Archive for the ‘Crispr’ Category

Imagine editing one gene and curing a debilitating disease.Three small biotech companies with combined annual sales of less than $50 million Crispr Therapeutics (CRSP), Intellia Therapeutics (NTLA) and Editas Medicine (EDIT) say that soon could be a reality.

X All three biotech stocks went public in 2016 to bet big on a simple premise: Altering specific genes can create curative medicines.An estimated 5,000 diseases could be cured by changing one targeted gene, says former Intellia Chief Executive Nessan Bermingham.

The World Health Organization has a higher estimate for what are known as monogenic diseases and says it's actually north of 10,000.

"People have been talking about (personalized medicine) for 20 years and yet we've never had a system to allow us to do it before," Bermingham told Investor's Business Daily before stepping down from his role on Dec. 31."And for the first time ever, we actually have a system to do it and that system would be based on your personalized genome."

That system is known as CRISPR, and it's where Crispr, Intellia and Editas are putting their chips. It's a cheaper and faster gene editing method and, according to Bermingham, the key to advancing personalized medicine. Some analysts think CRISPR technology could provide the platform for the next generation of giant biotech companies.

CRISPR the technology not to be confused with Crispr Therapeutics, the company builds on a project that sequenced the human genome. The first map cost $2.7 billion and was completed in 2003.

Since then, the cost to map an individual's genome has dropped precipitously and could come down to just hundreds of dollars in the next few years, Bermingham says. Large-data analytics also have a part to play in sifting through the genome.

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When the first human genome was mapped, investigators were "absolutely horrified" to find just 20,000 genes in the human body that code proteins, Bermingham says. That was down from estimates of 100,000. Essentially, these protein-coding genes serve as words in the genetic language.

Investigators also found regions of DNA that were initially thought to have no purpose. These were controversially called "junk DNA" that does not code protein. But, as it turns out, these sequences do have a key purpose in regulating the expression of genes.

All together, the better understanding of the human genome has allowed these biotech companies to utilize CRISPR, an acronym for the technology known asClustered Regularly Interspaced Short Palindromic Repeats.

There is a caveat, however. In January, a paper published by bioRxiv said there may be evidence that human immune systems may fight off the major form of genome editing that uses an enzyme called Cas9, thus rendering the science ineffective. The paper, however, has yet to be peer reviewed.

The process, developed at various universities, essentially uses specialized strands of DNA thatact as molecular "scissors." Those scissors are capable of editing other DNA at specific points, and allow biotech companies to edit, add or remove faulty genes responsible for diseases.

There are varying types of scissors. Crispr, Intellia and Editas are using the Cas9 CRISPR technology, ARK Invest analyst Manisha Samy told IBD. She estimates Cas9 can reach 70%-80% of the human genome. Developing new scissors can expand the reach into more genes and diseases, she says.

Gene editing isn't new, she adds. Older techniques called TALENs and zinc finger nucleases have been around for some time. Notably, biotech companyBluebird Bio (BLUE) is using a variation of TALENs, and Sangamo Therapeutics (SGMO) is using a method of zinc finger nucleases.

She likens CRISPR technology to a word processor.

"We think CRISPR gene editing is analogous to a DNA word processor with two functions: find and delete," she said in a January 2017 report. "In addition, scientists are working on a rudimentary paste function, allowing CRISPR to insert appropriate DNA code to repair mutations."

Older technologies used by biotech companies are more like old-fashioned typewriters, requiring actual cutting and pasting, she says. CRISPR technology is also cheaper and easier to use than TALENs and zinc fingers, says JMP Securities analyst Mike King.

"What's so powerful about CRISPR is it's so easy to use," he told IBD. "High school students are doing experiments in the biology lab to knock out genes. Zinc fingers takes a lot of talent and time. You have to fiddle with them a lot. The systems created under CRISPR are quite robust."

In January, bioRxiv an online archive and distribution service for unpublished reports in the life sciences field published a paper casting doubt on the durability of CRISPR gene therapy over time, suggesting the body could build an immunity to it. Analysts and biotech companies are not worried, however, saying either this is a nonissue or there's time for the science to catch up.

Many companies working in CRISPR are doing so using the Cas9 enzyme, short for CRISPR associated protein 9. Cas9 is derived from two bacteria that cause infections in humans at high rates, meaning some immune systems could have developed immunities to them.

Would CRISPR gene editing, using that enzyme, work in those patients?

It depends, Crispr Therapeutics said in a follow-up email to IBD. It's important to note the lead investigator and writer on the bioRxiv paper wasMatthew Porteus, a scientific founder and advisory board member for Crispr Therapeutics.

When the gene editing is done ex vivo, or outside the body, the Cas9 enzyme is degraded and, therefore, essentially gone by the time the cells are reintroduced to the patient, Crispr told IBD.

For in vivo applications, when gene editing is done inside the body, Crispr Therapeutics says it uses several approaches to ensure transient expression of the Cas9 enzyme. Because of that, "we do not expect pre-existing immunity to Cas9 to cause any issues," the firm said.

Ark's Samy also noted that other enzymes are in use. Editas is also using the Cpf1 enzyme. This enzyme is derived from other bacteria and could overcome some of the immunity challenges involving Cas9.

Intellia told IBD in a follow-up email that in clinical testing, its delivery system for treatment in rodents and non-human primates has yet to falter. Further, Intellia notes it's using an advanced form of Cas9 and none of the donors had a pre-existing immunity in its study.

The data are still early. Editas has done its own work in immune responses to CRISPR genome editing and will present a paper in the future, JMP's King said in a Jan. 8 note to clients. Management has indicated it found immune responses to be "much lower" than those reported in the other paper.

"Immune responses are not uncommon," Samy said. "Scientists have worked for decades on evading immune recognition. There are numerous workarounds that can be implemented to reduce any potential side effects with Cas9 and we have proved this in a number of other therapeutic modalities."

Among the biotech companies, Crispr Therapeutics is ahead of the competition from a regulatory standpoint. On Dec. 7, the firm submitted its first application for a clinical trial testing its gene therapy, known as CTX001, in a blood disorder known as beta thalassemia.

The company is working with Vertex Pharmaceuticals (VRTX) in beta thalassemia, as well as sickle cell disease. The therapies are part of Crispr's ex vivo programs, where gene editing is done on cells outside the body before they are reintroduced to the patient. Crispr is also looking at in vivo therapies for the liver, muscles and lungs.

According to a Crispr news release, the trial is set to begin in Europe in 2018 in adult patients. This is expected to be the first in-human trial of a gene editing treatment based on CRISPR technology. Crispr also plans to file an application to begin testing for CTX001 in treating sickle cell disease in the U.S. in 2018.

Intellia also has in vivo and ex vivo programs in gene editing, and also is working in sickle cell disease. It's furthest along in a partnership with Regeneron Pharmaceuticals (REGN) for a therapy to treat what's known as transthyretin amyloidosis, a condition characterized by the buildup of abnormal protein deposits throughout the body.

Alnylam Pharmaceuticals (ALNY) and Ionis Pharmaceuticals (IONS) also are working separately to treat the disease using different methods called RNA interference and antisense technology, respectively.

Meanwhile, Editas is working on an injected treatment for an inherited eye disease known as Leber congenital amaurosis, which is characterized by severe loss of vision at birth. It is also using gene editing in sickle cell disease and beta thalassemia.

Intellia and Editas also are expected to start in-human trials in 2018, analysts say, though Intellia has not said when it will begin testing.

Regulators are getting more comfortable with the idea of gene editing, Crispr Therapeutics President Sam Kulkarni told IBD. The benefit of gene editing and potential trouble with it is that it's meant to be a permanent fix. The biotech companies are working to ensure they hit a bull's-eye every time out.

"We've shown you we can make this edit and it's done in a precise fashion using (targets the industry calls) molecular ZIP codes," he said. "We eliminate edits happening outside places you want them to happen. And we manufacture these in a high-quality fashion, understanding the pharmacology."

Both Kulkarni and Intellia's Bermingham who was succeeded byJohn Leonard, a former AbbVie (ABBV) executive say there's room for all three big players in the group.

Sizing the market is a challenge, ARK's Samy says. No matter how you slice it, the numbers are big and a lot will depend on which diseases companies target and how they set pricing.

If CRISPR is able to address all monogenic diseases diagnosed each year, that's a $75 billion market globally, she says. Addressing all these diseases for people already living with diagnoses would be a $2 trillion market.

"One product is not going to cure everything," she said. "Whenever you're seeing volatility between these three main CRISPR companies, it doesn't really make sense because there's room for all of them and more when it comes to CRISPR."

Kulkarni says it's unlikely the market will remain at just three publicly traded biotech companies with CRISPR technology in the long run. The technology is just that remarkable.

"Once in a lifetime may be a little bit of a stretch, maybe not," he said. "But it's definitely a once in a generation type of advance in the field. The last time this kind of excitement happened in the biotech field was when antibodies were applied as therapeutic modalities. On the basis of that, technology companies like Genentech (now owned byRoche (RHHBY)) were created."

He added: "Here we have the basis of a CRISPR platform to create the next big biotech giants."

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CRISPR Gene Editing And 3 Biotech Companies Blaze New Path To ...

China is taking the lead in the global race to perfect gene therapies.

Scientists have genetically engineered the cells of at least 86 cancer and HIV patients in the country using Crispr-Cas9 technology since 2015, the Wall Street Journal reports (paywall). Although no formal scientific papers have been written about these experiments, doctors told journalists at the WSJ that some patients have improved. There have also been least 15 deaths, seven of which were in one trial. Scientists report all of these deaths were related to patients previous conditions and not Crispr treatment.

These therapies, which involved taking the immune cells from hospital patients, editing the cells, and transfusing them back into the body, are the first to use Crispr-Cas9 in living humans.

In 2013 scientists first used (paywall) Crispr on on human DNA, and in 2017, US scientists at Oregon Health & Science University reported using the technology to edit human embryos. (The embryos were not allowed to develop further.) It took two years for the Oregon team to receive ethical approval for their experiment. It took the same amount of time for the University of Pennsylvania hospital and the US Food and Drug Administration to give Penn researchers the go-ahead to test a Crispr-based therapy on 18 cancer patients. That trial is expected to begin later this year. Scientists at the Cambridge, Massachusetts-based Crispr Therapeutics also hope to start phase I clinical trials using Crispr to treat patients with a genetic disorder called beta-thalassemias.

Crispr trials on humans have been relatively slow to develop in the US and UK in part due to concerns over how the risk of the procedure is communicated to patients. The Penn scientists first had to consult with an advisory board from the National Institutes of Health set up specifically to evaluate the potential risks and benefits of Crispr therapies, then get approval from the US Food and Drug Administration.

The FDA approved three gene therapies for treatment in 2017, none of which use Crispr. Two of these therapies treat late-stage forms of cancer, and both rely on editing the patients immune cells. The third, which targets a rare form of childhood blindness, works by modifying cells in the eye.

The Chinese ministry of health has to approve all gene-therapy clinical trials in China, but these regulations appear relatively relaxed. According to the WSJ, at Hangzhou Cancer Hospital, for example, a proposal to test a cancer treatment that modifies patients immune cells was approved in a single afternoon. One member of the hospitals approval committee told the WSJ that she did not really understand the science laid out for her in a 100-page document, but was told that the side effects were mild. This was enough for her to give it the go-ahead.

The truth, though, is that there is a dearth of data on the safety of Crispr on humans, and many scientists in the field are concerned that the treatment may cause unintended mutations or may not work at all.

If any of these Crispr treatments are proven successful under scientific scrutiny, theyd be the first of their kind.

Correction: An earlier version of this article stated that about half of the deaths in Crispr trials were related to the gene therapy. It has been corrected to reflect that doctors say all of the deaths in the Crispr trials were related to patients previous conditions.

Read this next: A highly successful attempt at genetic editing of human embryos has opened the door to eradicating inherited diseases

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Chinese scientists already used Crispr gene editing on 86 ...

Your DNA is your bodys most closely guarded asset. To reach it, any would-be-invaders have to get under your skin, travel through your bloodstream undetected by immune system sentries, somehow cross a cell membrane, and finally find their way into the nucleus. Most of the time, thats a really good thing. These biological barriers prevent nasty viruses from turning your cells into disease-making factories.

But theyre also standing between patients with debilitating genetic diseases and their cures. Crispr, the promising new gene editing technology, promises to eradicate the world of human sufferingbut for all the hype and hope, it hasnt actually cured humans of anything, yet. Medical researchers have the cargo, now they just have to figure out the delivery route.

The first US trials of Crispr safety are set to begin any day now, with Europe expected to follow later this year. Chinese scientists, meanwhile, have been testing Crispr humans since 2015, as The Wall Street Journal recently reported, with mixed success. These first clinical forays involve removing cells from patients bodies, zapping them with electricity to let Crispr sneak in, then infusing them back into their bodies, to either better fight off cancer or to produce a missing blood protein. But that wont work for most rare genetic diseasesthings like cystic fibrosis, Duchennes muscular dystrophy, and Huntingtons. In the 34 trillion-cell sea that is your body, an IV bag full of Crisprd cells simply wont make a dent.

This is the same problem that has plagued the stop-and-go field of gene therapy for nearly three decades. Traditional gene therapy involves ferrying a good copy of a gene inside a harmless virus, and brute-forcing it into a cells DNA. Crisprs cutting action is much more elegant, but its bulk and vulnerability to immune attacks make it just as difficult to deliver.

