Archive for the ‘Crispr’ Category

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A leading genome-editing researcher is urging extra caution as drug companies race to turn the landmark technology he helped create into human medicine.

In a paper published today in Nature Medicine, Feng Zhang of the Broad Institute of MIT and Harvard and colleague David Scott argue that researchers should analyze the DNA of patients before giving them experimental medicines that alter their genes with the breakthrough technology CRISPR. The suggestion, among others in the paper, stems from a deeper look at the wide array of subtle differences in human DNA.

Zhang is a key inventor of CRISPR-Cas9, which describes a two-part biological system that slips into the nucleus of cells and irreversibly alters DNA. One part is an enzyme, natures molecular scissors, which cuts DNA. The second part is a string of ribonucleic acid (RNA) that guides the enzyme to the proper spot. In five years since its invention, CRISPR-Cas9 has become a mainstay of biological research, and researchers including Zhang (pictured above) have moved quickly to improve upon its components. His work is at the center of a long-running patent battle to determine ownership of the technology.

Zhang and Scotts recommendation taps into a long-running debate in the gene-editing field about off-target effectsthe fear of misplaced cuts causing unintended harm. Most recently, the FDA took up a similar issue at a meeting to assess a type of cell therapy, known as CAR-T, for kids with leukemia. The FDA highlighted the risk that the cells, which have certain genes edited to make them better cancer fighters, may cause secondary cancers long after a patients leukemia has been cured. (FDA advisors unanimously endorsed the therapys approval nonetheless.)

Some researchers say there should be near certainty that gene altering techniques wont go awry before testing in humans, caution that stems in part from gene therapy experiments in the U.S. and Europe nearly 20 years ago that killed an American teenager and triggered leukemia in several European boys.

While no medicine is risk-free, other researchers say the tools to gauge risk have improved.

Andy May, senior director of genome engineering at the Chan Zuckerberg Biohub in San Francisco, calls Zhang and Scotts recommendation for patient prescreening a good discussion point, but the danger is someone will pick up on this and say you cant push forward [with a CRISPR drug] until everyone is sequenced.

Its an extremely conservative path to take, says May, who until recently was the chief scientific officer at Caribou Biosciences, a Berkeley, CA-based firm in charge of turning the discoveries of UC Berkeleys Jennifer Doudna and her colleagues into commercial technology. (May was also a board member of Cambridge, MA-based Intellia Therapeutics (NASDAQ: NTLA), which has exclusive license to use Caribous technology in human therapeutics.)

Berkeley is leading the challenge to Zhangs CRISPR patents and last week filed the first details in its appeal of a recent court decision in favor of Zhang and the Broad Institute.

Zhang sees prescreening as a form of companion diagnostic, which drug companies frequently use to identify the right patients for a study. A whole genome sequencewhich costs about $1,000could filter out patients unlikely to benefit from a treatment or at higher risk of unintended consequences, such as cancer. In the long run, it could also encourage developers to create more variations of a treatment to make genome-editing based therapeutics as broadly available as possible, said Zhang.

Its well known that human genetic variation is a hurdle in the quest to treat genetic diseases either by knocking out disease-causing genes or replacing them with healthy versions. But Zhang and Scott use newly available genetic information to deepen that understanding. In one Broad Institute database with genetic information from more than 60,000 people, they find one genetic variation for every eight letters, or nucleotides, in the exomethat is, the sections of DNA that contain instructions to make proteins. (There are 6 billion nucleotides in each of our cells.) The wide menu of differences is, in effect, an open door to misplaced cuts that CRISPRs enzymes might be prone to.

Zhang and others are working on many kinds of enzymes, from variations on the workhorse Cas9, to new ones entirely. He and Scott found that the deep pool of genetic variation makes some forms of the Cas enzyme more likely than others to go awry, depending on the three-nucleotide sequence they lock onto in the targeted DNA.

Zhang and Scott write that CRISPR drug developers should avoid trying to edit DNA strings that are likely to have high variation. In their paper, they examine 12 disease-causing genes. While more common diseases, such as those related to high cholesterol, will contain higher genetic variation because of the broader affected population, every gene, common or not, contains regions of high and low variation. Zhang and Scott say developers can build strategies around the gene regions they are targeting.

For example, going after a more common disease might require a wider variety of product candidates, akin to a plumber bringing an extra-large set of wrenches, with finer gradations between each wrench, to a job site with an unpredictable range of pipe sizes.

CRISPR companies say they are doing just that. We have always made specificity a fundamental part of our program, says Editas Medicine CEO Katrine Bosley. Zhang is a founder of Editas (NASDAQ: EDIT), which has exclusive license to the Broads Next Page

Alex Lash is Xconomy's National Biotech Editor. He is based in San Francisco.

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CRISPR Pioneer Zhang Preaches Extra Caution In Human Gene ... - Xconomy

Theres still a way to go from editing single-cell embryos to a full-term designer baby. Credit: ZEISS Microscopy, CC BY-SA

The announcement by researchers in Portland, Oregon that they've successfully modified the genetic material of a human embryo took some people by surprise.

