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October 23, 2017

A Dose of CRISPR: Can Gene Editing Cut it in the Clinic?

Top Scientists Are in a Race to Be First with an Approved CRISPR-Based Treatment

A Dose of CRISPR: Can Gene Editing Cut it in the Clinic?

Poseida researchers in the lab.

  • It’s one of the highest-stakes races in all of biopharma. Top scientists around the globe are jockeying to be first with an approved CRISPR-based treatment. The breakthrough gene editing technique, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), arrived on the scene just a few years ago. But already a handful of intriguing initial human studies, including some in embryos, have helped fire up the field. Now, dozens of CRISPR-based trials are planned worldwide and in a new twist, China seems to be ahead of the pack, with the U.S. trying to catch up.

    “Gene editing is exploding,” says Rhonda Bassel-Duby, professor of molecular biology, UT Southwestern Medical Center, whose group has done groundbreaking work with CRISPR and Duchenne muscular dystrophy models. The rise of CRISPR has also revived interest in older gene–editing techniques, such as zinc fingers and TALENs. Start-up Homology Medicines recently raised $127 million for a little known editing technique based on viruses.

    Faster, cheaper, easier to use, CRISPR is already a clear winner on the lab bench. “The CRISPR revolution has been one of the most monumental technical advances in the gene editing field,” said Christos Georgiadis of the Great Ormond Street Institute of Child Health, University College London (UCL), U.K. It provides targeted genomic knockout efficiencies that are “unprecedented,” he adds.

    But many also think CRISPR can be used to create a host of new cures. It also offers a means to tweak other therapies, such as those based on T cells or stem cells, including the breakout CAR-T cancer treatments, the first of which (Novartis’ Kymria) was just approved.

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    Significant research funding has flowed to CRISPR in recent years.

    The market for CAR-T is expected to be worth more than $8 billion within ten years, according to research by Coherent Market Insights. However, those therapies are hampered by the fact that they require removing, altering, then re-administering a patients’ own cells, which is a lot of handling and added expense. CRISPR, experts think, might be able to solve this problem. “Could CRISPR make these less individualized?” asks Rachel Haurwitz, president and CEO of Caribou Biosciences. That would turn an autologous treatment into an allogeneic one—a big win.

    The first CRISPR-based trial was conducted by a team lead by Lu You at Sichuan University, Chengdu, China in October 2016. Those researchers injected a lung cancer patient with immune cells edited to knockout the activity of PD-1—a famous “brake” protein that keeps the immune system from attacking cancer cells.  In the wake of this news, renowned cancer researcher Carl June was quoted as saying “I think this is going to trigger ‘Sputnik 2.0,’” essentially, a duel between the U.S. and China. That race is heating up fast. New Scientist recently reported that “as many as 20 human trials” of CRISPR would soon be launched, mainly in China. Currently, nine trials of CRISPR-based therapeutics are listed on ClinicalTrials.gov, although several are not yet recruiting.

    Nagging concerns remain, however. Skeptics point to the potential for off-target effects (a recent paper in Nature Methods set off a signficant firestorm from leaders in the field), delivery challenges, the hurdles that are typical to any product undergoing regulatory review, and now some re-invigorated rival technologies.

    Sangamo, which is developing zinc finger protein (ZFP)-based gene editing technology for more than 13 years, is still square in the game. The company has one product already in clinical trials and three more headed there. (See Sidebar “Can Zinc Fingers Zip Along?”) Transcription activator-like effector nucleases (TALENs) have also entered the clinic, at least in a 2015 “first in man” study of a single patient with B-cell acute lymphoblastic leukemia. More such trials are planned and Thermo Fisher Scientific recently relaunched TALENs as a genome–editing tool that “performs comparably or better than CRISPR.” The company is “focusing on using them to edit parts of the genome where CRISPR is either inefficient or completely non-functional.”