The challenge is getting gene editors to the right place at the right time in the right amount, says Dan Anderson, an MIT chemical engineer and one of the scientific founders of Crispr Therapeutics. Thats a problem people have been working on for a long time. As of today there certainly is no one way to cure every disease with a single delivery formulation.

And its unlikely there will be anytime soon. So for now, most Crispr companies are taking more of a whatever works approach, borrowing mostly from gene therapys few success stories. One of those is a small, harmless helper virus called AAV, well-suited for carrying genetic instructions into a living cell. AAV wont make you sick, but it can still sneak into your cells and hijack their machinery, making them a perfect Trojan horse in which to put good stufflike a correct copy of a gene, or instructions for how to make the protein-RNA pair that forms the Crispr complex. Crisprs instructions are quite long, so they often cant fit inside one virus.

But once you get around that, theres an even bigger downside to AAV; once it ferries Crispr inside a cell, theres no good way to control its expression. And the longer Crispr hangs around, the greater the chance it could make unwanted cuts.

Delivering Crispr into the cell directly, as opposed to teaching the cell to build it, would provide more control. But doing that means enveloping the unwieldy, charged protein complex in a coating of fat particlesone that can simultaneously shield it from the immune system, get it across a cell membrane, and then release it to do its cutting work unencumbered. Although the technology is improving, its still not very efficient.

The big threeCrispr Therapeutics, Editas Medicine, and Intellia Therapeuticsas well as the latest newcomer, Casebia, are all investing in AAV and lipid nanoparticles, and testing both for their first rounds of treatment. Were leveraging existing delivery technologies, while exploring and developing the next generation, says Editas CEO Katrine Bosley. We will use whatever works best for a given target.

But industry isnt the only one feeling the urgency. This week the National Institutes of Health announced it will be awarding $190 million in research grants over the next six years, in part to push gene editing technologies into the mainstream. The focus of the Somatic Cell Genome Editing program is to dramatically accelerate the translation of these technologies to the clinic for treatment of as many genetic diseases as possible, NIH Director Francis Collins said in a statement Tuesday. Which could encourage some of the more exotic, experimental delivery systems out in the research worldstrategies like Crispr-covered gold beads, yarn-like ball structures called DNA nanoclews, and shape-shifting polymers to get the editor where it needs to go.

In October, UC Berkeley researchers Kunwoo Lee, Hyo Min Park, and Nirhen Murthy used those gold nanoparticles to repair the muscular dystrophy gene in mice. Theyre now expanding that work in a startup the trio cofounded called GenEdit. They plan to develop a suite of nanoparticle delivery vehicles optimized to different tissues, starting with muscles and the brain. Then theyll partner with the folks making the Crispr payloads. That will make it the first company devoted solely to Crispr delivery. The gene editing world is filling up with products to deliverbut even Amazon needs UPS.

Originally posted here:
Crisprs Next Big Challenge: Getting Where It Needs to Go | WIRED

Remove and replace

Science / Alamy Stock Photo

By Michael Le Page

The CRISPR genome-editing method may just have become even more powerful. Uri David Akavias team at McGill University in Canada has managed to repair mutations in 90 per cent of target cells using CRISPR the best success rate yet.

The CRISPR approach is very good at disabling genes, but using the technique to fix them is much harder, because it involves replacing a faulty sequence with another. This typically works in less than 10 per cent of target cells.

To make the process more efficient, Akavias team physically linked the replacement DNA with the CRISPR protein that finds and cuts the faulty sequence. This ensures that the replacement DNA is there ready to be slotted in once the cut is made. Weve taped the [replacement] text to the scissors, says Akavia.

The team also used a polymer

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New CRISPR method could take gene editing to the next level

A

new paper points to a previously unknown hurdle for scientists racing to develop therapies using the revolutionary genome-editing tool CRISPR-Cas9: the human immune system.

In a study posted Friday on the preprint site bioRxiv, researchers reported that many people have existing immune proteins and cells primed to target the Cas9 proteins included in CRISPR complexes. That means those patients might be immune to CRISPR-based therapies or vulnerable to dangerous side effects the latter being especially concerning as CRISPR treatments move closer to clinical trials.

But researchers not involved with the study said its findings, if substantiated, could be worked around. (Papers are posted to bioRxiv before being peer-reviewed.) Many of the first planned CRISPR clinical trials, for example, involve removing cells from patients, fixing their DNA, and then returning them to patients. In that case, its possible that there will be few or no CRISPR proteins remaining for the immune system to detect.

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They also noted that scientists are already studying other types of CRISPR that use different proteins, which could stave off the immune responses.

At the end of the day, Im not that concerned about it, said Daniel Anderson of the Massachusetts Institute of Technology, who has studied the delivery of CRISPR therapies and who was not involved with the new study. But we want to do some experiments to learn more.

The new study should not put the brakes on developing CRISPR therapies, agreed Dr. Matthew Porteus of Stanford, a senior author of the paper and who is himself at work on a CRISPR-based therapy for sickle cell disease. But he said he and his colleagues investigated the immune issues because he felt they were being overlooked as the excitement around CRISPR grew.

Like any new technology, you want to identify potential problems and engineer solutions for them, Porteus said. And I think thats where were at. This is an issue that should be addressed.

(Porteus and Anderson are both scientific founders of CRISPR Therapeutics, one of the most prominent companies exploring CRISPR-based therapies.)

CRISPR has gained fame in recent years as researchers have deployed it to correct an array of disease-causing mutations in cells in the lab and in animal models, with hopes that the same results can be achieved in people. There are different types of CRISPR systems, but the most well known is dubbed CRISPR-Cas9; it includes Cas9 proteins that cut DNA so that it can be edited. Cas9 proteins come from bacteria.

For the study, the researchers decided to check for immune signals against two of the most common types of Cas9 proteins used, those from the bacteria S. aureus (called SaCas9) and those from S. pyogenes (called SpCas9). In their samples of blood from 22 newborns and 12 adults, the scientists found that 79 percent of donors had immune proteins, called antibodies, against SaCas9, and 65 percent had antibodies against SpCas9.

The researchers then searched for immune cells called T cells. They discovered that about half of the donors had T cells that specifically targeted SaCas9, so that if the immune cells detected that protein on the surface of a cell, they would rally a response to try to destroy it. The researchers did not find anti-SpCas9 T cells, though they said the cells might still have been present.

Its not surprising so many of the donors had antibodies and T cells against the Cas9 proteins, experts said. That simply means that those people had been exposed to the bacteria containing the proteins in the past, and other studies have found that, at any given time, 40 percent of people are colonized by S. aureus and 20 percent of schoolchildren have S. pyogenes. The bacteria only sometimes cause disease.

But what then does that previous exposure mean for our receptiveness to CRISPR therapies?

A lot remains unclear, Porteus said. Its not known how severe the immune response would be, and whether it would trigger a dangerous inflammatory attack or just render the treatment useless.

Experts also said that perhaps the immune responses could be avoided. If the CRISPR complex does its editing after the cells are removed from the patient whats called ex vivo or in a place like the eye that is isolated from the immune system, then the antibodies and T cells might not detect any Cas9 proteins. Even in in vivo therapies in which CRISPR complexes would be ferried into cells in a patients body much depends on what kind of delivery system is used and whether the Cas9 proteins become expressed on the outside of the cells in which the editing is taking place.

Porteus said he and his team decided to post the paper on bioRxiv because they wanted CRISPR researchers to start thinking now about possible immune system challenges. The team has also submitted the paper to a journal for peer review and publication.

As a cautionary tale about the importance of asking these questions now, Porteus pointed to what happened with gene therapy in 1999. In that case, a patient in a trial died after an immune system attack, likely because he had preexisting antibodies against a virus used as part of the therapy. The death led to years lost in gene therapy development, experts say. (Patients who have preexisting antibodies to viruses used in gene therapies are now generally excluded from trials.)

I would hate to see the field have a major setback because we didnt address this potential issue, Porteus said. We should learn from that.

Roland Herzog, a gene therapy expert at the University of Florida, agreed that the hype around CRISPR meant that possible immune issues were not being given enough credence.

I suspect that the field has not been aware of it sufficiently, he said. Its not a show stopper, he added about the paper, but the field needs to know about this, that its a potential problem that they need to work around or fix.

One possible fix is simply using a different protein or enzyme in the CRISPR complex, one that doesnt come from such common bacteria. If people havent been exposed to the bacterial protein previously, then they wont have specific antibodies or T cells ready to attack.

New Cas editing enzymes are being described all the time from bacterial species that are not human pathogens (and so there would be no chance to develop the pre-existing antibodies), Jacob Corn, of the University of California, Berkeley, who was not involved with the new paper, wrote in an email. I also know some people have already been working on making Cas enzymes that would be invisible to the immune system.

He added: The field moves very fast!

General Assignment Reporter

Andrew is a general assignment reporter at STAT.

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CRISPR hits a snag: Our immune systems may attack the treatment

2018 is supposed to be the year of CRISPR in humans. The first U.S. and European clinical trials that test the gene-editing tool's ability to treat diseasessuch as sickle-cell anemia, beta thalassemia, and a type of inherited blindnessare slated to begin this year.

But the year has begun on a cautionary note. On Friday, Stanford researchers posted a preprint (which has not been peer reviewed) to the website biorXiv highlighting a potential obstacle to using CRISPR in humans: Many of us may already be immune to it. Thats because CRISPR actually comes from bacteria that often live on or infect humans, and we have built up immunity to the proteins from these bacteria over our lives.

Its the first time this concern has been aired so publicly, and the preprint kicked off something of a firestorm. We had no anticipation it would be picked up so broadly on social media. I dont even have a Twitter account. I just heard this from others, says Matthew Porteus, a pediatrician and stem-cell researcher at Stanford who led the study and is working on a clinical trial for sickle-cell anemia.

Not all CRISPR therapies in humans will be doomed. We dont think this is the end of the story. This is the start of the story, says Porteus. There are likely ways around the problem of immunity to CRISPR proteins, and many of the early clinical trials appear to be designed around this problem.

Porteus and his colleagues focused on two versions of Cas9, the bacterial protein mostly commonly used in CRISPR gene editing. One comes from Staphylococcus aureus, which often harmlessly lives on skin but can sometimes causes staph infections, and another from Streptococcus pyogenes, which causes strep throat but can also become flesh-eating bacteria when it spreads to other parts of the body. So yeah, you want your immune system to be on guard against these bacteria.

The human immune system has a couple different ways of recognizing foreign proteins, and the team tested for both. First, they looked to see if people have molecules in their blood called antibodies that can specifically bind to Cas9. Among 34 people they tested, 79 percent had antibodies against the staph Cas9 and 65 percent against the strep Cas9.

Then, they looked to see if a particular type of immune cells called T cells can recognize the Cas9 proteins. This time they studied T cells from 13 healthy adults. Six of themor 46 percentreacted to the staph Cas9. None of them did against the strep Cas9.

The Stanford team only tested for preexisting immunity against Cas9, but anytime you inject a large bacterial protein into the human body, it can provoke an immune response. After all, thats how the immune system learns to fight off bacteria its never seen before. (Preexisting immunity can make the response faster and more robust, though.)

In statements to The Atlantic, three of the leading companies in CRISPR human therapyEditas Medicine, CRISPR Therapeutics, and Intellia Therapeuticsall downplayed the new findings, citing various ways their therapies could around the immune system. (Porteus is a scientific founder of CRISPR Therapeutics, though this study was performed independently.) A September 2017 presentation from a scientist at Editas Medicine also detailed some of the ways to test for immune reactions to CRISPR, anticipating a potential problem.

Here are some possible strategies to get around the immune system that are being discussed and tested:

Only use CRISPR outside of the body: Instead of delivering CRISPR/Cas9 into the body, you take cells out of the body, use CRISPR to edit their genes in a lab, and return Cas9-free cells. This is the strategy pursued by CRISPR Therapeutics for the inherited blood disorder thalassemia and in various trials using CRISPR to modify immune cells to attack cancer.

Only use CRISPR in places the immune system cannot reach: Some sites of the body are immunoprivileged, meaning the immune system cant really attack invaders there. The eye, which Editas Medicine is targeting for inherited blindness, is one of those sites.

Modify Cas9 or use a different CRISPR protein altogether: It may be possible to redesign Cas9 to hide it from the immune system or to find other bacterial proteins that can do the job of Cas9 without provoking the immune response. Many different bacteria have CRISPR systems. We already have lots of Cas enzymes and could get many more, George Church, a geneticist at Harvard and a founding scientific advisor of Editas, wrote in an email.

Express Cas9 only transiently:Once Cas9 has made its edit, it doesnt need to stick around. A spokesperson for Intellia noted that its still unclear how the immune system responds to continuous versus transient expression of Cas9. The company says its lipid-nanoparticle delivery system can get cells to make Cas9 only transiently, but enough for the editing to happen in rodents and non-human primates.

The one type of therapy where immune response may be most dangerous and unavoidable is when Cas9 is produced for a prolonged period of time in a non-immunoprivileged site. In the liver, for instance, the immune system could end up attacking the Cas9-making liver cells.

The danger of the immune system turning on a patients body hangs over a lot of research into correcting genes. In the late 1990s and 2000s, research into gene therapy was derailed by the death of 18-year-old Jesse Gelsinger, who died from an immune reaction to the virus used to deliver the corrected gene. This is the worst-case scenario that the CRISPR world hopes to avoid.

