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Episode 6: Delivering CRISPR

By Brinley Macnamara
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Show Notes

With the discovery of CRISPR-Cas9, we gained the ability to precisely alter the human genome overnight. But how close are we to using CRISPR to cure diseases like sickle cell anemia and HIV?


Full text of transcript

Dr. Heath Farris (00:04):

Cationic lipid nanoparticles is such a mouthful, but I feel like it’s a household word, like, everyone would know what cationic lipid nanoparticles are by now.

Brinley Macnamara (00:13):

Hello and welcome to MITRE’s Tech Futures Podcast. I’m your host, Brinley Macnamara. At MITRE, we offer a unique vantage point and objective insights that we share in the public interest. And in this podcast series, we showcase emerging technologies that will affect the government and our nation in the future.

Brinley Macnamara (00:32):

Today, we’re talking about Dr. Heath Farris’ recent MITRE investigation into a breakthrough gene editing technology called CRISPR. And in the episode, we’re going to pay special attention to emerging techniques for precisely delivering CRISPR-based gene therapies into the human body to treat and even form the basis of potential cures to a broad range of diseases. Dr. Farris recently won MITRE’s prestigious Best Paper Award for his work on CRISPR, so I was excited to get the chance to chat with him about his work.

Brinley Macnamara (01:04):

But before we dive in, I want to say a huge thank you to Dr. Kris Rosfjord, the Tech Futures Innovation Area Leader in MITRE’s Research and Development program. This episode would not have happened without her support. Now, without further ado, I bring you MITRE’s Tech Futures Podcast, episode number six.

Brinley Macnamara (01:32):

I’m going to start this episode with a disclaimer. Dr. Farris is a biologist who thinks biology is the greatest thing since sliced bread, so he may be just a tad bit prone to overestimating just how familiar we all are with cationic lipid nanoparticles. Nevertheless, there is no denying that cationic lipid nanoparticles, the delivery systems for the mRNA COVID-19 vaccines, are one of the most important drug delivery systems of the 21st century. Here’s Dr. Farris.

Dr. Heath Farris (02:03):

The cationic lipid nanoparticle technology actually uses the lipid uptake system of the cell. So, it is naturally brought into the cell. And when that comes into the cell, what is inside those lipid nanoparticles is released to this cytoplasm of the cell where your ribosomes are. And then that mRNA message is then translated into protein. And in this case, it’s translated into spike protein for the SARS-CoV-2 vaccine. That spike protein then is assembled and presented to the outside of the cell to stimulate your immune response. So, it is using the cell’s machinery to stimulate or to synthesize the vaccine.

Brinley Macnamara (02:52):

Now, you might be wondering, “Why are we talking about the delivery system for the COVID-19 vaccine in a podcast about delivery systems for CRISPR?” The answer is surprisingly simple. The payloads for the COVID-19 vaccine and CRISPR-based gene therapies both depend on one key ingredient and therefore have similar requirements for delivery into somatic cells. This one key ingredient is messenger RNA, typically abbreviated as mRNA.

Brinley Macnamara (03:22):

So, I’m wondering if you could explain what CRISPR is, and how was it first discovered?

Dr. Heath Farris (03:28):

So, CRISPR is actually a rudimentary immune system for bacteria and archaea. So, if you think about, if you’re a bacterium, what would be your biggest threat, one of their biggest threats is being invaded by a virus. So, that’s their biggest enemy, other than disinfectants, I guess, but out in nature, it’s going to be a virus. So, over evolutionary time, they’ve developed a way to fight against an invading virus. So, how do they have a memory of that? Just like our immune systems have B cells that are our memory that create our memory cells for antibodies, they create a memory by storing part of the genome of the virus that’s invading them. And if they see that virus again, they use CRISPR to go in and chop up the genome of the invading virus before it can kill them.

Brinley Macnamara (04:24):

But while CRISPR, the so-called Swiss Army Knife of gene editing is stunningly precise, getting the CRISPR machinery, namely a piece of guide RNA and a piece of RNA that codes for a genome-cutting protein called Cas9, into exactly the right cells in the human body so it can do its precise cutting in exactly the right places while being careful to avoid healthy cells and unaffected tissues is a lot more complicated. And this is where Heath’s research into effective in vivo delivery systems for CRISPR comes into play. In vivo, by the way, is Latin for within the living. It should not be confused with in vitro, which typically refers to the practice of modifying cells when they’re outside of the living organism from which they were harvested.

Brinley Macnamara (05:08):

And according to Heath, a CRISPR delivery system must satisfy three key requirements to be considered a safe option for delivering gene therapies into the human body. The first key requirement is cargo capacity. Ideally, the delivery system should be able to carry all of the CRISPR components in a single vector. The second is low immunogenicity. In other words, the delivery system should not stimulate the immune system as this will doom the CRISPR components before they can reach their target cells. And the third and final requirement is targeting specificity. I.e. the delivery system should be able to target the specific cells that need editing while avoiding the ones that don’t.

