We asked a scientist to explain CRISPR to us—and how it’s being used in HIV research
Perhaps you’ve heard about a research technology called CRISPR (pronounced “crisper”) in the news. Since the technology was first developed, it has generated headlines as thousands of researchers have adopted this technology as a way to edit the genes of plant, animal and human cells. CRISPR has been used in everything from cancer research to genetically modifying citrus fruit, all while a patent battle has waged over who own this revolutionary technology.
BETA wanted to know more about this technology, and how it’s being used in HIV research. We turned to Molly OhAinle, PhD, a researcher at Fred Hutchinson Cancer Research Center, to explain more about how CRISPR is being used in HIV research, and what her lab is learning about HIV with this technology.
BETA: Could you first tell us—what does CRISPR stand for, and what is it?
Molly OhAinle, PhD: CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. It’s actually a defense mechanism against viruses that bacteria have in their genome. “Cas9” is the name of a bacterial enzyme that can cut DNA. When people talk about CRISPR, they’re actually referring to the “CRISPR-Cas9,” system which is a way of doing very specific gene editing in cells. You can target and use the Cas9 enzyme as “scissors” to cut DNA in a very specific way.
How and when is gene editing helpful? In other words, what are the implications of changing a cell’s DNA?
Our genes control everything from the color of our eyes to how susceptible we are to certain diseases. If we know what genes are responsible for certain traits—and can change those genes in a very targeted way—we have the potential to change the genetic makeup of our cells. We could cure genetic diseases, or reduce our susceptibility to certain viruses.
What’s exciting about this technology?
CRISPR is specific, flexible and cheap. You can program very specific cutting to happen at any place in the genome simply by providing a 20 nucleotide sequence [nucleotides are the “building blocks” of DNA]. It’s inexpensive and readily available for researchers to use in the lab. And it’s flexible—you can program CRISPR to DNA target using just a very short nucleotide sequence.
How are you applying CRISPR in HIV research?
I’m using CRISPR to better understand what the virus requires to infect cells and what cellular defenses block HIV infection. We know what some of these things are already, but we don’t have a complete understanding.
I’m using a “library” approach, which is a way we can test the effect of thousands of genes all at one time. We’re taking cells, and changing one part of the cellular DNA, and then testing them with virus. We want to see, if you knock out a certain gene, is the virus better able to replicate?
If the virus replicates more easily without a certain gene, it suggests that the gene you knocked out is important for normal cellular defense against infection.
One exciting part of our research, that I presented at CROI this year, involved using the virus against itself. We were able to “trick” the virus into carrying the CRISPR genome out of the cell. We’re excited because it’s a new approach, and a new idea for how these types of screenings can be done.
How is CRISPR being used in cure research?
There are a few different ways that CRISPR is being used in HIV cure research. One strategy uses CRISPR to edit normal cellular genes so that the virus can no longer infect the cells in a person’s immune system (or is less likely to infect those cells). You can either use CRISPR to add antiviral genes to people’s cells that make them impossible to infect. Or, you can use CRISPR to delete genes in host cells that makes them impossible to infect. One example of how this would work is the CCR5 mutation (which cured Timothy Ray Brown, the “Berlin Patient”). People who have a deletion in this gene are resistant to HIV infection. You could do the same thing with CRISPR—take cells and edit out the CCR5 gene.
It also might be possible to use CRISPR to remove viral DNA from infected immune cells. When HIV makes copies of itself, it integrates itself into the cellular DNA of our immune cells. This is a big challenge in curing people from HIV, because it means that you need to delete the virus from the cells that are infected, or the virus needs to be inactivated. It’s possible that CRISPR can be used to remove viral DNA from infected cells—which is exciting.
Another strategy, the one that our lab is pursuing, is to identify all of the potential anti-HIV genes in humans, and then eventually find ways to turn them on to prevent virus reactivation.
This concept seems so strange—to take immune cells, change them, and then put them back into people. Do you think this will be a feasible way to cure HIV?
Immunotherapy is certainly something that people are doing now. I work at Fred Hutch, and a lot of the cancer research and treatment being done here is to edit cells and then put them back into patients to try and kill their tumors. So there is similar work being done. There are, however, big challenges in this type of approach as the cost and logistics of immunotherapy are not likely to be scale-able to confront the global HIV pandemic.
Want to read more about HIV cure research on BETA? Read an HIV cure Q&A with HIV cure researchers at the University of California San Francisco, and about how a social scientist is investigating some of the difficult ethical and moral dilemmas that crop up in HIV cure research.