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Obstacle to Using CRISPR in Humans? The Immune System - The ...

Ever since 2012, when researchers first discovered that bacterial immune systems could be hijacked to edit DNA in living creatures, CRISPR has been hailed as a maker of revolutions. This was the year that prediction felt like it was starting to come true. U.S. scientists used the CRISPR gene editing technique to treat a common genetic heart disease in a human embryo. Many morediseases were successfully treated in mice using CRISPR. Hell, a particularly enthusiastic biohacker even spontaneously injected himself with muscle-growth genes while giving a talk at a conference.

But if 2017 was the year that the potential of CRISPR began to come into focus, 2018 may be the year that potential begins to be realized.

Next year, the first human trials of CRISPR-based treatments in the U.S. and Europe are slated to begin.

This month, biotech firm CRISPR Therapeutics became the first to submit a clinical trial application to European regulators. Tests are set to begin next year for its therapy that combines CRISPR gene editing and stem cell therapy to treat the blood disorder beta thalassemia. CEO Samarth Kulkarni told Gizmodo that the company also plans to file an application to conduct a clinical trial using a similar therapy to treat sickle cell disease in the first half of 2018. In 2018, the first human is going to get dosed with CRISPR in the clinic, Kulkarni told Gizmodo. And were going to be the first ones to do it.

Both disorders are genetic, caused by mutations to the genes that produce hemoglobin, a protein essential to ensuring that red blood cells ferry oxygen throughout the body. Without that oxygen, people can suffer from severe anemia, developmental delays, damage to organs, and pulmonary hypertension. The idea is extract stem cells from patients bone marrow and correct the faulty genes with CRISPR, a gene-editing technique that allows scientists to cut and paste tiny snippets of genetic code. Then those edited cells would be infused back into the body, where they would multiply, eventually outnumbering the diseased cells. Sickle cell disease and beta thalassemia are good candidates for CRISPR because in many cases, they are caused by a mutation to one single DNA letter.

At Stanford, a different spin on using CRISPR to treat sickle cell disease is also moving toward clinical trials. Matthew Porteus, who heads the research, said that his group expects to file a clinical trial application with the FDA by the end of 2018 and begin trials in 2019. Our New Years resolution for 2018 is to gather the data so we can file a [trial application] by the end of the year, so we can start a clinical trial in 2019, Porteus told Gizmodo. We just need to check off all the boxes.

Chinese scientists, meanwhile, used CRISPR for the first time on a human in 2016, and conducted a second human trial this year, setting off a biomedical duel between the U.S. and China and sparking concerns that the trials were irresponsibly premature. The first U.S. human CRISPR trial was slated to begin this summerat the University of Pennsylvania, after receiving a regulatory stamp of approval to proceed last year. It is unclear what has caused that trials delay.

Porteus said that he expects 2018 will bring many more preclinical studies demonstrating how CRISPR might be used to treat different diseases. In 2017, there were several such studies, addressing devastating diseases and conditions such as Huntingtons disease, Lou Gherigs disease, and an inherited form of hearing loss in mice.

There is going to be a lot of behind-the-scenes work of turning those into a real clinical protocol, Porteus said. He also predicted 2018 will see applications for more clinical trials, though most likely ones the involve simply deleting a problematic gene rather than correcting it.

George Church, the famed Harvard geneticist, told Gizmodo that he expects CRISPR will get much more precise in the coming year. He also expects an uptick in research on how to use CRISPR to solve problems that dont have other good solutions, like eliminating zoonotic diseases such as Lyme disease and malaria by using whats known as a gene drive to alter the DNA of wild species, or even growing transplantable organs in pigs.

The MIT synthetic biologist Kevin Esvelt said he expects there to be more gene therapy progress using a brand-new CRISPR technique that relies on base editing, or chemically altering a single letter of DNA rather than using CRISPR to actually cut through DNAs double helix to change it. The only prediction Im absolutely confident of making is that 2018 will see CRISPR continue to markedly accelerate research, both by simplifying previously difficult tasks and by making it possible to conduct experiments we could never previously contemplate, Esvelt said. Beyond that, theres no telling.

Hank Greely, a bioethicist at Stanford, told Gizmodo that he expects to see advancement with CRISPR outside of biomedicine. Among his predictions: Several groups will come up with completely new and unexpected uses for CRISPR, he said. And someone, somewhere will do a gene-drive trial in a controlled but non-laboratory environment.

Greely also predicts that CRISPR inventors will win a Nobel prize. (Though theres no telling which of CRISPRs inventorsits a bitterly disputed claim that award would go to.)

There are still significant hurdles, though, to reaching a future in which molecular cutting and pasting can act as a one-time cure-all for any genetic disease. For one, treating diseases that require editing DNA while its still inside the human body, such as amyotrophic lateral sclerosis,is a lot harder (and riskier) than removing cells, editing them in a lab, and putting them back into the body, as researchers will do in the trials slated to start in the next two years. But addressing many diseases will require whats known as in-vivo treatment. And scientists are still working to figure out the best way to deliver therapies inside the body effectively.

For ex-vivo treatments, the limit now is just whether we can do the work. I dont think there are obvious technical challenges. We just need to move into the clinic and test them out, Porteus said. For for in-vivo treatments, there is a lot of room for improvement.

Greely said that while some CRISPR clinical trials will start soon, they wont wrap up in 2018. Even when science is moving at a breakneck speed, like it is with CRISPR, it still tends to move more slowly than we wish it would.

And we may also realize that the high-tech solution is not always the best option.

Harvard geneticist Church said CRISPR may be due for a reality check. For example, he said, families may decide to undergo genetic counseling before having kids to assess their risk of passing on genetic diseases, rather than having children and treating them with CRISPR therapies likely to be $1 million per dose.

Whatever is in store for 2018, its important to remember that in the realm of science, progress is never a straight line.

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In 2018, We Will CRISPR Human Beings - gizmodo.com

In fewer than five years, the gene-editing technology known as Crispr has revolutionized the face and pace of modern biology. Since its ability to find, remove, and replace genetic material was first reported in 2012, scientists have published more than 5,000 papers mentioning Crispr. Biomedical researchers are embracing it to create better models of disease. And countless companies have spun up to commercialize new drugs, therapies, foods, chemicals, and materials based on the technology.

Usually, when weve referred to Crispr, weve really meant Crispr/Cas9a riboprotein complex composed of a short strand of RNA and an efficient DNA-cutting enzyme. It did for biology and medicine what the Model T did for manufacturing and transportation; democratizing access to a revolutionary technology and disrupting the status quo in the process. Crispr has already been used to treat cancer in humans, and it could be in clinical trials to cure genetic diseases like sickle cell anemia and beta thalassemia as soon as next year.

But like the Model T, Crispr Classic is somewhat clunky, unreliable, and a bit dangerous. It cant bind to just any place in the genome. It sometimes cuts in the wrong places. And it has no off-switch. If the Model T was prone to overheating, Crispr Classic is prone to overeating.

Even with these limitations, Crispr Classic will continue to be a workhorse for science in 2018 and beyond. But this year, newer, flashier gene editing tools began rolling off the production line, promising to outshine their first-generation cousin. So if you were just getting your head around Crispr, buckle up. Because gene-editing 2.0 is here.

Crisprs targeted cutting action is its defining feature. But when Cas9 slices through the two strands of an organisms DNA, the gene-editor introduces an element of risk. Cells can make mistakes when they repair such a drastic genetic injury. Which is why scientists have been designing ways to achieve the same effects in safer ways.

One approach is to mutate the Cas9 enzyme so it can still bind to DNA, but its scissors dont work. Then other proteinslike ones that activate gene expressioncan be combined with the crippled Cas9, letting them toggle genes on and off (sometimes with light or chemical signals) without altering the DNA sequence. This kind of epigenetic editing could be used to tackle conditions that arise from a constellation of genetic factors, as opposed to the straightforward single mutation-based disorders most well-suited to Crispr Classic. (Earlier this month, researchers at the Salk Institute used one such system to treat several diseases in mice, including diabetes, acute kidney disease, and muscular dystrophy.)

Other scientists at Harvard and the Broad Institute have been working on an even more daring tweak to the Crispr system: editing individual base pairs, one at a time. To do so, they had to design a brand-new enzymeone not found in naturethat could chemically convert an A-T nucleotide pairing to a G-C one. Its a small change with potentially huge implications. David Liu, the Harvard chemist whose lab did the work, estimates that about half of the 32,000 known pathogenic point mutations in humans could be fixed by that single swap.

I dont want the public to come away with the erroneous idea that we can change any piece of DNA to any other piece of DNA in any human or any animal or even any cell in a dish, says Liu. But even being where we are now comes with a lot of responsibility. The big question is how much more capable will this age get? And how quickly will we be able to translate these technological advances into benefits for society?"

Crispr evolved in bacteria as a primitive defense mechanism. Its job? To find enemy viral DNA and cut it up until there was none left. Its all accelerator, no brake, and that can make it dangerous, especially for clinical applications. The longer Crispr stays in a cell, the more chances it has to find something that sort of looks like its target gene and make a cut.

To minimize these off-target effects, scientists have been developing a number of new tools to more tightly control Crispr activity.

So far, researchers have identified 21 unique families of naturally occurring anti-Crispr proteinssmall molecules that turn off the gene-editor. But they only know how a handful of them work. Some bind directly to Cas9, preventing it from attaching to DNA. Others turn on enzymes that outjostle Cas9 for space on the genome. Right now, researchers at UC Berkeley, UCSF, Harvard, the Broad, and the University of Toronto are hard at work figuring out how to turn these natural off-switches into programmable toggles.

Beyond medical applications, these will be crucial for the continued development of gene drivesa gene-editing technology that quickly spreads a desired modification through a population. Being able to nudge evolution one way or the other would be a powerful tool for combating everything from disease to climate change. Theyre being considered for wiping out malaria-causing mosquitoes, and eradicating harmful invasive species. But out in the wild, they have the potential to spread out of control, with perhaps dire consequences. Just this year Darpa poured $65 million toward finding safer gene drive designs, including anti-Crispr off-switches.

Despite decades of advances, theres still so much scientists dont understand about how bugs in your DNA can cause human disease. Even if they know what genes are coded into a cells marching orders, its a lot harder to know where those orders get delivered, and how they get translated (or mistranslated) along the way. Which is why groups at Harvard and the Broad led by Crispr co-discoverer Feng Zhang are working with a new class of Cas enzymes that target RNA instead of DNA.

Since those are the instructions that a cells machinery reads to build proteins, they carry more information about the genetic underpinnings of specific diseases. And because RNA comes and goes, making changes to it would be useful for treating short-term problems like acute inflammation or wounds. The system, which theyre calling Repair, for RNA Editing for Programmable A to I Replacement, so far only works for one nucleotide conversion. The next step is to figure out how to do the other 11 possible combinations.

And scientists are finding new Cas enzymes all the time. Teams at the Broad have also been working to characterize cpf1a version of Cas that leaves sticky ends instead of blunt ones when it cuts DNA. In February, a group from UC Berkeley discovered CasY and CasX, the most compact Crispr systems yet. And researchers expect to turn up many more in the coming months and years.

Only time will tell if Crispr-Cas9 was the best of these, or merely the first that captured the imagination of a generation of scientists. We dont know whats going to wind up working best for different applications, says Megan Hochstrasser, who did her PhD in Crispr co-discoverer Jennifer Doudnas lab and now works at the Innovative Genomics Institute. So for now I think it makes sense for everyone to be pushing on all these tools all at once.

It will take many more years of work for this generation of gene-editors to find their way out of the lab into human patients, rows of vegetables, and disease-carrying pests. That is, if gene-editing 3.0 doesnt make them all obsolete first.

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Crispr Isnt Enough Any More. Get Ready for Gene Editing 2.0

For many people today, amyotrophic lateral sclerosis, aka ALS or Lou Gehrigs disease, is most commonly linked with both the fundraising Ice Bucket Challenge and one its most famous patients, the physicist Stephen Hawking. However, it could soon have a brand-new distinction the next disease to be treatable using CRISPR-Cas9 gene-editing technology.

In work carried out by researchers at University of California, Berkeley, scientists have been able to disable the defective genethat triggers ALS in mice. While they didnt get rid of the disease permanently, the treatment did extend the mices life span by 25 percent. The therapy delayed the onset of the muscle-wasting symptoms that characterize ALS, which ultimately become fatal when they spread to the muscles which control breathing.

Some diseases, like Lou Gehrigs disease, are caused by gene mutations that lead a protein in our cells to malfunction, David Schaffer, a professor of chemical and biomolecular engineering and director of the Berkeley Stem Cell Center, told Digital Trends. A very promising approach is to disable or delete that mutated gene. CRISPR/Cas9 is a highly promising technology to do so, but this capability needs to be delivered to the target cells. We put together CRISPR-Cas9 with a highly promising gene delivery, based on a virus, in order to disable the disease causing gene SOD1 in an animal model of ALS.

The mice in the study were genetically engineered to exhibit a mutated human gene that is responsible for around 20 percent of all inherited forms of ALS. The team then used a specially engineered virusthat deliversa gene encoding the Cas9 protein,which in turn disabled the mutant gene responsible for ALS. The treated mice lived one month longer than the typical four-month life span of mice with ALS. An average healthy mouse lives for around two years.

