Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4 ⁺ T cells

SUMMARY

Type I interferon (IFN) upregulates proteins that inhibit HIV within infected cells. Prior studies have identified IFN-stimulated genes (ISGs) that impede lab-adapted HIV in cell lines, yet the ISG(s) that mediate IFN restriction in HIV target cells, primary CD4 ⁺ T cells, are unknown. Here, we interrogate ISG restriction of primary HIV in CD4 ⁺ T cells by performing CRISPR-knockout screens with a custom library that specifically targets ISGs expressed in CD4 ⁺ T cells. Our investigation identifies previously undescribed HIV-restricting ISGs (HM13, IGFBP2, LAP3) and finds that two factors characterized in other HIV infection models (IFI16 and UBE2L6) mediate IFN restriction in T cells. Inactivation of these five ISGs in combination further diminishes IFN’s protective effect against diverse HIV strains. This work demonstrates that IFN restriction of HIV is multifaceted, resulting from several effectors functioning collectively, and establishes a primary cell ISG screening model to identify both single and combinations of HIV-restricting ISGs.

Graphical abstract

In brief

Itell et al. interrogate mediators of IFN restriction of HIV directly in primary HIV target cells, CD4 ⁺ T cells, utilizing customized CRISPR-KO screens. This unbiased strategy identifies ISGs not previously known to inhibit HIV. Inactivating several ISGs together reveals cumulative effects, underscoring the multifaceted nature of IFN restriction of HIV.