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Gene-Editing Advance Puts More Gene-Based Cures Within Reach

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Prime Editing
Caption: The prime editing system (left) contains three parts: two enzymes, Cas9 and reverse transcriptase, and an engineered guide RNA, pegRNA. Unlike regular CRISPR gene editing, prime editing nicks just one strand of the DNA molecule (right) and then uses RNA and reverse transcriptase to direct highly targeted changes to a cell’s DNA. Credit: Broad Institute of MIT and Harvard, Cambridge, MA.

There’s been tremendous excitement recently about the potential of CRISPR and related gene-editing technologies for treating or even curing sickle cell disease (SCD), muscular dystrophy, HIV, and a wide range of other devastating conditions. Now comes word of another remarkable advance—called “prime editing”—that may bring us even closer to reaching that goal.

As groundbreaking as CRISPR/Cas9 has been for editing specific genes, the system has its limitations. The initial version is best suited for making a double-stranded break in DNA, followed by error-prone repair. The outcome is generally to knock out the target. That’s great if eliminating the target is the desired goal. But what if the goal is to fix a mutation by editing it back to the normal sequence?

The new prime editing system, which was described recently by NIH-funded researchers in the journal Nature, is revolutionary because it offers much greater control for making a wide range of precisely targeted edits to the DNA code, which consists of the four “letters” (actually chemical bases) A, C, G, and T [1].

Already, in tests involving human cells grown in the lab, the researchers have used prime editing to correct genetic mutations that cause two inherited diseases: SCD, a painful, life-threatening blood disorder, and Tay-Sachs disease, a fatal neurological disorder. What’s more, they say the versatility of their new gene-editing system means it can, in principle, correct about 89 percent of the more than 75,000 known genetic variants associated with human diseases.

In standard CRISPR, a scissor-like enzyme called Cas9 is used to cut all the way through both strands of the DNA molecule’s double helix. That usually results in the cell’s DNA repair apparatus inserting or deleting DNA letters at the site. As a result, CRISPR is extremely useful for disrupting genes and inserting or removing large DNA segments. However, it is difficult to use this system to make more subtle corrections to DNA, such as swapping a letter T for an A.

To expand the gene-editing toolbox, a research team led by David R. Liu, Broad Institute of MIT and Harvard, Cambridge, MA, previously developed a class of editing agents called base editors [2,3]. Instead of cutting DNA, base editors directly convert one DNA letter to another. However, base editing has limitations, too. It works well for correcting four of the most common single letter mutations in DNA. But at least so far, base editors haven’t been able to make eight other single letter changes, or fix extra or missing DNA letters.

In contrast, the new prime editing system can precisely and efficiently swap any single letter of DNA for any other, and can make both deletions and insertions, at least up to a certain size. The system consists of a modified version of the Cas9 enzyme fused with another enzyme, called reverse transcriptase, and a specially engineered guide RNA, called pegRNA. The latter contains the desired gene edit and steers the needed editing apparatus to a specific site in a cell’s DNA.

Once at the site, the Cas9 nicks one strand of the double helix. Then, reverse transcriptase uses one DNA strand to “prime,” or initiate, the letter-by-letter transfer of new genetic information encoded in the pegRNA into the nicked spot, much like the search-and-replace function of word processing software. The process is then wrapped up when the prime editing system prompts the cell to remake the other DNA strand to match the new genetic information.

So far, in tests involving human cells grown in a lab dish, Liu and his colleagues have used prime editing to correct the most common mutation that causes SCD, converting a T to an A. They were also able to remove four DNA letters to correct the most common mutation underlying Tay-Sachs disease, a devastating condition that typically produces symptoms in children within the first year and leads to death by age four. The researchers also used their new system to insert new DNA segments up to 44 letters long and to remove segments at least 80 letters long.

Prime editing does have certain limitations. For example, 11 percent of known disease-causing variants result from changes in the number of gene copies, and it’s unclear if prime editing can insert or remove DNA that’s the size of full-length genes—which may contain up to 2.4 million letters.

It’s also worth noting that now-standard CRISPR editing and base editors have been tested far more thoroughly than prime editing in many different kinds of cells and animal models. These earlier editing technologies also may be more efficient for some purposes, so they will likely continue to play unique and useful roles in biomedicine.