With headlines referring to "groundbreaking" research and "designer babies," you might wonder what the scientists actually accomplished. This was a big step forward, but hardly unexpected. As this kind of work proceeds, it continues to raise questions about ethical issues and how we should we react.

What did researchers actually do?

For a number of years now we have had the ability to alter genetic material in a cell, using a technique called CRISPR.

The DNA that makes up our genome comprises long sequences of base pairs, each base indicated by one of four letters. These letters form a genetic alphabet, and the "words" or "sentences" created from a particular order of letters are the genes that determine our characteristics.

Sometimes words can be "misspelled" or sentences slightly garbled, resulting in a disease or disorder. Genetic engineering is designed to correct those mistakes. CRISPR is a tool that enables scientists to target a specific area of a gene, working like the search-and-replace function in Microsoft Word, to remove a section and insert the "correct" sequence.

In the last decade, CRISPR has been the primary tool for those seeking to modify genes human and otherwise. Among other things, it has been used in experiments to make mosquitoes resistant to malaria, genetically modify plants to be resistant to disease, explore the possibility of engineered pets and livestock, and potentially treat some human diseases (including HIV, hemophilia and leukemia).

Up until recently, the focus in humans has been on changing the cells of a single individual, and not changing eggs, sperm and early embryos what are called the "germline" cells that pass traits along to offspring. The theory is that focusing on non-germline cells would limit any unexpected long-term impact of genetic changes on descendants. At the same time, this limitation means that we would have to use the technique in every generation, which affects its potential therapeutic benefit.

Earlier this year, an international committee convened by the National Academy of Sciences issued a report that, while highlighting the concerns with human germline genetic engineering, laid out a series of safeguards and recommended oversight. The report was widely regarded as opening the door to embryo-editing research.

That is exactly what happened in Oregon. Although this is the first study reported in the United States, similar research has been conducted in China. This new study, however, apparently avoided previous errors we've seen with CRISPR such as changes in other, untargeted parts of the genome, or the desired change not occurring in all cells. Both of these problems had made scientists wary of using CRISPR to make changes in embryos that might eventually be used in a human pregnancy. Evidence of more successful (and thus safer) CRISPR use may lead to additional studies involving human embryos.

What didn't happen in Oregon?

First, this study did not entail the creation of "designer babies," despite some news headlines. The research involved only early stage embryos, outside the womb, none of which was allowed to develop beyond a few days.

In fact, there are a number of existing limits both policy-based and scientific that will create barriers to implanting an edited embryo to achieve the birth of a child. There is a federal ban on funding gene editing research in embryos; in some states, there are also total bans on embryo research, regardless of how funded. In addition, the implantation of an edited human embryos would be regulated under the federal human research regulations, the Food, Drug and Cosmetic Act and potentially the federal rules regarding clinical laboratory testing.

Beyond the regulatory barriers, we are a long way from having the scientific knowledge necessary to design our children. While the Oregon experiment focused on a single gene correction to inherited diseases, there are few human traits that are controlled by one gene. Anything that involves multiple genes or a gene/environment interaction will be less amenable to this type of engineering. Most characteristics we might be interested in designing such as intelligence, personality, athletic or artistic or musical ability are much more complex.

Second, while this is a significant step forward in the science regarding the use of the CRISPR technique, it is only one step. There is a long way to go between this and a cure for various disease and disorders. This is not to say that there aren't concerns. But we have some time to consider the issues before the use of the technique becomes a mainstream medical practice.

So what should we be concerned about?

Taking into account the cautions above, we do need to decide when and how we should use this technique.

Should there be limits on the types of things you can edit in an embryo? If so, what should they entail? These questions also involve deciding who gets to set the limits and control access to the technology.

We may also be concerned about who gets to control the subsequent research using this technology. Should there be state or federal oversight? Keep in mind that we cannot control what happens in other countries. Even in this country it can be difficult to craft guidelines that restrict only the research someone finds objectionable, while allowing other important research to continue. Additionally, the use of assisted reproductive technologies (IVF, for example) is largely unregulated in the U.S., and the decision to put in place restrictions will certainly raise objections from both potential parents and IVF providers.

Moreover, there are important questions about cost and access. Right now most assisted reproductive technologies are available only to higher-income individuals. A handful of states mandate infertility treatment coverage, but it is very limited. How should we regulate access to embryo editing for serious diseases? We are in the midst of a widespread debate about health care, access and cost. If it becomes established and safe, should this technique be part of a basic package of health care services when used to help create a child who does not suffer from a specific genetic problem? What about editing for nonhealth issues or less serious problems are there fairness concerns if only people with sufficient wealth can access?

So far the promise of genetic engineering for disease eradication has not lived up to its hype. Nor have many other milestones, like the 1996 cloning of Dolly the sheep, resulted in the feared apocalypse. The announcement of the Oregon study is only the next step in a long line of research. Nonetheless, it is sure to bring many of the issues about embryos, stem cell research, genetic engineering and reproductive technologies back into the spotlight. Now is the time to figure out how we want to see this gene-editing path unfold.

Explore further: In US first, scientists edit genes of human embryos (Update)

This article was originally published on The Conversation. Read the original article.