Brinley Macnamara (05:50):

And the decades-long quest to engineer in vivo delivery systems that satisfy these three requirements has yielded several viable candidates, each of which fall into one of three categories: viral vector systems, physical systems, and chemical systems. The first category of CRISPR delivery systems, viral vector systems, is based on methods of reengineering viruses so that, rather than wreaking havoc on their host cells, they will instead assemble the CRISPR-Cas9 complex upon entering the host cell wherein the target DNA can then be edited. I asked Heath about the pros and cons of this delivery system.

Dr. Heath Farris (06:30):

For viral vector systems, advantages and disadvantages are really going to depend on which virus you’re talking about. So, for instance, for adeno-associated viruses, those are great because they’re less likely to stimulate your immune response, so they’re less likely to stimulate an immune reaction to them, but they also are limited on the capacity of what they can carry. They can’t carry large amounts of nucleic acid, so they cannot carry all the components of CRISPR. So, you have to deliver the CRISPR components in multiple virion particles. So, it complicates your delivery mechanism. So, instead of infecting the cell with one virion, you’ve got to infect the cell with two or three virions, depending on the size of your CRISPR components. So, you’re limited.

Dr. Heath Farris (07:28):

Now, when you think of things like retroviruses, you could package all of the CRISPR components into retroviruses, but retroviruses then are going to incorporate themselves into your genome. So, you increase your risk of mutating your genome in a place where you don’t want to mutate it.

Dr. Sybil Russell (07:49):

The viral vector delivery mechanisms can be expensive or they’re less cost-effective.

Brinley Macnamara (07:56):

That’s Dr. Sybil Russell talking. She’s MITRE’s Health Innovation Area Leader. She’s also a pediatric hospitalist, so I was curious to hear her thoughts on some of the limitations of viral vector delivery systems.

Dr. Sybil Russell (08:08):

A lot of times, they require eukaryotic production systems. In addition, occasionally, there can be host, pre-existing or, in the case of vaccines, vaccine-induced anti-vector immunity. So, there are several potential side effects of using viral vectors. And so, those are some of the main reasons why researchers are looking at other delivery systems.

Brinley Macnamara (08:34):

The second category of CRISPR delivery systems, physical systems, leverage advanced techniques to inject the CRISPR components directly into individual cells that need editing. But according to Heath, they come with some considerable limitations.

Dr. Heath Farris (08:50):

A good example of that is microinjection, where you are literally, on a microscopic level, holding a cell, using a microscope and a microneedle to inject nucleic acid into the nucleus. An example of using that would be if you’re trying to affect a CRISPR edit at the fertilization stage of reproduction such that you would get an edit at the zygote stage where you have an edit that edits every cell of an organism. So, it’s a very “limited” technique. I’m putting limited in air quotes because it’s a very powerful technique because I just described a way that you can modify all of the cells of an animal if you start at the right stage of development.

Brinley Macnamara (09:44):

When I asked Heath about the delivery system that he thinks holds the most promise for driving improvements in gene therapy, he was resolute in his response. “Chemical systems,” he said. And this is the third and final category of CRISPR delivery systems that we’ll discuss in this episode. By the way, the delivery system for the COVID-19 mRNA vaccines, cationic lipid nanoparticles, falls within this category, as do other promising delivery systems, like extracellular vesicles and dendrimers. And, of course, I was curious to know about why Heath thinks chemical delivery systems hold so much promise.

Dr. Heath Farris (10:23):

Well, one of the major advantages is you can pack all of the components of CRISPR into one vector. So, it can all be housed. So, it has the capacity for carrying it. They’re non-immunogenic, so that’s great because you’re not going to stimulate an immune response. And there is potential for directing its location. And when I say that, there… and the science is not there yet, the science behind it, the research behind it, is not there, but there is work being done to direct these particles to tissue-specific receptors. So, getting them to go to the locations where you want them to go in the body before they’re filtered out. But I like them because it’s more of a synthetic way that can be very dialed-in and tuned to the tissue. So, I think it’s going to up the chances of actually being able to deliver CRISPR where we need it to go in the body.

Brinley Macnamara (11:33):

So, CRISPR has been investigated as a potential basis for a cure for sickle cell anemia. And so, I’m wondering, how would a CRISPR-based cure for sickle cell anemia work?

Dr. Shmona Simpson (11:45):

So, sickle cell disease is caused by an inherited mutation of the gene that codes for beta hemoglobin. And this is what carries the oxygen in our red blood cells.

Brinley Macnamara (11:57):

That’s Dr. Shmona Simpson talking. Shmona recently joined MITRE as a Principal in biomedical innovation. Shmona is also an immunogeneticist. And throughout her career, she’s been a strong advocate for increased global investment in cures for sickle cell anemia.

Dr. Shmona Simpson (12:13):

And when this is defective, it creates a multi system disorder that we know as sickle cell disease, which is very serious.