    One major task will be tweaking CRISPR, or its competitors, to make them clinical grade products. “A key step in going from the lab to a therapeutic is making a high–quality nuclease and qualifying its activity and specificity,” says Edward Rebar, vice president of technology at Sangamo. The focus will have to be on reducing off-target effects, improving delivery, creating robust reagents with dependable effects, and being able to detect all of any treatment’s effects. 

  • The Rise of CRISPR

    While ZFPs, TALENs, and others might stay in the race, most of the attention now is in the CRISPR arena.  Developed approximately five years ago, CRISPR caps almost 30 years of research on gene editing. It contains a dual RNA structure, one part of which binds naturally to a complementary DNA sequence and an endonuclease enzyme that snips and degrades nucleotides. The system is natural to the bacterial immune system, helping them defend against the DNA of attacking viruses.  Key details of this process were published in a landmark Science paper in 2012, and it soon became the basis for a widely used DNA editing technique. The most popular approach uses the CRISPR/Cas9 complex although CRISPR/Cpf1 is now also coming into use also.

    The system works with elegant simplicity. The CRISPR-associated (Cas) proteins recognize the sequence, hold the endonucleases in place, and then unwind the target DNA so the sequence becomes visible to the matching CRISPR RNA (also called the “guide” RNA). That sequence binds its target, thereby allowing the proteins to cut both strands at the chosen spot. While understanding all this was helpful, the really big breakthrough was the realization that it is possible to program the protein, using a single RNA, to cleave almost any DNA sequence. That sealed the technology’s status as a breakthrough, and is why CRISPR/Cas9 is often referred to as “programmable molecular scissors.” 

    CRISPR/Cas9 can recognize as few as 20 base pairs of complementary sequence, as long as that sequence is followed by a protospacer associated motif (PAM). That PAM serves as the binding signal for the complex. By mixing in a short DNA sequence, the system can be used to correct single-base mutations.  It can also either shut down or ramp up gene expression, and to edit messenger RNA or non-coding sequences.  This technology has already transformed plant and microbial research, and is having a similar impact on the development of animal models.

  • CRISPR Contenders

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    Poseida researchers in the lab.

    Preclinical studies with CRISPR have been enticing. It has, for example, shrunk human prostate cancer tumors in mouse xenografts and the group Basel-Duby works with at UT used it to successfully treat mice with Duchenne–like muscular dystrophy. And then there are those studies of embryos, which have shown that it is indeed possible to repair genes even at that early stage. These reports have prompted more labs and companies to look at clinical applications of the technology. But while many large pharmaceutical companies and biotechs are using CRISPR or looking at incorporating it in their pipelines, largely because of patent issues, there are few companies using the platform as the backbone of their business.

    As noted earlier, one of the most attractive targets is the chimeric antigen receptor T Cell (CAR-T) therapeutics that have gotten so much attention. Poseida is one of the companies with an eye on that market. CEO Eric Ostertag said their NextGEN CRISPR technology solves many of the problems inherent in other gene editing techniques. “First–generation CRISPR is great, but it is an inherently sloppy system,” he said. “It will cut your 20 base–pair target but it may also make unwanted cuts at similar sites that could differ from the target by as many as 5 nucleotides.” TALENs and ZFPs, he says “Are quite clean in terms of specificity, but they require expertise in reagent design and construction.”

    Poseida’s technology uses a Cas9 protein that is mutated so that is has no nuclease activity. It’s also bound to a nuclease called Clo051, which Ostertag describes as an “obligate heterodimer.” In this system, the Cas9 guide RNA only works as a binding protein to determine site specificity. And the nuclease only cuts when the two fused proteins come together at the same target site, at the same time. “That increases specificity because it is more similar to the earlier dimeric systems,” Ostertag noted. Poseida is using this technology with the CAR-T therapeutics in their pipeline, which include treatments for multiple myeloma, prostate cancer, and other malignancies.

    Crispr Therapeutics AG, Editas Medicine, and Intellia Therapeutics are all “pure play” CRISPR-based therapeutic developers with co-founders who helped pioneer the technology. All of these are also leaning heavily on deals with pharmaceutical companies. 