Hopefully, were this to be carried over to humans, those time spans would beextended.There are challenges that remain before extending into human studies, such as using an improved virus optimized for humans, but we think there is a clear path to doing so, Schaffer said.

A paper describing the work was recently published in the journal Science Advances.

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With CRISPR, geneticists have a powerful new weapon in the ...

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The CRISPR system uses a guide RNA (yellow) to direct the Cas9 enzyme (white) to a specific location in a cells DNA (blue) for cutting.

Credit: CRISPR Therapeutics

The gene editing technology CRISPR is one step closer to treating genetic diseases in humans. Last week, Crispr Therapeutics filed an application with European regulatory authorities to begin clinical trials for its CRISPR therapy CTX001 in a genetic blood condition called beta-thalassemia. The biotech firm expects to begin the trialthe first industry-sponsored study of a CRISPR drugnext year.

Samarth Kulkarni, CRISPR Therapeutics CEO

It is a momentous occasion for both our company and the field, says Samarth Kulkarni, CEO of Crispr Therapeutics. In early 2018, the firm will also ask the U.S. Food & Drug Administration for permission to use CTX001 to treat sickle cell disease. Vertex Pharmaceuticals today announced a 50-50 partnership with CRISPR Therapeutics to develop the drug in both beta-thalassemia and sickle cell.

Promising preclinical data presented at the American Society of Hematology (ASH) meeting in Atlanta this past weekend offered a glimpse of the strategies that Crispr Therapeutics and its many competitors are taking to treat the genetic blood diseases.

Since its conception in 2012, CRISPR has been swiftly adopted in research labs. By 2014, three biotech firms, each partly founded by one of the three inventors of CRISPR, had launched to transform the tool into a therapy. These three companies are now gearing up for their first-in-human studies, a breakneck pace for drug development.

CRISPR requires at least two basic components to edit genes: a guide RNA, which carries the code that specifies where to edit a genome, and an enzyme called Cas, which follows the guide RNA to make a cut in a cells DNA. Sometimes this cut is enough for a potential therapy. But to change the DNA or insert a new sequence, a third component, a template DNA, is required.

Both sickle cell disease and beta-thalassemia are caused by mutations in a gene that makes part of hemoglobin, the protein that carries oxygen throughout the blood. In sickle cell, the mutation causes normally donut-shaped red blood cells to warp into a crescent shape; the cells get stuck inside blood vessels, depriving tissues of oxygen. Beta-thalassemia is caused by mutations that prevent the production of fully functional hemoglobin, which for some people can cause severe anemia.

Instead of trying to fix the faulty DNA, Crispr Therapeutics and other companies are using the technology to reactivate a kind of hemoglobin found in infants. Everyone is born with high levels of a protein called fetal hemoglobin, which is mostly replaced with adult hemoglobin by three months of agethe same time that symptoms of sickle cell and beta-thalassemia appear. A gene called BCL11A represses the fetal hemoglobin production, but a rare genetic mutation in this gene is known to allow fetal hemoglobin production to continue.

Crispr Therapeutics lead drug candidate, CTX001, works by simply cutting BCL11A, basically removing the brakes on fetal hemoglobin production, Kulkarni says. On Sunday, the company presented results showing that its method edited over 90% of blood stem cells removed from patients with beta-thalassemia, dramatically increasing fetal hemoglobin in these cells.

Kulkarni says that extensive computer prediction, followed by cell and animal testing, has led them to a guide RNA in the CRISPR therapy that has no detectable off-target activitya potential side effect in which CRISPR accidently cuts the DNA in the wrong location. Stuart Orkin, a hematologist-oncologist at the Boston Childrens Hospital, says that off-target activity is one of the biggest safety concerns for gene editing in humans.

Crispr Therapeutics isnt the only company trying to increase fetal hemoglobin by targeting BCL11A. Intellia Therapeutics and Novartis have a partnership to do this with CRISPR. And Sangamo Therapeutics and Bioverativ are developing a similar therapy together using a different gene editing technology called zinc finger nucleases.

Meanwhile, Editas Medicine, another CRISPR company, presented an update at ASH on using its proprietary Cas enzyme, called Cpf1, to fix the mutation in the gene for adult hemoglobin. Charles Albright, chief scientific officer of Editas, says the company is simultaneously working on the fetal hemoglobin approach, but did not provide a timeline for when the sickle cell therapy would make it into clinical studies.

The hematology meeting also showcased many firms working on therapies for sickle cell and beta-thalassemia that dont require gene editing. Bluebird Bio, a gene therapy company, has ongoing clinical trials for both conditions using a virus to deliver a healthy copy of the hemoglobin gene into cells. Drug companies are also trying to treat sickle cell with small molecule drugs. Global Blood Therapeutics compound voxelotor, which increases hemoglobins ability to bind oxygen, is in Phase II and III clinical trials currently. And Epizyme is developing an inhibitor of an enzyme called histone methyltransferase, which could be another way to release the brakes on fetal hemoglobin production.

Everyone is working on these diseases because we know exactly what to do, and there are multiple different ways to get to the same end, a treatment, Orkin says. We dont know yet which program will be the bestBut the first one that is shown to be very effective and safe, could crowd out the others.

As it prepares to launch its first trial, Crispr Therapeutics has secured a contract manufacturer in Europe which will receive patient blood cells, edit them, and then ship them back to the clinical trial sites. Patients will then undergo chemotherapy or irradiation in preparation for their edited blood stem cells to be transplanted into the bone marrow, where they will hopefully produce healthier blood cells for life.

It is important that they do this very carefully, Orkin says. Because if there is a mistake or bad effect [from CRISPR], it will have repercussions beyond a single patient.

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CRISPR gene editing is coming to the clinic | Chemical ...

1987: CRISPR repeats were observed in bacterial genomes. The authors concluded, no sequence homologous to these has been found elsewhere in procaryotes, and the biological significance of these sequences is not known. Ishino et al. J. Bacteriology (1987) 169:5429-5433. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC213968/

2002: The term CRISPR was coined to describe the repetitive repeats observed in bacterial and archaeal genomes. Genes usually found associated with the CRISPR repeats were identified and named CRISPR Associated Proteins or Cas. Jansen et al. Mol. Microbiology. (2002) 43:1565-1575. http://www.ncbi.nlm.nih.gov/pubmed/11952905

2005: CRISPR spacer sequences were matched to foreign DNA. Bolotin et al. Microbiology (2005) 151:2551-2561. http://www.ncbi.nlm.nih.gov/pubmed/16079334

2006: CRISPR was first proposed to be a bacterial adaptive immune system. Makarova et al. Biol Direct (2006) 1:7. http://www.ncbi.nlm.nih.gov/pubmed/16545108.

2007: CRISPR loci were found to impart phage resistance in bacteria. It was determined that CRISPR sequences together with the Cas genes impart resistance and that resistance to specific phages was determined by the spacer sequences found between CRISPR repeats. Barrangou et al. Science. (2007) 315:1709-1712. http://www.ncbi.nlm.nih.gov/pubmed/17379808

2009: RNA guided RNA cleavage is first described. Hale et al. RNA (2008) 2:2572-2579. http://www.ncbi.nlm.nih.gov/pubmed/18971321

2010: The CRISPR/Cas system was identified as a bacterial and archeal immune system that targets and cleaves phage DNA. This system was found to be dependent on the bacteria containing CRISPR spacer sequences that match the phage DNA. Additionally researchers discovered that new spacer sequences could be inserted into the bacterial/archeal chromosome making the CRISPR/Cas system an adaptive immune system. Garneau et al. Nature. (2010) 468:67-71. http://www.ncbi.nlm.nih.gov/pubmed/21048762

2011: Cas9 from Streptococcus pyogenes was found to associate with two RNA molecules coined crRNA and tracrRNA and that all these components are required for protection against phage infection. Deltcheva et al. Nature (2011) 471:602-607. http://www.ncbi.nlm.nih.gov/pubmed/21455174

2012: Cas9 was found to be an endonuclease capable of introducing DSB in DNA and that this process is dependent on complementary binding of the crRNA to the target DNA. Two nuclease domains were found in Cas9 with the HNH domain cleaving the complementary strand and the RuvC-like domain cutting the non-complementary strand. Jinek et al. Science (2012) 337:816-821. http://www.ncbi.nlm.nih.gov/pubmed/22745249

2013: The CRISPR/Cas9 system was used to edit targeted genes in both human and mouse cells using designed crRNA sequences. Cong et al. Science (2013) 339:819-823. http://www.ncbi.nlm.nih.gov/pubmed/23287718

First use in plants. Li et al. Nat Biotechnol (2013) 8:688-691. http://www.ncbi.nlm.nih.gov/pubmed/23929339

Also first use in plants ? Nekrasov et al. Nat Biotechnol (2013) 8:691-693. http://www.ncbi.nlm.nih.gov/pubmed/23929340.

2014: The crystal structure of Cas9 complexed with both gRNA and targeted DNA was elucidated. Nishimasu et al. Cell (2014) 156:935-949. http://www.ncbi.nlm.nih.gov/pubmed/24529477

PAMs are identified as a key component of DNA target integration. Anders et al. Nature (2014) 513:569-573. http://www.ncbi.nlm.nih.gov/pubmed/25079318

sgRNA and Cas9 are directly delivered into cells without the use of a vector intermediate. Ramakrishna et al. Genome Res (2014) 24:1020-1027. http://www.ncbi.nlm.nih.gov/pubmed/24696462

2015: CRISPR/Cas9 was used to edit tri-chromosomal pre-implantation human embryos. Researchers attempted to repair the HBB locuswhich, when mutated, results in -thalassemia blood disorders. The researchers were unable to effectively repair the mutated locus and many off-target cleavages were observed. Liang et al. Protein and Cell (2015) 6:363-372. http://www.ncbi.nlm.nih.gov/pubmed/25894090

2015: An international moratorium is called for making heritable changes to the human genome using gene editing.At an international meeting convened by the National Academy of Science of the United States, the Institute of Medicine, The Chinese Academy of Sciences, and the Royal Society of London scientists called for a moratorium on making inheritable changes to the human genome. None of these groups have regulatory authority to prevent such research from taking place, however previous moratoriums where widely accepted in 1975 when an international group met in California to discuss gene editing in all species.http://www.nytimes.com/2015/12/04/science/crispr-cas9-human-genome-editing-moratorium.html?_r=0

2016: The USDA determines CRISPR/Cas9 edited crops will not be regulated as GMOs. Due to the lack of foreign DNA and the inability to distinguish CRISPR modified crops from those created by traditional plant breeding the USDA has determined that gene edited crops will not be regulated like traditional GMOs.http://www.nature.com/news/gene-edited-crispr-mushroom-escapes-us-regulation-1.19754

2016: The first human trial to use CRISPR gene editing gets approval from the NIH. A National Institute of Health advisory committee approved the use of CRISPR/Cas9 gene editing in a cancer therapy trial. The treatment will use CRISPR/Cas9 technology to edit the patients own T cells to target cancer.http://www.nature.com/news/first-crispr-clinical-trial-gets-green-light-from-us-panel-1.20137

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CRISPR Timeline CRISPR Update

The CRISPR-Cas9 gene editing tool shows incredible promise in treating a wide range of diseases, from HIV to cancer. But the technology isn't without controversy, as the long term effects of cutting DNA in living organisms isn't fully known. Now, scientists from the Salk Institute have modified CRISPR to work without making any cuts, switching targeted genes on and off instead, and demonstrated its effectiveness by treating diabetes, muscular dystrophy and other diseases in mice.

The CRISPR gene-editing tool is one of the most important scientific breakthroughs in years, with the potential to reverse the effects of disease or even snip them out of the genome at the embryo stage. But as exciting as it is, a recent study found that the cut-and-paste method may introduce unintentional mutations into the genome, and although this study was later contested, safety remains a concern at this early stage in the technology.

"Although many studies have demonstrated that CRISPR-Cas9 can be applied as a powerful tool for gene therapy, there are growing concerns regarding unwanted mutations generated by the double-strand breaks through this technology," says Juan Carlos Izpisua Belmonte, senior author of the study. "We were able to get around that concern."

The Salk scientists adapted the regular CRISPR mechanism to influence gene activation without actually changing the DNA itself. The Cas9 enzyme normally does the cutting, so the team used a dead form of it called dCas9 that can still target genes but doesn't damage them. The active ingredients this time are transcriptional activation domains, which act like molecular switches to turn specific genes on or off. These are coupled to the dCas9, along with the usual guide RNAs that help them locate the desired section of DNA.

There's just one problem with this technique: normally the CRISPR system is loaded into a harmless virus called an adeno-associated virus (AAV), which carries the tool to the target. But the entire protein, consisting of dCas9, the switches and the guide RNAs, is too big to fit inside one of these AAVs. To work around that issue, the researchers split the protein into two, loading dCas9 into one virus and the switches and guide RNAs into another. The guide RNAs were tweaked to make sure both parts still ended up at the target together, and to make sure the gene was strongly activated.

To test how well the new technique worked, the researchers experimented with mice that had three different diseases kidney damage, type 1 diabetes and muscular dystrophy. In each case, the mice were treated with specialized CRISPR systems to increase the expression of certain genes, which would hopefully reverse the symptoms.