As for prime editing, additional research is needed before we can consider launching human clinical trials. Among the areas that must be explored are this technology’s safety and efficacy in a wide range of cell types, and its potential for precisely and safely editing genes in targeted tissues within living animals and people.

Meanwhile, building on all these bold advances, efforts are already underway to accelerate the development of affordable, accessible gene-based cures for SCD and HIV on a global scale. Just last month, NIH and the Bill & Melinda Gates Foundation announced a collaboration that will invest at least $200 million over the next four years toward this goal. Last week, I had the chance to present this plan and discuss it with global health experts at the Grand Challenges meeting Addis Ababa, Ethiopia. The project is an unprecedented partnership designed to meet an unprecedented opportunity to address health conditions that once seemed out of reach but—as this new work helps to show—may now be within our grasp.

References:

[1] Search-and-replace genome editing without double-strand breaks or donor DNA. Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A, Liu DR. Nature. Online 2019 October 21. [Epub ahead of print]

[2] Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Nature. 2016 May 19;533(7603):420-424.

[3] Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR. Nature. 2017 Nov 23;551(7681):464-471.

Links:

Tay-Sachs Disease (Genetics Home Reference/National Library of Medicine/NIH)

Sickle Cell Disease (National Heart, Lung, and Blood Institute/NIH)

Cure Sickle Cell Initiative (NHLBI)

What are Genome Editing and CRISPR-Cas9? (National Library of Medicine/NIH)

Somatic Cell Genome Editing Program (Common Fund/NIH)

David R. Liu (Harvard, Cambridge, MA)

NIH Support: National Institute of Allergy and Infectious Diseases; National Human Genome Research Institute; National Institute for General Medical Sciences; National Institute of Biomedical Imaging and Bioengineering; National Center for Advancing Translational Sciences


Nano-Sized Solution for Efficient and Versatile CRISPR Gene Editing

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Nanocapsule for Gene Editing
Caption: Nanocapsule containing its gene-editing payload.
Credit: Guojun Chen and Amr Abdeen, University of Wisconsin-Madison

If used to make non-heritable genetic changes, CRISPR gene-editing technology holds tremendous promise for treating or curing a wide range of devastating disorders, including sickle cell disease, vision loss, and muscular dystrophy. Early efforts to deliver CRISPR-based therapies to affected tissues in a patient’s body typically have involved packing the gene-editing tools into viral vectors, which may cause unwanted immune reactions and other adverse effects.

Now, NIH-supported researchers have developed an alternative CRISPR delivery system: nanocapsules. Not only do these tiny, synthetic capsules appear to pose a lower risk of side effects, they can be precisely customized to deliver their gene-editing payloads to many different types of cells or tissues in the body, which can be extremely tough to do with a virus. Another advantage of these gene-editing nanocapsules is that they can be freeze-dried into a powder that’s easier than viral systems to transport, store, and administer at different doses.

In findings published in Nature Nanotechnology [1], researchers, led by Shaoqin Gong and Krishanu Saha, University of Wisconsin-Madison, developed the nanocapsules with specific design criteria in mind. They would need to be extremely small, about the size of a small virus, for easy entry into cells. Their surface would need to be adaptable for targeting different cell types. They also had to be highly stable in the bloodstream and yet easily degraded to release their contents once inside a cell.

After much hard work in the lab, they created their prototype. It features a thin polymer shell that’s easily decorated with peptides or other ingredients to target the nanocapsule to a predetermined cell type.

At just 25 nanometers in diameter, each nanocapsule still has room to carry cargo. That cargo includes a single CRISPR/Cas9 scissor-like enzyme for snipping DNA and a guide RNA that directs it to the right spot in the genome for editing.

In the bloodstream, the nanocapsules remain fully intact. But, once inside a cell, their polymer shells quickly disintegrate and release the gene-editing payload. How is this possible? The crosslinking molecules that hold the polymer together immediately degrade in the presence of another molecule, called glutathione, which is found at high levels inside cells.

The studies showed that human cells grown in the lab readily engulf and take the gene-editing nanocapsules into bubble-like endosomes. Their gene-editing contents are then released into the cytoplasm where they can begin making their way to a cell’s nucleus within a few hours.

Further study in lab dishes showed that nanocapsule delivery of CRISPR led to precise gene editing of up to about 80 percent of human cells with little sign of toxicity. The gene-editing nanocapsules also retained their potency even after they were freeze-dried and reconstituted.

