activity.