In the kidney-damaged mice, the team targeted two genes that play a role in kidney function. Sure enough, there was an increase in the levels of a protein linked to those genes, and kidney function improved. In the diabetic mice, the targeted genes were those that promote the growth of insulin-producing cells, and after treatment, the mice were found to have lower blood glucose levels. And finally, the treatment also worked to reverse the symptoms of muscular dystrophy.

After that promising start, further work is underway on the system. The researchers plan to try to apply the technique to other cell types to help treat other diseases, and conduct more safety tests before human trials can begin.

The research was published in the journal Cell.

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CRISPR breakthrough treats diseases like diabetes without ...

C

RISPR-Cas9 is complicated.

Thats why scientists, entrepreneurs, and journalists like me have spent the past few years reaching for metaphors to try to make the mechanics of the revolutionary genome-editing technology easier for laypeople to understand. In text and imagery, weve drawn parallels to everything from garage tools to divine interventions.

But it must be said: Some of these analogies are better than others. To compile the definitive ranking, I sat down with STATs senior science writer Sharon Begley, a wordsmith who has herself compared CRISPR to 1,000 monkeys editing a Word document and the kind of dog you can train to retrieve everything from Frisbees to slippers to a cold beer.

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Sharon and I evaluated each of the metaphors we found by considering these three questions: Is it creative? Is it clear? And is it accurate? Below, our rankings of CRISPR analogies, ordered from worst to best:

This is not how it works. This is not at all how it works.

We see where these marketers got started with their pun: Genetics researchers do indeed use the term knock out to refer to eliminating an existing gene in, say, a mouse.

But a blunt instrument like a boxing glove vastly undersells CRISPRs precision. It also suggests, wrongly, that CRISPRs powers extend to leaving genes bruised and battered. For these reasons, this ad wins the ignoble prize as the worst CRISPR metaphor we could track down.

The hand of God is a familiar trope to describe advances in biotech. Elucidating CRISPR this way is sinful.

If God were in the business of editing the genome, we expect that She would make fewer mistakes than CRISPR, which is known foroff-target effects. Were wondering, too, if the holy light emanating from the hand of a CRISPR-ing God is meant to imply that She is among those researchers interested in combining CRISPR with optogenetics?

Most damningly, though, this metaphor does nothing to explain how CRISPR actually works.

The framing of CRISPR as a method to remove ticking time bombs lurking within our DNA is true enough: Researchers do want to use the technology to take out genetic mutations that cause deadly diseases.

But this visual metaphor confuses the biology. The destructive power in DNA lies in the base pairs themselves, not in between them, where this red canister is placed. And again, this does nothing to shine light on CRISPRs mechanism of action.

We had high hopes for this analogy, which came courtesy of the National Institutes of Health. But alas, it mostly disappoints.

The idea, as we understand it, is that CRISPR-Cas9 acts to modify precisely the correct segments of DNA, similar to how a handyman uses a particular wrench to loosen or tighten a nut or bolt of a specific size and shape.

But were scratching our heads to come up with a real-life construction scenario where whats visualized here would actually happen.We get the sense that someone in pursuit of a fresh analogy came up with this one only after concluding that all the good analogies were already taken.

This analogy is so 2012. Sure, an eraser is a fine way to think about CRISPRs powers to delete. But that only goes halfway what about CRISPRs powers to add or replace? And it loses the physicality of CRISPR-Cas9s cutting action for no good reason. (In the interests of full disclosure, we must admit that STAT has used this one in the past. Apologies.)

The notion of CRISPR as a surgeons scalpel nicely captures its cutting action. But points are deducted for the suggestion that CRISPR is as precise as a surgeons tool must be.

We like the simple explanatory power of a plain-old pair of scissors to describe CRISPR-Cas9s cutting action. Its better than the scalpel metaphor at conveying the technology isablunt instrument. But points are deducted for not addressing CRISPRs powers to add or replace.

This analogy comes by way ofthe authority:Feng Zheng, the groundbreaking Massachusetts Institute of Technology scientist who helped create CRISPR-Cas9.

Zhengs comparison is a good one overall especially when he explains how it works with the song Twinkle Twinkle Little Star. But its still an imperfect one, because it implies greater precision than CRISPR actually allows.

To continue the analogy: If you use CRISPR to search for the and replace it with this, it would work as intended sometimes. But because CRISPR sometimes finds something it shouldnt, you might also wind up with jumbled words describing the study of the divine as thisology and a book of synonyms as athissaurus.

We really like this comparison, exemplified bywriter Aime Lutkins turn of phrase describing CRISPR assort of like organic matter Photoshop.

To be sure, youre not literally cutting anything, as CRISPR-Cas9 does, when you use the Adobe image editing software. But we saw explanatory power in the fact that Photoshop lets you make zoomed-in changes, down to the level of a single pixel just as CRISPR can make changes at the level of the As, Ts, Cs, and Gs that make up the genetic code.

And as anyone whos been victim of a bad Photoshop job knows, theres plenty of room for the tool to go awry.

Folks, we have a winner: A Swiss Army knife is the best analogy we found for what CRISPR can and cant do.

Like the other cutting instruments on our list, a Swiss Army knife gets points as a good visual because CRISPR-Cas9 literally cuts DNA. But a Swiss Army knife breaks out of the pack because it has different blades for different tasks comparable to CRISPRs ability to cut something out, introduce a single one-letter change, or make an insertion without a deletion. Swiss Army knives also strike the right middle ground between a precise cut and a blunt cut, a good way to think about CRISPRs capabilities.

And if thats not enough: Both CRISPR and Swiss Army knives have recently been at the center of heated legalfights over intellectual property.

Business Reporter

Rebecca covers the business of biopharma.

Originally posted here:
The best and worst analogies for CRISPR, ranked

In the last five years, biology has undergone a seismic shift as researchers around the globe have embraced a revolutionary technology called gene editing. It involves the precise cutting and pasting of DNA by specialized proteinsinspired by nature, engineered by researchers. These proteins come in three varieties, all known by their somewhat clumsy acronyms: ZFNs, TALENs, and CRISPRs. But its Crispr, with its elegant design and simple cell delivery, thats most captured the imagination of scientists. Theyre now using it to treat genetic diseases, grow climate-resilient crops, and develop designer materials, foods, and drugs.

So how does it work?

When people refer to Crispr, they're probably talking about Crispr-Cas9, a complex of enzymes and genetic guides that together finds and edits DNA. But Crispr on its own just stands for Clustered Regularly Interspaced Palindromic Repeatschunks of regularly recurring bits of DNA that arose as an ancient bacterial defense system against viral invasions.

Viruses work by taking over a cell, using its machinery to replicate until it bursts. So certain bacteria evolved a way to fight back. They deployed waves of DNA-cutting proteins to chop up any viral genes floating around. If the bacteria survived the attacks, they'd incorporate tiny snippets of virus DNA into their own genomeslike a mug shot of every foe theyd ever come across, so they could spot each one quicker in the future. To keep their genetic memory palace in order, they spaced out each bit of viral code (so-called guide RNAs) with those repetitive, palindromic sequences in between. It doesn't really matter that they read the same forward and backward; the important thing is that they helped file away genetic code from viral invaders past, far away from more essential genes.

And having them on file meant that the next time a virus returned, the bacteria could send out a more powerful weapon. They could equip Cas9a lumpy, clam-shaped DNA-cutting proteinwith a copy of that guide RNA, pulled straight out of storage. Like a molecular assassin, it would go out and snip anything that matched the genetic mug shot.

Thats what happens in the wild. But in the lab, scientists have harnessed this powerful Crispr system to do things other than fight off the flu. The first step is designing a guide RNA that can sniff out a particular block of code in any living cellsay, a genetic defect, or an undesirable plant trait. If that gene consists of a string of the bases A, A, T, G, C, scientists make a complementary strand of RNA: U, U, A, C, G. Then they inject this short sequence of RNA, along with Cas9, into the cell theyre trying to edit. The guide RNA forms a complex with Cas9; one end of the RNA forms a hairpin curve that keeps it stuck in the protein, while the other endthe business enddangles out to interact with any DNA it comes across.

Once in the cell's nucleus, the Crispr-Cas9 complex bumps along the genome, attaching every time it comes across a small sequence called PAM. This protospacer adjacent motif is just a few base pairs, but Cas9 needs it to grab onto the DNA. And by grabbing it, the protein is able to destabilize the adjacent sequence, unzipping just a little bit of the double helix. That allows the guide RNA to slip in and sniff around to see if it's a match. If not, they move on. But if every base pair lines up to the target sequence, the guide RNA triggers Cas9 to produce two pincer-like appendages, which cut the DNA in two.

The process can stop there, and simply take a gene out of commission. Or, scientists can add a bit of replacement DNAto repair a gene instead of knocking it out.

And they don't have to limit themselves to just Cas9. There's a whole bunch of proteins that can use an RNA guide. There's Cas3, which gobbles up DNA Pac-Man style. Scientists are using it to develop targeted antibiotics that can wipe out a strain of C. diff, while leaving your gut microbiome intact. And there's an enzyme called Cas13 that works with a guide that gloms onto RNA, not DNA. Called Sherlock, the system is being used to develop sensitive tests for viral infections. Researchers are working hard to add more implements to the Crispr toolkit, but at least right now, Cas9 is still the most widely used.

Crispr isnt perfect; sometimes the protein veers off course and makes cuts at unintended sites. So scientists are actively working on ways to minimize these off-target effects. And as it gets better, the ethical questions surrounding the technology are going to get a lot thornier. Hello, designer babies?! Figuring out where those lines get drawn is going to take more than science; it will require policymakers and the public coming to the table. Because pretty soon with Crispr, the question wont be can we do it, but should we?

Excerpt from:
How Does Crispr Gene Editing Work? | WIRED

The debate about Johnny Depps casting as Grindelwald in the Fantastic Beasts and Where To Find Them franchise rages on. A quick recap: Depp was cast as Grindelwald a few years ago, but it was kept under wraps, as his casting was part of a big twist at the end of the first film.

But last summer, just before Fantastic Beasts was released, Amber Heard, his now ex-wife, accused Depp of domestic abuse. Videos of Depp throwing bottles and glasses and shouting at Heard, photos of Heards bruises, and text exchanges between Heard and Depps manager, all made their way into the press. The couple later released a joint statement saying neither party had lied for financial gain and that there wasnever any intent of physical or emotional harm.

The latest developments come as the press for the second Fantastic Beasts film, The Crimes of Grindelwald kicks into gear. The title, and images of Depp in character, reignited a debate over whether someone accused of domestic abuse should be given such a high-profile role, especially in a progressive childrens franchise. Depp has continuously denied all allegations since the divorce as salacious false stories.

On Tuesday, in an interview with Entertainment Weekly, Fantastic Beasts director David Yates explicitly defended Depps character, calling the concerns of audiences a dead issue. Yates attempted to positively contrast the allegations against Depps with those made against Harvey Weinstein and Kevin Spacey.

Honestly, theres an issue at the moment where theres a lot of people being accused of things, he said.[But] with Johnny, it seems to me there was one person who took a pop at him and claimed something.

Its very different [to instances] where there are multiple accusers over many years that need to be examined and we need to reflect on our industry that allows that to roll on year in and year out. Johnny isnt in that category in any shape or form. So to me, it doesnt bear any more analysis. It's a dead issue.

Yates also seemed to find it relevant that hehas had no direct experience of Depp being abusive towards him. He added: I can only tell you about the man I see every day: Hes full of decency and kindness, and thats all I see. Whatever accusation was out there doesnt tally with the kind of human being Ive been working with.

Its an interesting departure from Yatess previous take on the issue, which emphasised Depps talent over his private actions, separating art from artist. The whole principal of casting the movie was go with the best actor, he said last year. In this business, its a weird old business. Youre brilliant one week, people are saying odd things the next, you go up and down. But no one takes away your pure talent. Johnny Depp is a real artist.

Its possible that after the widely commended decisions from studios and directors to have both Harvey Wenstein and Kevin Spacey removed from their cinematic projects, Yates has felt the need to change tack. Instead of saying that the personal actions of an actor are irrelevant to their professional roles an argument that Hollywood and the public seem to have moved beyond he tries to separate Depp from those men by emphasising the differences in the actions themselves.

In 2016, J K Rowling simply said of Depps casting,Im delighted. Hes done incredible things with that character, again ensuring the focus stayed solely on talent rather than Depps character as a colleague or friend.

Those comments cause some controversy, and in the days after, she tweeted a couple of cryptic quotes seemingly referencing the situation. First, Those only who can bear the truth will hear it. - Arthur Helps. Then, Arguments cannot be answered by personal abuse; there is no logic in slander, and falsehood, in the long run, defeats itself - R G Ingersoll. When a fan messaged her to say, We know you'd never support abuse, Rowling, whose first husband Jorge Arantes has admitted to acting abusively,replied Thank you x. Its impossible to say from these quotes what her position actually is. Is the truth she references a belief that Depp is not really an abuser? Or is she hinting that she would like to re-cast the role, or condemn Depps casting, but is contractually unable to?

Since then, shes been silent on the issue. Although Rowlings actual thoughts on the situation are unclear, supporters of Depp see these cryptic tweets, the casting, and her general lack of condemnation of Depp, as evidence that she supports him. If you look up the hashtags #JohnnyDeppIsInnocent and #JohnnyDeppIsMyGrindelwald, J K Rowling immediately appears as a related person and related search term, as so many Depp supporters are mentioning the two in the same breath either thanking J K Rowling for her support, or using her name to argue that Depp must be innocent if even J K Rowling herself thinks so. Some have even used the hashtag #JohnnyDeppIsJKRowlingsGrindelwald.

