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New advances in CRISPR gene-editing could lead to an HIV cure

The researchers are seeking to engineer new treatments that could become permanent cures.

New advances in CRISPR gene-editing could lead to an HIV cure
A 3D illustration of HIV. Artem_Egorov/iStock

The Human Immunodeficiency Virus (HIV) virus is a small, unassuming virus with only 12 proteins and a genome only a third of the size of SARS-CoV-2. Yet, it manages to hijack the body’s cells to replicate and spread across systems with impressive speed and agility. How does it do this?

Scientists at Northwestern Medicine are using new advances in CRISPR gene-editing technology to uncover this mystery and hopefully lead to a new permanent treatment for the virus, according to a statement published by the institution on Friday. Through this process, they stumbled upon 86 genes that may play a role in the way HIV replicates including over 40 that had never been examined before in the context of HIV infection.

Important tools in fighting HIV

“The existing drug treatments are one of our most important tools in fighting the HIV epidemic and have been amazingly effective at suppressing viral replication and spread,” said Northwestern’s Judd Hultquist, a co-corresponding author. “But these treatments aren’t curative, so individuals living with HIV have to follow a strict treatment regimen that requires continual access to good affordable health care — that’s simply not the world we live in.”

Hultquist's study looked at T cells. These powerful cells that are targeted by HIV were isolated from donated human blood and hundreds of their genes were further knocked out using CRISPR-Cas9 gene editing. They were then infected with HIV in order to be studied. The researchers found that when these cells lost a gene important for viral replication it resulted in decreased HIV infection, while when cells lost an antiviral factor it resulted in increased HIV infection.

Treatments that become cures

“This is a really great proof-of-concept that the steps and processes that we took to perform the study were robust and well thought out,” Hultquist explained. “That nearly half of the genes we found were previously discovered increases confidence in our dataset. The exciting part is that over half — 46 — of these genes had never before been looked at in the context of HIV infection, so they represent new potential therapeutic avenues to look into.”

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Hultquist now hopes that her work will lead to engineering new treatments that can become permanent cures. The study was published in the journal Nature Communications.

Abstract:

Human Immunodeficiency Virus (HIV) relies on host molecular machinery for replication. Systematic attempts to genetically or biochemically define these host factors have yielded hundreds of candidates, but few have been functionally validated in primary cells. Here, we target 426 genes previously implicated in the HIV lifecycle through protein interaction studies for CRISPR-Cas9-mediated knock-out in primary human CD4+ T cells in order to systematically assess their functional roles in HIV replication. We achieve efficient knockout (>50% of alleles) in 364 of the targeted genes and identify 86 candidate host factors that alter HIV infection. 47 of these factors validate by multiplex gene editing in independent donors, including 23 factors with restrictive activity. Both gene editing efficiencies and HIV-1 phenotypes are highly concordant among independent donors. Importantly, over half of these factors have not been previously described to play a functional role in HIV replication, providing numerous novel avenues for understanding HIV biology. These data further suggest that host-pathogen protein-protein interaction datasets offer an enriched source of candidates for functional host factor discovery and provide an improved understanding of the mechanics of HIV replication in primary T cells.

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