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Science Diction Podcast | CRISPR

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CRISPR is a technology that can target and edit specific genes to make agricultural crops more drought tolerant and disease resistant. It can also be used as a cost-effective and versatile research method with the potential to eliminate otherwise deadly diseases.

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SCIENCE DICTION PODCAST: Episode 13

Amy Manning-Boğ, Ph.D.
There is a technology available to us that can target and edit specific genes to make agricultural crops more drought tolerant and disease resistant. It can also be used as a cost-effective and versatile research method, and it has the potential to eliminate otherwise deadly diseases.

Dr. Julie Lucas is an expert in infectious disease with an emphasis on emerging pathogens and pathogens important to biosecurity and public health. She’s a trained biochemist and molecular biologist who has spent the last several years working on ways to use the new genetic engineering tool to detect those pathogens.

Today on the show – CRISPR – what that acronym stands for, why ensuring its responsible use is critical, and how it may help us find new pathogens before they impact human health. I’m Amy Manning-Bog, and this is Science Diction from MRIGlobal.

Julie Lucas, Ph.D.
Scientists have been thinking about the possibility of gene editing for decades. I mean, basically once they realized that mutations in DNA could help contribute to disease, and the initial probably discovery in terms of application was in the 1970s when restriction enzymes were discovered.

These allowed scientists to cut and paste DNA for the first time and create what’s called recombinant DNA, which are hybrid sequences that had never existed before. And this laid the groundwork for gene therapy.

Gene therapy did add new genes, but these new sequences might land near silencing regulatory DNA or they might disrupt healthy genes, which kind of makes the problem worse, right? Scientists really wanted to find better tools to control the gene editing process.

In the early 2000s, they synthesized artificial proteins, and that included the zinc finger nucleuses and these allowed for the precise targeting mutation in the genomes. It was a much, much better approach than what the restriction enzymes were able to do. And this really paved the way for CRISPR.

CRISPR stands for clustered regularly interspaced short palindromic repeats.

Amy Manning-Boğ, Ph.D.
Mouthful.

Julie Lucas, Ph.D.
Yes. That’s why we always just refer to it as CRISPR. So it’s DNA clusters, and there are sequences that were exactly that – regularly interspaced, and they were palindromic in that they could read the same way frontwards and backwards, and they were repeating.

Between them were what scientists called spacers. These spacers are identical to viruses that infect bacteria called bacteriophages. You talked about these, I believe in a previous podcast.

Amy Manning-Boğ, Ph.D.
Yes, with Kristin Bates.

Julie Lucas, Ph.D.
Oh, really?

CRISPR actually has been around in terms of its bacteriophage immune response for like 30 years. But it really wasn’t until about 15 years ago when Doudna and Charpentier identified their applications to gene editing that they really revolutionized the field.

Amy Manning-Boğ, Ph.D.
What’s its utility in bacteria?

Julie Lucas, Ph.D.
It’s a defense mechanism for bacteria. Imagine it as a tiny molecular shield that bacteria will use to protect themselves from the bacteriophages and the bacteria store snippets of the viral DNA in their own genome.

These snippets are like the mugshots of past offenders. And when a new virus attacks, the CRISPR system scans its genetic material, and if it finds it, and with any sorted snippet, then it sounds the alarm.

Armed with information, the CRISPR system targets and chops up the viral DNA, so it renders the invader bacteria harmless. But really the beauty of it lies in its adaptability, so the bacteria can update their CRISPR database with new viral snippets enhancing their defense over time.

CRISPR really helps bacteria survive in a viral like battlefield by remembering past foes and swiftly neutralizing new threats. It’s like their genetic security detail.

Amy Manning-Boğ, Ph.D.
How are we scientists taking advantage of this?

Julie Lucas, Ph.D.
One of the most common ways is to use its use as genetic scissors. So imagine these molecular scissors as precision tools that scientists use to edit DNA. CRISPR systems can be programmed to seek out specific genes within an organism’s DNA.

It’s like having a GPS for genes. You can plug in the address, tell it where you want to go, and it will. That’s the power of CRISPR right there. Extremely targeted.

Once the CRISPR system locates its target gene, it snips it like a skilled tailor cutting fabric. This cut allows scientists to either disable a faulty gene or insert new genetic material.