Domestic violence is by nature a more difficult crime to discuss that serial instances of documented workplace sexual harassment it happens at home, with few or no witness, to people in complex existing romantic relationships.

In Amber Heards own words, When it happens in your home, behind closed doors, with someone you love, its not as straightforward as if a stranger did this. Clearly, Hollywood still finds allegations of domestic violence easier to swallow than workplace harassment.

See the article here:
CRISPR: can gene-editing help nature cope with climate change?

Genome editing (also called gene editing) is a group of technologies that give scientists the ability to change an organism's DNA. These technologies allow genetic material to be added, removed, or altered at particular locations in the genome. Several approaches to genome editing have been developed. A recent one is known as CRISPR-Cas9, which is short for clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9. The CRISPR-Cas9 system has generated a lot of excitement in the scientific community because it is faster, cheaper, more accurate, and more efficient than other existing genome editing methods.

CRISPR-Cas9 was adapted from a naturally occurring genome editing system in bacteria. The bacteria capture snippets of DNA from invading viruses and use them to create DNA segments known as CRISPR arrays. The CRISPR arrays allow the bacteria to "remember" the viruses (or closely related ones). If the viruses attack again, the bacteria produce RNA segments from the CRISPR arrays to target the viruses' DNA. The bacteria then use Cas9 or a similar enzyme to cut the DNA apart, which disables the virus.

The CRISPR-Cas9 system works similarly in the lab. Researchers create a small piece of RNA with a short"guide" sequence that attaches (binds) to a specific target sequence of DNA in a genome. The RNA also binds to the Cas9 enzyme. As in bacteria, the modified RNA is used to recognize the DNA sequence, and the Cas9 enzyme cuts the DNA at the targeted location. Although Cas9 is the enzyme that is used most often, other enzymes (for example Cpf1) can also be used. Once the DNA is cut, researchers use the cell's own DNA repair machinery to add or delete pieces of genetic material, or to make changes to the DNA by replacing an existing segment with a customized DNA sequence.

Genome editing is of great interest in the prevention and treatment of human diseases. Currently, most research on genome editing is done to understand diseases using cells and animal models. Scientists are still working to determine whether this approach is safe and effective for use in people. It is being explored in research on a wide variety of diseases, including single-gene disorders such as cystic fibrosis, hemophilia, and sickle cell disease. It also holds promise for the treatment and prevention of more complex diseases, such as cancer, heart disease, mental illness, and human immunodeficiency virus (HIV) infection.

Ethical concerns arise when genome editing, using technologies such as CRISPR-Cas9, is used to alter human genomes. Most of the changes introduced with genome editing are limited to somatic cells, which are cells other than egg and sperm cells. These changes affect only certain tissues and are not passed from one generation to the next. However, changes made to genes in egg or sperm cells (germline cells) or in the genes of an embryo could be passed to future generations. Germline cell and embryo genome editing bring up a number of ethical challenges, including whether it would be permissible to use this technology to enhance normal human traits (such as height or intelligence). Based on concerns about ethics and safety, germline cell and embryo genome editing are currently illegal in many countries.

Gupta RM, Musunuru K. Expanding the genetic editing tool kit: ZFNs, TALENs, and CRISPR-Cas9. J Clin Invest. 2014 Oct;124(10):4154-61. doi: 10.1172/JCI72992. Epub 2014 Oct 1. Review. PubMed: 25271723. Free full-text available from PubMed Central: PMC4191047.

Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell. 2014 Jun 5;157(6):1262-78. doi:10.1016/j.cell.2014.05.010. Review. PubMed: 24906146. Free full-text available from PubMed Central: PMC4343198.

Komor AC, Badran AH, Liu DR. CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes. Cell. 2017 Apr 20;169(3):559. doi:10.1016/j.cell.2017.04.005. PubMed: 28431253.

Lander ES. The Heroes of CRISPR. Cell. 2016 Jan 14;164(1-2):18-28. doi:10.1016/j.cell.2015.12.041. Review. PubMed: 26771483.

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What are genome editing and CRISPR-Cas9?

Designer babies, the end of diseases, genetically modified humans that never age. Outrageous things that used to be science fiction are suddenly becoming reality. The only thing we know for sure is that things will change irreversibly.

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SOURCES AND FURTHER READING:

The best book we read about the topic: GMO Sapiens

https://goo.gl/NxFmk8

(affiliate link, we get a cut if buy the book!)

Good Overview by Wired:http://bit.ly/1DuM4zq

timeline of computer development:http://bit.ly/1VtiJ0N

Selective breeding: http://bit.ly/29GaPVS

DNA:http://bit.ly/1rQs8Yk

Radiation research:http://bit.ly/2ad6wT1

inserting DNA snippets into organisms:http://bit.ly/2apyqbj

First genetically modified animal:http://bit.ly/2abkfYO

First GM patent:http://bit.ly/2a5cCox

chemicals produced by GMOs:http://bit.ly/29UvTbhhttp://bit.ly/2abeHwUhttp://bit.ly/2a86sBy

Flavr Savr Tomato:http://bit.ly/29YPVwN

First Human Engineering:http://bit.ly/29ZTfsf

glowing fish:http://bit.ly/29UwuJU

CRISPR:http://go.nature.com/24Nhykm

HIV cut from cells and rats with CRISPR:http://go.nature.com/1RwR1xIhttp://ti.me/1TlADSi

first human CRISPR trials fighting cancer:http://go.nature.com/28PW40r

first human CRISPR trial approved by Chinese for August 2016:http://go.nature.com/29RYNnK

genetic diseases:http://go.nature.com/2a8f7ny

pregnancies with Down Syndrome terminated:http://bit.ly/2acVyvg( 1999 European study)

CRISPR and aging:http://bit.ly/2a3NYAVhttp://bit.ly/SuomTyhttp://go.nature.com/29WpDj1http://ti.me/1R7Vus9

Help us caption & translate this video!

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CRISPR - youtube.com

The acronyms might not be quite as catchy as CRISPR, but what new genetic tools dubbed REPAIR and ABE lack in whimsy they promise to make up in utility. These advances, unveiled last week, solve two of the problems hobbling CRISPR, the revolutionary genome-editing technique: that its idea of editing is often like 1,000 monkeys editing a Word document, and that making permanent changes to DNA might not be the best approach.

Together, the discoveries, described in separate studies, show that five years after scientists demonstrated that CRISPR can edit DNA, bioengineers are still racing to develop the most efficient, precise, versatile and therefore lucrative genome-editing tools possible.

One reason these are so exciting is, they show the CRISPR toolbox is still growing, said chemical engineer Gene Yeo of the University of California San Diego. There are going to be a lot more, and its not going to stop anytime soon. His lab has been working on one of the CRISPR advances but was not involved in either of the two new studies; its personally frustrating to get beaten, he added.

One discovery, led by biochemist David Liu of Harvard University, extends his 2016 invention of a way to change a single DNA letter, or base, on the 3-billion-letter-long human genome. Classic CRISPR cuts DNA with a molecular scissors and leaves the cell to repair the breach willy-nilly, introducing the problem of 1,000 monkeys editing away. In contrast, Lius base editor replaces the molecular scissors with something like a pencil wielded by an expert forger: It is an enzyme that literally rearranges atoms, cleanly and without collateral damage that the cell needs to fix.

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As in classic CRISPR, this version finds its way to a target on the genome via a molecule that acts like a bloodhound. Attached to the bloodhound is the atom-rearranger, which in Lius 2016 version turned the DNA letter G into A. Thousands of genetic diseases arise because a gene has a G where it should have an A, so the edit might one day treat or prevent them.

But other inherited disorders need different alphabetical magic. Thats what Liu, postdoctoral fellows Nicole Gaudelli and Alexis Komor, and their colleagues report in a paper in Nature: Their new ABE (adenine base editor) can turn A into G. Attached to CRISPRs bloodhound molecule, ABE works at virtually any target site in genomic DNA, Liu said.

In tests so far, it changed DNA in more of the lab-grown human cells that it was slipped into than standard CRISPR.

About half of the 32,000 known disease-causing, single-letter mutations have one of the misspellings that ABE can fix, Liu said. They include sickle cell, Tay-Sachs, and cystic fibrosis, raising hopes that ABE could be used to treat these diseases, or (in early embryos) prevent them. In tests of cells growing in lab dishes, ABE reversed the mutation that causes hereditary hemochromatosis in about 30 percent of the cells, and changed another gene into a form that prevents sickle cell disease even in people who have its disease-causing mutation.

As with all forms of CRISPR, before ABE helps any patients, scientists will have to test whether its safe and effective. But having the molecular machine is a good start, said Liu, a cofounder of the CRISPR company Editas Medicine Inc., based in Cambridge. He and his colleagues have filed for patents on ABE.

Harvard biologist George Church, who tied for first in the race to make CRISPR work in human cells, called base editing especially interesting. Changing a single DNA letter, he said, means fewer worries about the editing enzyme [in classic CRISPR] later going rogue or silent. He also expects that crops with a single base change will not be designated as transgenic, reducing regulatory barriers to commercialization.

In a separate study, CRISPR pioneer Feng Zhang of Cambridges Broad Institute discovered along with his colleagues a new version of CRISPR that can edit RNA, DNAs friskier cousin. While DNA mostly sits sedately in cells and issues orders to make proteins that keep life living, RNA zips around the cell carrying out those orders, and then disappears. That makes RNA a tantalizing target: By editing the errant orders (RNA) rather than their issuer (DNA), scientists might be able to make temporary, reversible genetic edits, rather than CRISPRs permanent ones.

Editing DNA is hard to reverse, but once you stop providing the RNA-editing system, the changes will disappear over time, said Zhang, also a cofounder of Editas. That might make it possible to treat conditions where you dont need a permanent edit, such as when the immune system is in overdrive and causing inflammation.

To create what Zhang and his colleagues call REPAIR (RNA editing for programmable A to I [G] replacement), they fused an enzyme that binds to RNA with one that changes the RNA letter A (adenosine) to inosine, a molecule similar to the RNA letter G (guanosine), they report in Science.

In tests on human cells growing in the lab, REPAIR corrected misspellings in the RNA that was made by disease-causing DNA in this case, Fanconi anemia, an inherited and devastating bone marrow disease, or nephrogenic diabetes insipidus, a serious inborn kidney disease.

The furious race to improve CRISPR, via ABE or REPAIR or whatever comes next, Church said, is a reminder of how far CRISPR is from precise genome-editing in humans.

Excerpt from:
CRISPR gene editing gets new tools, and acronyms

Scientists have used a popular gene editing tool called CRISPR to snip out a tiny piece of DNA from one particular gene in a white button mushroom. The resulting mushroom doesn't brown when cut. Adam Fagen/Flickr hide caption

Scientists have used a popular gene editing tool called CRISPR to snip out a tiny piece of DNA from one particular gene in a white button mushroom. The resulting mushroom doesn't brown when cut.

There's a genetic technology that scientists are eager to apply to food, touting its possibilities for things like mushrooms that don't brown and pigs that are resistant to deadly diseases.

And food industry groups, still reeling from widespread protests against genetically engineered corn and soybeans (aka GMOs) that have made it difficult to get genetically engineered food to grocery store shelves, are looking to influence public opinion.

The technology is called Clustered Regularly Interspaced Short Palindromic Repeats, or CRISPR. It's a technique that Alison Van Eenennaam, an animal genetics professor at University of California, Davis, says can de-activate a gene. Or, as she puts it: "It's editing. It's like going into a Word document and basically replacing one letter, maybe that instead of 'wind,' you want it to say 'wine,' " she says.

Skeptics, like Dana Perls with the environmental group Friends of the Earth, say food companies are trying to distance themselves from terms like GMO and genetic engineering that have caused them trouble with consumers.

"These new gene editing technologies like CRISPR are genetic engineering. And if this is genetic engineering, then call it that," says Perls. She says these producers are just trying to pull the wool over consumers' eyes with a strong public relations push.

Dozens of crops and livestock developed with CRISPR technology are years from the market, though the U.S. Department of Agriculture already said it won't regulate CRISPR-developed products like other genetically engineered food, since no foreign genetic material is introduced in the process. The Food and Drug Administration will decide which new products are safe.

To get ahead of any criticism, a group of heavyweights in the food industry have joined forces to form the Coalition for Responsible Gene Editing in Agriculture, which is funded by members like the U.S. Pork Board, Monsanto, Syngenta and Bayer.

The board's CEO, Bill Even, says the food industry missed a chance to do this when the earlier wave of genetically engineered food made it to the market.

"There was never any conversation with consumers around what is this and what did it mean," he says. "Fast forward now today, there's a lot of debate around GMOs and food. The public rightly [is] ... interested in knowing what's in their food."

People don't often trust big companies, says Charlie Arnot, who leads the coalition and is the CEO of the Center for Food Integrity. But when it comes to CRISPR, there are three key strategies Arnot says will help get consumers on board.

First: CRISPR is not a secret.

"Those in technology have to be more transparent and be much more engaged in a public conversation and dialogue, in order to answer those questions, address the skepticism and ultimately result in earning consumer trust in what they're doing in gene editing," he says.