Dr. Shmona Simpson (12:22):

So, CRISPR is being used to treat this in two ways. The obvious approach is by correction of the beta hemoglobin. And the second approach, which is very interesting, is by blocking expression of the BCL11A gene. And this gene actually helps a person, when blocked, to revert back to their fetal hemoglobin, which actually doesn’t sickle. And so, by increasing their fetal hemoglobin, it’ll improve the symptoms of the sickle cell anemia. And this is very exciting because, for this particular disease, despite the low efficiency of transfer, you’re still getting a very strong phenotypic effect.

Dr. Shmona Simpson (13:13):

So, what I mean by that is that sickle cell is one of these diseases where even a nominal amount of oxygen transfer in the fetal hemoglobin will create phenotypic effect. And so, it’s probably going to be a highly successful gene therapy because even though the transfer may not be as efficient, we’re still getting an effect, which is not true for every other disease that you could cure with gene therapy. The efficiency typically needs to be a lot higher. So, sickle cell disease is really exciting because we have a chance to, with our current therapeutic method, actually really change the lives of the patients. The challenge now is going to be ensuring that these gene therapies are safe and effective in the long term.

Brinley Macnamara (14:10):

When I talk to CRISPR researchers like Heath, there’s a palpable sense among them that the programmable gene editor that is CRISPR will inevitably drive future breakthroughs in medicine. Breakthroughs that we’ve been waiting more than a generation for, like cures to sickle cell anemia, HIV, and perhaps even one day cures to cancer.

Brinley Macnamara (14:31):

Before the discovery of CRISPR-Cas9, gene therapy was so indefinite that it was considered by most to be a perilous endeavor. Just under 10 years ago, this reality changed overnight. Suddenly, highly precise and reliable gene editing became astoundingly definite, with efficiency of in vivo mammalian genome editing rising from single digits to over 50% in some cases. Moreover, the large-scale deployment of cationic lipid nanoparticles for delivery of the COVID-19 vaccine has shown us that the rapid refinement of novel delivery systems for CRISPR is also inevitable. Our government sponsors must be aware of both the miracles and the dangers that these refinements will bring.

Brinley Macnamara (15:24):

This show was written by me. It was produced and edited by Dr. Kris Rosfjord, Dr. Heath Farris, and myself. Our guests were Dr. Heath Farris, Dr. Sybil Russell, and Dr. Shmona Simpson. The music in this episode was brought to you by Arthur Benson, Ooyy, Yi Nantiro, and Truvio. We’d like to give a special thanks to Dr. Kris Rosfjord, the Technology Futures Innovation Area Leader, for all her support. Copyright 2022. MITRE PRS # 22-0497. February 8th, 2022.

Brinley Macnamara (16:00):

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Meet the Guests

Dr. Heath Farris

Dr. Heath Farris is a Department Chief Scientist at The MITRE Corporation, leading mission-focused research and development in the areas of CRISPR genome modification detection, SARS-CoV-2 and dengue virus host cell interactions, and the recovery and analyses of trace genomic biomarkers for human identification.  During his tenure at MITRE, Dr. Farris has led projects to develop and explore applications for bacterial protein antimicrobial agents and to leverage advanced sequencing technologies for characterizing the genome, transcriptome, and epigenome in viral, bacterial, and mammalian organisms. He retains a B.S. in microbiology and a M.S. and Ph.D. in molecular biology from The University of Alabama.

Dr. Sybil Russell

Dr. Sybil Russell is a Chief Scientist in the Health Innovation Lab and the Health Innovation Area Lead of the MITRE Innovation Program where she focuses on funding research projects in health, public health, and health policy. She is a researcher, board certified practicing physician, public health expert, and teacher. Prior to joining MITRE, she worked at the Johns Hopkins University School of Medicine as a Medical Director and Pediatric Hospitalist. She continues to practice at Johns Hopkins as a Pediatric Hospitalist and has taught at several medical schools over the past 15 years. She has earned a B.A. in political science and a B.S. in cell and molecular biology from Tulane University, an M.D. from Emory University School of Medicine, and an M.P.H. from Johns Hopkins Bloomberg School of Public Health.

Dr. Shmona Simpson

Dr. Shmona Simpson is a Principal for Biomedical Innovation at the MITRE Corporation, leading work at the intersection of health equity, R&D, and public health. She is a viral immunologist and global health consultant, specializing in infectious disease prevention, control, and the development of medical countermeasures. Shmona’s prior roles include Strategist with the Bill & Melinda Gates Foundation identifying new areas of programmatic investment, Strategic Medtech Consultant, Immunologist with the UK Government and Senior Research Advisor to a UK Overseas Territory. She started her career in global health with the Wellcome Trust Unit in Vietnam. Shmona holds an MPH and DPhil in Clinical Medicine from Oxford University, where she was a Rhodes Scholar.