You can think of the DNA as a massive book with chapters, and CRISPR is the editor of the book. You could either add in paragraphs or take out sentences depending on what you want to do.

Because it’s so versatile, scientists have found lots of different ways to use CRISPR. They can use it to treat genetic diseases, create genetically modified organisms, which are GMOs, detect pathogens, and even explore gene therapies.

Amy Manning-Boğ, Ph.D.
Now we’ll talk about something near and dear to your heart. Diagnostics.

Julie Lucas, Ph.D.
Yes. More recently, CRISPR has had an impact in diagnostics. So the first papers describing diagnostic application with CRISPR were not until 2017, so many years after the gene therapy applications were published, and the diagnostic applications utilize different Cas enzymes than for gene editing.

The enzymes that are used for diagnostics are mainly what are called Cas12 and Cas13 enzymes. These have simpler requirements for assay design, which makes them more suitable for molecular approaches.

What’s important is that these enzymes, there’s really two flavors of them, but they have the ability to detect either RNA or DNA, so you can detect pathogens with both types of genomes.

Amy Manning-Boğ, Ph.D.
The pandemic had an impact on accelerating so many scientific applications. Is this the case for CRISPR as well?

Julie Lucas, Ph.D.
Yes. When you’re looking at infectious disease diagnostics in general, the pandemic really accelerated it as a field. CRISPR was certainly a part of that. There was an urgent need for accurate rapid diagnostic tests for SARS-CoV-2 and CRISPR scientists really stepped up to the plate to provide a solution.

The pandemic really accelerated what were called the point of need diagnostics. CRISPR is uniquely suited for that because of its simple applications. That time period is really when the first emergency use authorization for CRISPR test was approved by the FDA, which really helped to advance the diagnostic field for CRISPR.

Amy Manning-Boğ, Ph.D.
All of these breakthroughs are occurring due to gene editing with CRISPR, but the technology is not without controversy.

Julie Lucas, Ph.D.
The rise of CRISPR Cas9 is really fascinating. It’s like we’ve found a way to rewrite the instruction manual for life itself, which is exciting, but it’s also daunting.

You can apply it to human health, you can apply it to research, you can apply it to, I mean, who knows where it can go. That’s probably part of the controversy—because there’s a flip side of that coin.

I think that’s why people are concerned about it, because it can do so many different things. It’s so versatile because not only is it precise, but it’s relatively easy from a scientific perspective to make it precise.

In response, scientists, ethicists, and policy makers, along with the wider public are all rolling up their sleeves to figure out what are the best ways to handle CRISPR’s use responsibly. What we really need to do is make sure we set up clear rules, that we have open discussions, and that we ensure everything is done fairly and transparently.

It’s going to be a really tricky path, and we’re going to need a mix of a deliberation across domains, courage and caution. We need to be aware of how our choices now will weave into the broader fabric of life, literally.

Amy Manning-Boğ, Ph.D.
Absolutely. Turning our focus to a remarkable achievement in the scientific community. It’s been widely celebrated that the Nobel Prize in chemistry was awarded to two imminent scientists for their pioneering contributions to the CRISPR technology.

This recognition not only underscores the profound impact of their work, but also marks a significant milestone. Julie, will you please elaborate on their trailblazing work?

Julie Lucas, Ph.D.
The Nobel Prize in chemistry was justly awarded to Emmanuelle Charpentier and Jennifer Doudna for their monumental contributions to the development of CRISPR Cas9 gene editing technology.

This came about because of Emmanuelle Charpentier’s initial discovery of the RNA molecule, a tracrRNA, which is essential in the CRISPR mechanism. And that laid the groundwork for this breakthrough.

Jennifer Doudna’s expertise in RNA biology was then synergized with Charpentier’s findings, leading to the collaborative development of a simplified system for gene editing that’s both precise and efficient.

Their work has indeed revolutionized the way we approach genetic research and therapy, and it offers new horizons in biomedical research and beyond. This collaborative spirit underscores a fundamental truth in science is that advancements in science are not the work of just one or two people, but are built upon the collective effort of many.