Second, the coalition wants to show that it shares the same values that shoppers do. So, its members are sponsoring and attending events like CRISPRcon to engage in public discussions about the technology and its potential animal welfare, societal and environmental benefits.

"If people trust you, science doesn't matter. If people don't trust you, science doesn't matter," Arnot says. "It only matters after you cross that trust threshold. So you really have to engage in that values-based dialogue to build trust, and then you're given the permission to introduce the science."

And that's the third strategy: These companies want consumers to know that CRISPR isn't like other forms of genetic engineering. CRISPR changes the way genes are expressed; it doesn't necessarily add genetic material from another species, although it can be used that way.

"That's going to be the path that will ultimately lead to greater trust," Arnot says. "If we shortcut that path, we run the risk of potentially having this significantly beneficial technology not be accepted."

But persuading consumers to buy into CRISPR will be an uphill battle for Arnot and other industry groups. Food and environmental advocacy groups already are asking questions about CRISPR, as well as raising concerns over tracing genetically edited food in the system and the potential lack of regulatory oversight.

This story comes to us from Harvest Public Media, a reporting collaboration that focuses on agriculture and food production. Kristofor Husted is based at member station KBIA in Columbia, Mo.

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Amid GMO Strife, Food Industry Vies For Public Trust In ...

The CRISPR Pill made headlines with its implications in the fight against Superbugs.

But CRISPR technology originated from research into gene splicing and genetic editing capabilities. Since DNA is the fundamental building block of existence, what CRISPR claims it can do is bold and a little terrifying.

What are the real-world applications and implications of this biotech?

The above image comes from a YouTube video produced by the McGovern Institute for Brain Research at MIT from 2014. You can see that it involves gene splicing. One of the faculty members, Feng Zhang, led a team of researchers at MIT on the project, but many groups have looked into CRISPR-Cas9 biotech.

As early as 1993, researcher Francisco Mojica of the University of Alicante in Spain tinkered with CRISPR. Fun fact: the CRISPR DNA sequenceandCas-9 enzyme are a naturally occurring defense mechanism in various bacteriamost notably the kind that causes strep throat.

Yeswe derived gene editing biotech from that pestering, cold weather (but also any time weather because its bacteria based) illness.

But dont worry: the CRISPR-Cas9 strand operates similarly to bacteriophages.

It repeats a series of the same DNA sequences with unique sequences peppered in. These clusters became known as clustered regularly interspaced short palindromic repeats.

Though Ruud Jansen first used the term CRISPR in 2002, Mojica adopted the initialization throughout his research in discovering that CRISPR is basically an adaptive immune system.

This led others to tinker with the bacteria-based defense mechanism, as well. In 2005, Alexander Bolotin of the French National Institute for Agricultural Research discovered the unusual Cas-9 protein displaying nuclease activity. He specifically noted it in the Streptococcus thermophilus bacteria as opposed to other bacteria. Bolotin also discovered a PAM(protospacer adjacent motif) which allows for target recognition.

From there, a plethora of scientists and researchers began to experiment with CRISPR and Cas-9 DNA sequences.

Knowing how something came to be is all fine and good, but exactly how does CRISPR work? Simple: it acts similarly to how viruses do when they attack organisms human or otherwise. Copies of the attacking virus DNA are made with temporary RNA. Then, these copies attach themselves to the attacked organism, forcing replication. This is how viruses infect things and its also how bacteriophages work, too.

Since researchers can now harness the power of CRISPR-Cas9 (bacterias own natural defense system against infection) many believe they can utilize this against antibiotic resistant strains of bacteria.

So, DNA has four amino-acid bases: adenine (A), thymine (T), guanine (G), and cytosine (C).

DNA will target any sequence acting a bit off to forego any potential damage. However, the CRISPR-Cas9 system operates differently since it can read 20 bases in any sequence. This elf-eyes-esque sight allows for better tailoring to a specific gene. There is even an online tool you can use to design a target sequence and how the RNA should interact with it.

While the implications of this are monstrous, the real world applications do meet with a few stumbling blocks. One such block: the fact that the enzymes sometimes cut at the wrong place. Clearly, when it comes to gene editing, you want to be able to hit your mark every time.

While the research into gene editing biotech has come a very long way, genetically engineered babies are still a bit further down the roador are they? Researchers in Portland, Oregon successfully edited a human embryo in 2017.

However, this falls under the category of germlinecells or reproductive cells. While the editing of somatic (or non-reproductive) cells is generally not controversial, editing reproductive cells raises several ethical dilemmas.

Despite this moral hang-up, use of CRISPR-Cas9 gene editing tech is already underwayeven in robotics. Transcriptics robotic lab added this biotech to its list of services in 2015 in hopes to save time and money in the gene editing process. China instigated human trials in 2016, and we dont even need to mention the implications regarding infectious diseases like Malaria.

We may have far to go with genetic editing and the fight against superbugs and viruses. But, we have taken very necessary and BIG first steps.

With how far genetics has come in the last 30 years, we have to wonder how advancements in robotics and biotech will propel things even further.

See the original post here:
The Latest Guide to Understanding CRISPR-Cas9

T

he acronyms might not be quite as catchy as CRISPR since, really, what is? but what new genetic tools dubbed REPAIR and ABE lack in whimsy they promise to make up in utility. These advances announced Wednesday solve two of the problems hobbling CRISPR, the revolutionary genome-editing technique: that its idea of editing is often like 1,000 monkeys editing a Word document, and that making permanent changes to DNA might not be the best approach.

Together, the discoveries, described in separate studies, show that five years after scientists demonstratedthat CRISPR can edit DNA, bioengineers are still racing to develop the most efficient, precise, versatile and therefore lucrative genome-editing tools possible.

One reason these are so exciting is, they show the CRISPR toolbox is still growing, said chemical engineer Gene Yeo of the University of California, San Diego. There are going to be a lot more, and its not going to stop anytime soon. His lab has been working on one of the CRISPR advances but was not involved in either of the two new studies its personally frustrating to get beaten, he added.

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One discovery, led by biochemist David Liu of Harvard University, extends his 2016 inventionof a way to change a single DNA letter, or base, on the 3-billion-letter-long human genome. Classic CRISPR cuts DNA with a molecular scissors and leaves the cell to repair the breach willy nilly, introducing the problem of 1,000 monkeys editing away. In contrast, Liusbase editor replaces the molecular scissors with something like a pencil wielded by an expert forger: It is an enzyme that literally rearranges atoms cleanly and without collateral damage that the cell needs to fix.

As in classic CRISPR, this version finds its way to a target on the genome via a molecule that acts like a bloodhound. Attached to the bloodhound is the atom-rearranger, which in Lius 2016 version turned the DNA letterG into A. Thousands of genetic diseases arise because a gene has a G where it should have an A,so the edit might one day treat or prevent them.

But other inherited disorders need different alphabetical magic. Thats what Liu, postdoctoral fellows Nicole Gaudelli and Alexis Komor, and their colleagues report in a paper in Nature: Their new ABE (adenine base editor) can turn A into G.Attached to CRISPRs bloodhound molecule, ABE works at virtually any target site in genomic DNA, Liu said.

In tests so far, it changed DNA in more of the lab-grown human cells thatit was slipped into than standard CRISPR (for all its fame, CRISPR often bungles the job). ABE also seems to make fewer off-target edits: In one test, it mistakenly hit four of the 12 off-target sites, compared to CRISPRs nine, and made that mistake in 1.3 percent of cases compared to 14 percent for CRISPR, Liu said.

About half of the 32,000 known disease-causing, single-letter mutations have one of the misspellings that ABE can fix, Liu said. They include sickle cell, Tay-Sachs, and cystic fibrosis, raising hopes that ABE could be used to treat these diseases, or (in early embryos) prevent them.In tests of cells growing in lab dishes, ABE reversed the mutation that causes hereditary hemochromatosis in about 30 percent of the cells, and changed another gene into a form that prevents sickle cell disease even in people who have its disease-causing mutation.

As with all forms of CRISPR, before ABE helps any patients, scientists will have to test whether its safe and effective. But having the molecular machine is a good start, said Liu, a co-founder of the CRISPR company Editas Medicine. He and colleagues have filed for patents on ABE.

Harvard biologist George Church, who tied for first in the race to make CRISPR work in human cells, called base editing especially interesting. Changing a single DNA letter, he said, means fewer worries about the editing enzyme [in classic CRISPR] later going rogue or silent. He also expects that crops with a single base change will not be designated as transgenic, reducing regulatory barriers to commercialization.

In a separate study, CRISPR pioneer Feng Zhang of the Broad Institute and his colleagues discovered a new version of CRISPR that can edit RNA, DNAs friskier cousin. While DNA mostly sits sedately in cells and issues orders to make proteins that keep life living, RNA zips around the cell carrying out those orders, and then disappears. That makes RNA a tantalizing target: By editing the errant orders (RNA) rather than their issuer (DNA), scientists might be able to make temporary, reversible genetic edits, rather than CRISPRs permanent ones.

Editing DNA is hard to reverse, but once you stop providing the RNA-editing system, the changes will disappear over time, said Zhang, also a co-founder of Editas. That might make it possible to treat conditions where you dont need a permanent edit, such as when the immune system is in overdrive and causing inflammation.

To create what Zhang and his colleagues call REPAIR (RNA editing for programmable A to I [G] replacement), they fused an enzyme that binds to RNA with one that changes the RNA letter A (adenosine) to inosine, a molecule similar tothe RNA letter G (guanosine), they report in Science.Other labs, including that of CRISPR developer Jennifer Doudna of the University of California, Berkeley, have also developed RNA editors, including one using the same Cas13 enzyme. But REPAIRs creators say theirs is more efficient and less error-prone.

In tests on human cells growing in the lab, REPAIR corrected misspellings in theRNA that was made by disease-causing DNA in this case, Fanconi anemia, an inherited and devastating bone marrow disease, or nephrogenic diabetes insipidus, a serious inborn kidney disease. Although the DNA still had its disease-causing mutations, 23 percent and 35 percent, respectively, of the RNA made by those defective genes was REPAIRed. Those levels might be high enough to treat the diseases. Some 5,800 inherited diseases are the result of the G-to-A glitch that REPAIR can fix, including epilepsy and Duchenne muscular dystrophy.

Both REPAIR and ABE might venture where CRISPR stumbles: in mature cells, like neurons, that dont divide. In unpublished research, Liu said, he and his team have shown that ABE can edit genes in neurons, raising the possibility of treating devastating neurological diseases with ABE.

The furious race to improve CRISPR, via ABE or REPAIR or whatever comes next, Church said, are potent reminders of how far CRISPR is from precise genome-editing in humans.

Senior Writer, Science and Discovery

Sharon covers science and discovery.

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Scientists have used a new gene-editing technique to create pigs that can keep their bodies warmer, burning more fat to produce leaner meat. Infrared pictures of 6-month-old pigs taken at zero, two, and four hours after cold exposure show that the pigs' thermoregulation was improved after insertion of the new gene. The modified pigs are on the right side of the images. Zheng et al. / PNAS hide caption

Scientists have used a new gene-editing technique to create pigs that can keep their bodies warmer, burning more fat to produce leaner meat. Infrared pictures of 6-month-old pigs taken at zero, two, and four hours after cold exposure show that the pigs' thermoregulation was improved after insertion of the new gene. The modified pigs are on the right side of the images.

Here's something that may sound like a contradiction in terms: low-fat pigs.

But that's exactly what Chinese scientists have created using new genetic engineering techniques.

In a paper published Monday in the Proceedings of the National Academy of Sciences, the scientists report that they have created 12 healthy pigs with about 24 percent less body fat than normal pigs.

The scientists created low-fat pigs in the hopes of providing pig farmers with animals that would be less expensive to raise and would suffer less in cold weather.

"This is a big issue for the pig industry," says Jianguo Zhao of the Institute of Zoology at the Chinese Academy of Sciences in Beijing, who led the research. "It's pretty exciting."

The genetically modified low-fat piglets Jianguo Zhao hide caption

The animals have less body fat because they have a gene that allows them to regulate their body temperatures better by burning fat. That could save farmers millions of dollars in heating and feeding costs, as well as prevent millions of piglets from suffering and dying in cold weather.

"They could maintain their body temperature much better, which means that they could survive better in the cold weather," Zhao said in an interview.

Other researchers call the advance significant.

"This is a paper that is technologically quite important," says R. Michael Roberts, a professor in the department of animal sciences at the University of Missouri, who edited the paper for the scientific journal. "It demonstrates a way that you can improve the welfare of animals at the same as also improving the product from those animals the meat."

But Roberts doubts the Food and Drug Administration would approve a genetically modified pig for sale in the United States. He's also skeptical that Americans would eat GMO pig meat.

"I very much doubt that this particular pig will ever be imported into the USA one thing and secondly, whether it would ever be allowed to enter the food chain," he says.

The FDA has approved a genetically modified salmon, but the approval took decades and has been met with intense opposition from environmental and food-safety groups.

Others say they hope genetically modified livestock will eventually become more acceptable to regulators and the public.

"The population of our planet is predicted to reach about 10 billion by 2050, and we need to use modern genetic approaches to help us increase the food supply to feed that growing population," says Chris Davies, an associate professor in the school of veterinary medicine at Utah State University in Logan, Utah.