    Crispr Tx was cofounded by Emmanuelle Charpentier, Ph.D., now director of the Max Planck Institute for Infection Biology in Berlin. Charpentier was one of the coauthors, along with Jennifer Doudna, on the pivotal 2012 Science paper describing the CRISPR/Cas9 gene–editing process.  CRISPR Therapeutics uses that specific approach, and has deals with Vertex Pharmaceuticals and Bayer Ag. Its pipeline contains projects for cystic fibrosis, Duchenne muscular dystrophy, hemophilia, sickle cell disease, and beta-thalassemia.  All of those programs are preclinical, although an IND has been filed for beta-thalassemia.

    Editas Medicine was founded by several leading lights in genome editing, including Feng Zhang, Ph.D., of the Broad Institute, who is currently one of the key patent holders in the CRISPR landscape. The company has a pivotal partnership with CAR-T developer Juno Therapeutics. That deal makes Editas eligible for roughly $700 million in milestone payments through 2020, as well as royalties.  Editas is using both Cas9- and Cpf1-based CRISPR systems.

    Vic Myer, Editas’ chief technology officer said the company’s first programs are in eye diseases, blood disorders such as sickle cell and beta thalassemia, and improving CAR-T. “Ophthalmic diseases are an attractive starting point for many reasons, including the fact that the eye is a relatively contained, immune–privileged organ,” he explained. That makes it less likely there will be systemic side effects. The company aims to file an IND in mid-2018 for Leber Congenital Amaurosis Type 10, which is an inherited form of retinal dystrophy. “We also think gene editing can make CAR-T more durable,” he said. “The T cells can adopt a phenotype called ‘exhaustion’, which makes the therapy less effective, we are working on editing out the signals that trigger that.” He adds that solid tumors had also been hard to crack with CAR-T, in part because they have an inhibitory microenvironment. “We are working on editing the T cells to overcome that,” Myer said.

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    Caribou Biosciences is among many companies currently racing to get CRISPR-based therapies into the clinic.

    Jennifer Doudna was a cofounder of Editas, but split with the group to find a new gene–editing–focused company Caribou Biosciences. Doudna is professor of chemistry and molecular and cell biology at UC–Berkeley. Caribou Biosciences has spun out several other companies in different fields, including Intellia Therapeutics, which is also focused on CRISPR/Cas9. The company’s initial programs are all in preclinical stages and use lipid nanoparticles to deliver edited genes to the liver. The most advanced of these programs is for transthyretin amyloidosis (ATTR).

    The company and has some high–profile deals, including one with Regeneron Pharmaceuticals and another with Novartis. “One of Caribou’s real advantages is the breadth of tools we have, including our wet lab and computational skills and expertise,” said CEO Rachel Haurwitz. The company has, for example, developed its own methodology for measuring off-target effects. The current business model is to focus on collaboration. “We are doing research for others while continuing to improve the platform,” she noted.

    Clearly, CRISPR comes with many caveats. There will likely be seemingly endless patent battles—dispute over who is entitled to which of the most important claims is still raging.  There are also the off–target effects, the ethical concerns, and the fact that most diseases are not caused by single mutations.

    And of course, there is the age–old delivery issue that has long dogged related fields, such as antisense and gene therapy. “Sure, you can do it in a dish, but how do you deliver it to particular cells in the body?” asked Joseph Bondy-Denomy, faculty fellow at the University of California, San Francisco. Right now, he pointed out, most companies are targeting the eye, the ear, the liver, and blood cells, which makes sense. But who will push that further? Denomy discovered “anti-CRISPRs” which are proteins that inhibit CRISPR function. He says we still have a lot to learn about CRISPRs to optimize the tool.

    But there is another major question with such a new technology: “What is everything that can happen when you ‘correct’ a genetic defect, particularly in a germ cell”?  As in many other fields, it’s possible the biggest stumbling blocks will be the ones we haven’t even yet realized exist. Still, the race is on and the rewards could be spectacular.

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