All of us as scientists stand on the shoulders of both our contemporaries and our predecessors. It’s a vivid reminder of the collaborative nature of scientific inquiry where each contribution, no matter the size, is a vital thread in the fabric of our collective understanding.

Amy Manning-Boğ, Ph.D.
Using what researchers have learned about the technology over the past 30 years, it’s possible to not only detect these diseases and develop therapeutics to address them, but Julie and her team are now using CRISPR to take on emerging pathogens.

Julie Lucas, Ph.D.
Emerging pathogens are the bugs that have newly appeared in a population or have existed, but are rapidly increasing in incidence or geographic range. Usually you hear about them in the news—SARS-CoV-2, mpox, and HIV are all examples.

Another way to think of emerging pathogens: when people travel, sometimes they take unwitting things with them, such as mosquitoes. Climate change can contribute to this as well. Mosquitoes range of certain species suddenly increase, and when that happens the mosquitoes are vectors for many nasty bugs.

Now you have a whole different group of people at risk to get vector-borne diseases. This has contributed to the emergence of diseases such as dengue, Zika virus, and West Nile virus, in additional parts of the world, including the U.S.

Amy Manning-Boğ, Ph.D.
For emerging pathogens, specifically, what benefits does CRISPR offer?

Julie Lucas, Ph.D.
Some current methods such as quantitative or qualitative PCR called qPCR or reverse transcriptase, QCR RTPCR, or even isothermal methods such as RPA or LAMP, they have limitations due to its costs, the sample-to-answer time, and personnel and equipment requirements, which limit widespread deployment.

Other methods can be more cost effective, but have trade-offs, like multi-flexibility. You can only multiplex a couple at a time, or there’s a limit upper limit to that readout, accessibility, sensitivity, specificity, and testing throughput.

Because CRISPR based diagnostic tools are very precise and sensitive, but do not need expensive laboratory equipment, they can enhance conventional procedures.

Amy Manning-Boğ, Ph.D.
So how does your use of CRISPR technology improve upon these methods?

Julie Lucas, Ph.D.
Well, a key component to the public health response to an emergency disease is being able to rapidly design and deploy an accurate specific test to the frontline scientists and laboratories so they can assess the disease spread, understand who has disease, who is at risk. Ultimately, of course, the goal is to control it.

The technology we have developed really enables that quick response from assay design through deployment because we are directly detecting the pathogen genomic material. 

If you look at those original papers from 2017, they actually used isothermal method, but they actually used an upfront application technique first, and then they actually used CRISPR as more as a detection part really for specificity.

They did that because the CRISPR by itself wasn’t sensitive enough to be able to detect the pathogen at relevant levels. What we’ve done is we actually are doing the direct detection, but have discovered ways to amplify the signal so that we can get the appropriate sensitivity.

Amy Manning-Boğ, Ph.D.
That’s really exciting. Let’s talk about organ transplantation. There’s been some news recently.

Julie Lucas, Ph.D.
Yes. Recently scientists and doctors were able to insert a pig kidney into a human. An interesting thing about this was that the pig was actually modified using CRISPR to remove certain pig genes that produce sugars or antibodies that our human immune systems would react to.

Now the human recipient of the kidney is less likely to reject it because their immune system doesn’t recognize it as foreign.

Of course, that would be a huge benefit to people who are on lists waiting for organs.

Amy Manning-Boğ, Ph.D.
We covered substantial ground today. Big picture, Julie, what do you envision for the future?

Julie Lucas, Ph.D.
Oh, wow. So I think CRISPR is going to continue to grow in its various different directions. We’re going to see a lot more in the gene therapy field in terms of helping those patients. And we’re going to see more in the agricultural field really increasing and pushing the envelope, especially with climate change. I think there’s going to be a much bigger need for that.

Diagnostics for CRISPR is in its infancy right now, so I think there’s a lot of room to grow there and lots of potential and exciting things that can happen in that field. It’s just going to keep growing and people are going to come up with even new and different ways, such as we talked about for the organ transplantation application and who knows what the next application is going to be.

I recently read about how people talked about HIV, where they actually could eradicate HIV because it integrates itself into your T-cell. When you can take it out of your T-cells, and now you don’t need the antiviral therapy for your lifetime anymore.

So there’s all kinds of different ways that people are going to come up with to apply it.