Zhao says he doubts the genetic modification would affect the taste of meat from the pigs.

"Since the pig breed we used in this study is famous for the meat quality, we assumed that the genetic modifications will not affect the taste of the meat," he wrote in an email.

The Chinese scientists created the animals using a new gene-editing technique known as CRISPR-Cas9. It enables scientists to make changes in DNA much more easily and precisely than ever before.

Pigs lack a gene, called UCP1, which most other mammals have. The gene helps animals regulate their body temperatures in cold temperatures. The scientists edited a mouse version of the gene into pig cells. They then used those cells to create more than 2,553 cloned pig embryos.

Next, scientists implanted the genetically modified cloned pig embryos into 13 female pigs. Three of the female surrogate mother pigs became pregnant, producing 12 male piglets, the researchers report.

Tests on the piglets showed they were much better at regulating their body temperatures than normal pigs. They also had about 24 percent less fat on their bodies, the researchers report.

"People like to eat the pork with less fat but higher lean meat," Zhao says.

The animals were slaughtered when they were six months old so scientists could analyze their bodies. They seemed perfectly healthy and normal, Zhao says. At least one male even mated, producing healthy offspring, he says.

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The powerful gene-editing tool CRISPR has been making headlines for its ability to edit DNA, which could one day transform how we fight cancer and other life-threatening diseases. Now, scientists have created a new version of CRISPR that can target and edit a different genetic building block: RNA.

The new tool, described in a study published today in Science, offers several advantages: its edits, for instance, arent permanent, which makes gene editing much safer. Researchers showed that the new system, called REPAIR, can work relatively efficiently in human cells. In the future, it could be used to treat diseases, as well as better understand the role that RNA plays in causing those diseases.

Its another tool in the toolbox.

Its another tool in the toolbox that we didnt have access to before, says Mitchell O'Connell, assistant professor in the Department of Biochemistry and Biophysics at the University of Rochester, who was not involved in the research. Its like developing new technology that makes you see things that you couldn't see before, or tweak things that you couldn't tweak.

The gene-editing tool CRISPR is based on a defense mechanism bacteria use to ward off viruses by cutting off bits of their DNA and pasting them elsewhere. Scientists have engineered that mechanism to tweak DNA, creating unusually muscular beagles, for instance, and mosquitoes that dont transmit malaria. But there are different types of CRISPR, with different types of molecular scissors. The gene-editing tool thats been making lots of headlines is called CRISPR-Cas9. The CRISPR used in todays study is called CRISPR-Cas13.

Instead of snipping DNA, this type of CRISPR targets another of the major biological molecules found in all forms of life, RNA. Most of the time, RNA is used inside the body to help DNA build proteins. And proteins play an important role in causing diseases. There are some advantages to editing RNA instead of DNA, says study co-author David Cox, a PhD student in the Zhang Lab at the Broad Institute of MIT and Harvard, which has been doing pioneering work on CRISPR. RNA is constantly being made and recycled inside cells, so an RNA edit is not permanent. (The edits could still be effective, though: the CRISPR system could be kept in cells for, say, months, allowing the scissors to keep editing RNA as it forms.) That makes the whole process safer. If you edit RNA and make a mistake, for instance, the faulty RNA will be degraded likely within 24 hours. Instead, if you edit DNA and make a mistake, that mistake is irreversible and could possible lead to cancer. Certain changes to DNA could also be passed on to future generations, while changes to RNA generally arent passed on.

there are still big risks involved.

Gene editing is very exciting, but there are still big risks involved, O'Connell tells The Verge. Targeting RNA rather than DNA is a safer strategy, particularly for things where you might not want to make permanent change.

To create the new editing tool, called REPAIR, the researchers combined CRISPR-Cas13 with a protein called ADAR. It works this way: the Cas13 enzyme is programmed to target a specific RNA sequence that might correspond to a disease mutation; the ADAR protein then makes the edit. In the study, the researchers showed that the system can edit specific RNA bases with 20 to 40 percent efficiency and up to 90 percent in some instances, says Cox. And the system made few mistakes: even though gene-editing tools are very precise, sometimes they snip pieces of genetic code they werent programmed to cut. These off-target cuts can be dangerous, and scientists want to make sure there are as few of them as possible.

A first version of REPAIR caused nearly 20,000 off-target cuts, says study co-author Omar Abudayyeh, also a PhD student in the Zhang Lab. That was a pretty disappointing moment, he tells The Verge. But then, the team tweaked the system in a way that reduced the number of off-target cuts to 10 to 20 per target site, making it much more precise and safe.

O'Connell says he was surprised by how well the system works. RNA has been targeted before in an effort to make drugs to treat disease, O'Connell says. But this CRISPR system makes the whole editing process much easier. In the future, this editing tool could be used to treat life-threatening diseases like hemophilia, as well as a heart condition called hypertrophic cardiomyopathy, which can lead to sudden death, Cox tells The Verge. Before that happens, the system needs to be optimized, and made much more precise. Researchers also need to show that it works in mice, other animals, and eventually in people. Its a long road to translate this into any sort of therapy, says study co-author Jonathan Gootenberg, another PhD student in the Zhang Lab.

You feel so empowered where youre in the lab.

Together with CRISPR-Cas9, this system really has the potential to revolutionize how we treat diseases. And thats the motivation that keeps Gootenberg, Cox, and Abudayyeh working hard in their lab. Abudayyeh says that when he was in med school, he met a woman with terminal lung cancer, who had maybe a few more months to live. You feel pretty hopeless in that situation because theres nothing you can do even as a doctor, he says. But thats also what inspired him to get into biotechnology.

You feel so empowered where youre in the lab, just thinking about new ways to make new technologies with the potential to hopefully actually help patients like that, Abudayyeh says. Its really exciting.

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Photo: LOREN ELLIOTT, Special To The Chronicle

A heat map illustrates how effectively mutated cells blocked HIV, in a UCSF lab.

A heat map illustrates how effectively mutated cells blocked HIV, in a UCSF lab.

How CRISPR gene-editing tech can fight HIV

Researchers at UCSF have received a three-year, $1.6 million grant to advance their work using novel gene-editing technology to make human blood cells less susceptible to HIV infection.

The grant, from biopharmaceutical giant Gilead Sciences, a global leader in sales of HIV treatments, will fund a team of scientists working to modify the DNA of a type of white blood cell to make them immune to HIV infection.

The cells, called T cells, have long been a focus of researchers seeking to improve HIV treatments. T cells help the immune system fight many diseases, including some cancers and flu viruses. They play a unique role in HIV because the virus targets and destroys T cells, and HIV-positive patients whose T cells become too depleted by the virus will progress to AIDS.

Using a gene-editing technique known as CRISPR, the UCSF researchers have already tested dozens of genes believed to play a role in how HIV spreads within the body. They do this by collecting blood samples from HIV-negative patients, altering the DNA of those cells, and then introducing the HIV virus to the modified cells in test tubes. Within two weeks, they can see whether the change to the gene has eliminated the cells ability to become infected with HIV.

CRISPR can be used to modify the DNA of plants, animals and other living organisms. It is considered a groundbreaking method because it is simpler and cheaper than other gene-editing techniques.

This is connecting CRISPR to HIV and opening up whole new avenues of research in understanding the interplay between human genetics and HIV, said Alex Marson, an assistant professor of microbiology and immunology at UCSF who leads the lab that received the Gilead grant.

The grant, announced this week, will allow Marsons lab to pursue an ambitious goal of uncovering why HIV remains dormant in some cells, only to awaken unpredictably, sometimes years later. Known as HIV latency, this characteristic of the virus is why HIV-positive patients must take antiretroviral drugs which are only effective in attacking the awake HIV for life.

The tricky thing about HIV, and one reason its so hard to cure, is that it can hide in the DNA of the human cells, said Joe Hiatt, a doctoral student of medicine and philosophy in Marsons lab and a leader in the research initiative. It becomes DNA and integrates into your DNA.

The problem has perplexed researchers for years. But Marson and Hiatt see potential for using CRISPR to discover which genes control HIV latency. They hope to use the gene-editing tool to create latent HIV cells in test tubes, and then modify the DNA in those cells to see which edits may coax the HIV out of hiding and make it susceptible to drugs. This will be the most challenging and complicated part of the research. If done successfully, it could lead to the development of drugs that target latent HIV and perhaps cure HIV permanently.

CRISPR technology is potentially revolutionary because HIV is a type of virus that will sneak its own genetic code into the genetic code of the human cell, said Ross Wilson, a scientist at UC Berkeleys Innovative Genomics Institute who is not involved in the grant. Its like hiding a book in a stack at the library, and the book has instructions to build a nasty bomb. To get rid of that information, you need to get it back out of the library. Weve never had the technology to do that inside the living cell until CRISPR came along. Its the first efficient way to do that inside living cells.

It is the first research initiative that Foster Citys Gilead, through its philanthropic program, has funded that involves using CRISPR as a tool in HIV cure-related research. While $1.6 million is not a huge amount, it comes with fewer restrictions than many government grants. The grant will fund a team of five researchers for three years.

It is one of five grants totaling $7.5 million, announced this week, that Gilead has awarded research institutions for HIV and AIDS-related initiatives. The others are to the University of Massachusetts Medical School; Dana-Farber Cancer Institute; Institute of Human Genetics, French National Center for Scientific Research and University of Montpellier; and Frederick National Laboratory for Cancer Research, AIDS and Cancer Virus Program.

A Gilead spokesman said that if the UCSF researchers discover how latent HIV can be targeted by drugs, the company will not necessarily have rights to licensing agreements or other commercial benefits. The grant is from the companys philanthropy program and is meant to support HIV research independent of Gileads business interests, he said.

Catherine Ho is a San Francisco Chronicle staff writer. Email: cho@sfchronicle.com Twitter: @Cat_Ho

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How CRISPR gene-editing tech can fight HIV - SFGate

Photos from Eadweard Muybridges study of a galloping horse have been recorded in bacterial DNA

Eadweard Muybridge/The LIFE Picture Collection/Gett

By Douglas Heaven

Life is an open book and were writing in it. A team at Harvard University has used the CRISPR genome-editing tool to encode video into live bacteria demonstrating for the first time that we can turn microbes into librarians that can pass records on to their descendants and perhaps to ours.

The technique could even let us create populations of cells that keep their own event logs, making records as biological processes like disease or brain development happen.

DNA is one of the best media for storing data we know of. Researchers have already crammed large amounts of information from books to digital images into tiny amounts of biological material. In theory, a gram of single-stranded DNA can encode 455 exabytes, or roughly 100 billion DVDs.

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Most previous DNA storage work has used artificial DNA: digital information is translated into a DNA sequence that is then synthesized.

However, using CRISPR lets you cut and paste the digital information directly into the DNA of a live organism, in this case a large population of E. coli.

Bacteria use the CRISPR/Cas9 system to record information in their DNA about viruses they encounter. And this machinery has been co-opted by researchers to enable us to precisely edit genomes.

In bacteria, each new entry gets stored upstream of the last one, which makes it possible to read off a history of events in the order they happened. Previous groups have created lifelogging cells by using CRISPR/Cas9 to mark the genome when a particular event occurs. But these marks just provide a tally of how many times something happens.

Seth Shipman at Harvard University and his colleagues have now used a version of CRISPR with a different enzyme, called CRISPR/Cas1-Cas2. This let them add a message to the genome rather than simply cut a notch.

The message was a recorded image of a human hand and five images showing a galloping horse, taken from Eadweard Muybridges 1878 photographic study of the animals motion, which has since been animated.

Seth Shipman

To get the DNA sequences encoding this data inside the cells, the team applied an electrical current that opened channels in the cells walls and the DNA flowed in. Once inside, CRISPR got to work.

To read the data back again, the team sequenced the DNA of more than 600,000 cells. The large number is necessary because most cells will not have edited their genome entirely accurately. Every cell isnt going to acquire every piece of information we throw at it, says Shipman. The more cells that are sampled, the better the reconstruction of the data. Fortunately, with modern sequencing tools, reconstruction is quick.

The five frames of a horse in motion showed that it is possible to capture data chronologically and replay them as a video. You get a physical record of events over time, says Shipman. For a long time we wanted to have some way of storing timing information inside cells, says Shipman. The CRISPR system is perfectly adapted to that.

This is a really neat paper, says Yaniv Erlich at Columbia University in New York. The team didnt store that much data and it is not clear that the CRISPR technique can compete with the storage capacity of synthetic DNA. But inserting information into living cells opens up a lot of possibilities, he says.

For a start, it lets you add to or change the stored information later. And because the data is written into the bacterial genomes, it gets passed down between generations. Mutations happen, but not nearly as many as you think, says Shipman certainly not enough to corrupt the data stored across a large population of cells.

Storing data in bacteria could even be a way to make important information survive a nuclear apocalypse. You could useDeinococcus radiodurans, a species that maintains its genome in extreme radiation conditions, says Erlich.

Shipman wants to turn cells into recording devices that document what takes place inside themselves. He is excited about the possibility of keeping a log book of events inside a living brain as it develops, showing how different brain cells acquire their distinct identities.

Its hard to understand what events make brain cells fully defined, says Shipman. You cant easily get in there to take a look. Taking a brain apart disrupts the whole process.

You could also get a cell to diarise what happens as it changes from healthy to diseased. Now that would be an account worth reading.

Journal reference: Nature, DOI: 10.1038/nature23017

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