But would the nanocapsules work in a living system? To find out, the researchers turned to mice, targeting their nanocapsules to skeletal muscle and tissue in the retina at the back of eye. Their studies showed that nanocapsules injected into muscle or the tight subretinal space led to efficient gene editing. In the eye, the nanocapsules worked especially well in editing retinal cells when they were decorated with a chemical ingredient known to bind an important retinal protein.  

Based on their initial results, the researchers anticipate that their delivery system could reach most cells and tissues for virtually any gene-editing application. In fact, they are now exploring the potential of their nanocapsules for editing genes within brain tissue.

I’m also pleased to note that Gong and Saha’s team is part of a nationwide consortium on genome editing supported by NIH’s recently launched Somatic Cell Genome Editing program. This program is dedicated to translating breakthroughs in gene editing into treatments for as many genetic diseases as possible. So, we can all look forward to many more advances like this one.

Reference:

[1] A biodegradable nanocapsule delivers a Cas9 ribonucleoprotein complex for in vivo genome editing. Chen G, Abdeen AA, Wang Y, Shahi PK, Robertson S, Xie R, Suzuki M, Pattnaik BR, Saha K, Gong S. Nat Nanotechnol. 2019 Sep 9.

Links:

Somatic Cell Genome Editing (NIH)

Saha Lab (University of Wisconsin-Madison)

Shaoqin (Sarah) Gong (University of Wisconsin-Madison)

NIH Support: National Eye Institute; National Institute of General Medical Sciences; National Institute of Neurological Disorders and Stroke; National Heart, Lung, and Blood Institute; Common Fund


More Progress Toward Gene Editing for Kids with Muscular Dystrophy

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Normal and treated muscles with DMD
Caption: Muscles of untreated mouse model of Duchenne muscular dystrophy (left) compared to muscles of similar mice one year after gene-editing treatment (right). Dystrophin production (green) is restored in treated animals, despite therapy-related immune response to the Cas9 editing enzyme (dark spots in white inset). Credit: Charles Gersbach, Duke University, Durham, NC

Thanks to CRISPR and other gene editing technologies, hopes have never been greater for treating or even curing Duchenne muscular dystrophy (DMD) and many other rare, genetic diseases that once seemed tragically out of reach. The latest encouraging news comes from a study in which a single infusion of a CRISPR editing system produced lasting benefits in a mouse model of DMD.

There currently is no way to cure DMD, an ultimately fatal disease that mainly affects boys. Caused by mutations in a gene that codes for a critical protein called dystrophin, DMD progressively weakens the skeletal and heart muscles. People with DMD are usually in wheelchairs by the age of 10, with most dying before the age of 30.

The exquisite targeting ability of CRISPR/Cas9 editing systems rely on a sequence-specific guide RNA to direct a scissor-like, bacterial enzyme (Cas9) to just the right spot in the genome, where it can be used to cut out, replace, or repair disease-causing mutations. In previous studies in mice and dogs, researchers directly infused CRISPR systems directly into the animals bodies. This “in vivo” approach to gene editing successfully restored production of functional dystrophin proteins, strengthening animals’ muscles within weeks of treatment.

But an important question remained: would CRISPR’s benefits persist over the long term? The answer in a mouse model of DMD appears to be “yes,” according to findings published recently in Nature Medicine by Charles Gersbach, Duke University, Durham, NC, and his colleagues [1]. Specifically, the NIH-funded team found that after mice with DMD received one infusion of a specially designed CRISPR/Cas9 system, the abnormal gene was edited in a way that restored dystrophin production in skeletal and heart muscles for more than a year. What’s more, lasting improvements were seen in the structure of the animals’ muscles throughout the same time period.

As exciting as these results may be, much more research is needed to explore both the safety and the efficacy of in vivo gene editing before it can be tried in humans with DMD. For instance, the researchers found that older mice that received the editing system developed an immune response to the bacterially-derived Cas9 protein. However, this response didn’t prevent the CRISPR/Cas9 system from doing its job or appear to cause any adverse effects. Interestingly, younger animals didn’t show such a response.

