How does HIV, armed with only nine genes, manage to hijack the immune system so effectively? For decades, researchers have known that the virus depends on human proteins to enter, replicate, and persist—yet the full roster of those host factors has remained elusive. One major reason: most HIV studies have relied on immortalized cell lines rather than the primary CD4+ T cells the virus actually infects in the body. As a result, scientists have lacked a comprehensive picture of how real human T cells respond when HIV attacks.
A new study from Gladstone Institutes and the University of California, San Francisco (UCSF), changes that. In the study, titled “Systematic Discovery of Pro- and Anti-HIV Host Factors in Primary Human CD4+ T Cells” and published in Cell, researchers report the first genome‑wide map of human genes that either promote or restrict HIV infection in primary human CD4+ T cells, offering a long‑sought blueprint of the host–virus interface.
“HIV has been a global crisis for over 40 years,” said Alex Marson, MD, PhD, director of the Gladstone‑UCSF Institute of Genomic Immunology and senior author of the study. “By studying human T cells, which are the primary target of the virus, we’ve finally mapped the genes—many of which were previously unknown—that influence whether or not they can be infected by HIV.”
Achieving this required overcoming a fundamental technical barrier. “One challenge of using real human T cells for research is they’re very difficult to infect with HIV; out of a whole dish of cells, typically only one or two percent would get infected,” said first author Ujjwal Rathore, PhD. After years of optimization, the team pushed infection rates to roughly 70%, enabling genome‑scale CRISPR perturbations in primary cells for the first time.
With that platform in hand, the researchers performed orthogonal genome‑wide CRISPR activation (CRISPRa) and CRISPR knockout (CRISPRn) screens in CD4+ T cells, systematically testing nearly every human gene. Disrupting genes revealed those HIV depends on, while overactivating genes exposed natural antiviral defenses that HIV normally suppresses. “Over‑activating the genes gave us a wealth of information,” said co–first author Eli Dugan, a PhD candidate in Marson’s lab. “We discovered natural antiviral proteins that were previously invisible because the virus could effectively silence them.”
Across both screens, the team identified hundreds of host factors that shape HIV infection. Among the most striking were two previously unrecognized antiviral proteins: PI16 and PPID (Cyp40). “PI16 interacts with host factors involved in HIV fusion and inhibits viral entry, whereas PPID, a paralog of the proviral cyclophilin CypA, binds capsid and reduces nuclear import of the HIV core,” wrote the authors. Targeted mutagenesis, along with structural modeling and evolutionary analyses, pinpointed residues essential for PPID’s restriction activity, and engineered variants were up to tenfold more potent, according to Dugan.
To test whether these defenses could counter real‑world viral strains, the team collaborated with HIV pioneer Jay Levy, MD, who provided isolates from the early AIDS epidemic. Elevated levels of PI16 or PPID restricted even these aggressive HIV strains.
“This was the first genome‑wide effort to show how human genes affect HIV infection in cells taken directly from human blood samples,” said Nevan Krogan, PhD, director of the HIV Accessory and Regulatory Complexes (HARC) Center. “Our findings could eventually lead to new treatments that help the body’s immune system resist the virus.”
Beyond identifying antiviral factors, the study offers the potential for a powerful new platform for probing HIV latency—the persistent reservoir that evades antiretroviral therapy. “Now, we have the platform to ask the biggest questions in the field,” Rathore said, “and hopefully learn how to eliminate hidden HIV that current drugs can’t reach.”
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