It’s worth noting that the immune systems of mice and people often respond quite differently. But the findings do highlight some possible challenges of such treatments, as well as approaches to reduce possible side effects. For instance, the latest findings suggest CRISPR/Cas9 treatment might best be done early in life, before an infant’s immune system is fully developed. Also, if it’s necessary to deliver CRISPR/Cas9 to older individuals, it may be beneficial to suppress the immune system temporarily.

Another concern about CRISPR technology is the potential for damaging, “off-target” edits to other parts of the genome. In the new work, the Duke team found that its CRISPR system made very few “off-target” edits. However, the system did make a surprising number of complex edits to the targeted dystrophin gene, including integration of the viral vector used to deliver Cas9. While those editing “errors” might reduce the efficacy of treatment, researchers said they didn’t appear to affect the health of the mice studied.

It’s important to emphasize that this gene editing research aimed at curing DMD is being done in non-reproductive (somatic) cells, primarily muscle tissue. The NIH does not support the use of gene editing technologies in human embryos or human reproductive (germline) cells, which would change the genetic makeup of future offspring.

As such, the Duke researchers’ CRISPR/Cas9 system is designed to work optimally in a range of muscle and muscle-progenitor cells. Still, they were able to detect editing of the dystrophin-producing gene in the liver, kidney, brain, and other tissues. Importantly, there was no evidence of edits in the germline cells of the mice. The researchers note that their CRISPR system can be reconfigured to limit gene editing to mature muscle cells, although that may reduce the treatment’s efficacy.

It’s truly encouraging to see that CRISPR gene editing may confer lasting benefits in an animal model of DMD, but a great many questions remain before trying this new approach in kids with DMD. But that time is coming—so let’s boldly go forth and get answers to those questions on behalf of all who are affected by this heartbreaking disease.

Reference:

[1] Long-term evaluation of AAV-CRISPR genome editing for Duchenne muscular dystrophy. Nelson CE, Wu Y, Gemberling MP, Oliver ML, Waller MA, Bohning JD, Robinson-Hamm JN, Bulaklak K, Castellanos Rivera RM, Collier JH, Asokan A, Gersbach CA. Nat Med. 2019 Feb 18.

Links:

Muscular Dystrophy Information Page (National Institute of Neurological Disorders and Stroke/NIH)

Gersbach Lab (Duke University, Durham, NC)

Somatic Cell Genome Editing (Common Fund/NIH)

NIH Support: National Institute of Arthritis and Musculoskeletal and Skin Diseases; National Institute of Biomedical Imaging and Bioengineering


Gene Editing in Dogs Boosts Hope for Kids with Muscular Dystrophy

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Dystrophin before and after treatment

Caption: A CRISPR/cas9 gene editing-based treatment restored production of dystrophin proteins (green) in the diaphragm muscles of dogs with Duchenne muscular dystrophy.
Credit: UT Southwestern

CRISPR and other gene editing tools hold great promise for curing a wide range of devastating conditions caused by misspellings in DNA. Among the many looking to gene editing with hope are kids with Duchenne muscular dystrophy (DMD), an uncommon and tragically fatal genetic disease in which their muscles—including skeletal muscles, the heart, and the main muscle used for breathing—gradually become too weak to function. Such hopes were recently buoyed by a new study that showed infusion of the CRISPR/Cas9 gene editing system could halt disease progression in a dog model of DMD.

As seen in the micrographs above, NIH-funded researchers were able to use the CRISPR/Cas9 editing system to restore production of a critical protein, called dystrophin, by up to 92 percent in the muscle tissue of affected dogs. While more study is needed before clinical trials could begin in humans, this is very exciting news, especially when one considers that boosting dystrophin levels by as little as 15 percent may be enough to provide significant benefit for kids with DMD.


Sharing a Story of Hope

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Whether by snail mail, email, or social media, it’s the time of year for catching up with family and friends. As NIH Director, I’m also fortunate to hear from some of the amazing people who’ve been helped by NIH research. Among the greetings to arrive in my inbox this holiday season is this incredible video from a 15-year-old named Aaron, who is fortunate enough to count two states—Alabama and Colorado—as his home.

As a young boy, Aaron was naturally athletic, speeding around the baseball diamond and competing on the ski slopes in freestyle mogul. But around the age of 10, Aaron noticed something strange. He couldn’t move as fast as usual. Aaron pushed himself to get back up to speed, but his muscles grew progressively weaker.


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