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Editing human embryos with CRISPR is moving ahead now's the ... - Phys.Org

A group of scientists in Oregon has successfully modified the genes of embryos using CRISPR, a cut-and-paste gene-editing tool.

The experiments, which have not yet been subject to peer review, were conducted by biologist Shoukhrat Mitalipov and colleagues at Oregon Health & Science University in Portland, MIT Technology Review reported. Mitalipov conducted the experiments on dozens of single-celled embryos, which were discarded before they could progress very far in development, according to Technology Review. This is the first time that scientists in the United States have used this approach to edit the genes of embryos.

The CRISPR/Cas9 gene-editing system is a simple "cut and replace" method for editing precise spots on the genome. CRISPRS are long stretches of DNA that are recognized by molecular "scissors" called Cas9; by inserting CRISPR DNA near target DNA, scientists can theoretically tell Cas9 to cut anywhere in the genome. Scientists can then swap a replacement gene sequence in the place of the snipped sequence. The replacement sequence then gets automatically incorporated into the genome by natural DNA repair mechanisms.

In 2015, a group in China used CRISPR to edit several human embryos that had severe defects, though none were allowed to gestate very long before being discarded. If rumors are to be believed, the new results are more promising than those earlier efforts, according to Technology Review. The Chinese technique led to genetic changes in some, but not all of the cells in the embryos, and CRISPR sometimes snipped out the wrong place in the DNA. According to Technology Review, the new technique was used in dozens of embryos that were created for in vitro fertilization (IVF), using the sperm of men who had severe genetic defects.

In general, editing the germ line meaning sperm, eggs or embryos has been controversial, because it means permanently changing the DNA that is passed on from one generation to the next. Some scientists have called for a ban on germ-line editing, saying the approach is incredibly risky and ethically dubious.

However, a National Academy of Sciences report published earlier this year suggested that embryo editing could be ethical in the case of severe genetic diseases.

Originally published on Live Science.

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Scientists Use CRISPR to Edit Human Embryos - Live Science

An artists conception of the DNA-cutting enzyme Cas9.

By Jon CohenJul. 26, 2017 , 9:00 AM

The University of California (UC) has fired another legal salvo in the prolonged patent battle over CRISPR, the revolutionary gene-editing technology that has spawned a billion-dollar industry.

UC leads a group of litigants who contend that the U.S. Patent Trial and Appeal Board (PTAB) wrongly sided with the Broad Institute in Cambridge, Massachusetts, and two partnersHarvard University and the Massachusetts Institute of Technology in Cambridgein February when it ruled that the Broad group invented the use of CRISPR in eukaryotic cells. After that ruling, UC moved the battleground to the U.S. Court of Appeals for the Federal Circuit. In a 25 July brief to the Federal Circuit, the UC group contends that PTAB ignored key evidence and made multiple errors.

The UC litigants indisputably first showed in 2012 that CRISPR could work in DNA of simpler organisms, and soon after filed a patent application on the gene-editing technique. They claim the Broad group learned from that disclosed invention and applied CRISPR to eukaryotic cells. The essential legal question is whether the Broads patent application is a novel, patentable invention, or whether it was obvious in the sense that anyone skilled in the artin other words, any trained molecular biologistwould have a reasonable expectation of success of using the CRISPR system to edit genes in eukaryotic cells.

The UC group contends PTAB ignored key decisions on these general questions made by the U.S. Supreme Court and the Federal Circuit. It reiterated its long-held claim that applying CRISPR to eukaryotic cells was so obvious that six different labs did it in the same time frame, which it complains the PTAB essentially dismissed as irrelevant. And its brief notes that patent examiners rejected similar eukaryotic cell CRISPR patent applications from Sigma-Aldrich and ToolGenfiled before the Broads patent applicationbecause it made claims that were non-novel or obvious in light of UCs disclosed work.

Jacob Sherkow,an intellectual property attorney at the New York Law School in New York City who has closely followed each round in the fierce battle, says the UC groups brief at times overplays these mistakes relative to the PTAB's analysis. He notes that the PTABs decision was thorough and the standards to overturn its decisions are high. While there were some interesting chestnuts in its briefsuch as UC pointing out that the PTAB virtually ignored some important patents pending at the time [the Broad] patent was filedI don't think that's going to be enough to win the day [for] UC, he says.

In a statement, the Broad Institutesuggested the UC will not prevail in its challenge:

Notably, the [UC]brief hinges on its argument that, although [UC]s work simply involved characterizing a purified enzyme in a test tube, it rendered obvious that genome editing could be made to work in living mammalian cells.

This is inaccurate, as the PTAB noted repeatedly in its decision.

Updated, 7/26/2017, 12:33 p.m.: Statement from the Broad Institute added.

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Ding, ding, ding! CRISPR patent fight enters next round | Science ... - Science Magazine

For the first time, scientists in the US have successfully edited the DNA of viable human embryos using the powerful gene-editing tool CRISPR, according to a report by MIT Technology Review. Gaining the ability to edit human DNA is the first step toward one day allowing scientists to prevent babies from being born with incurable diseases or disabilities. But further success with this kind of research is likely to raise the heated discussion on the ethical implications of genetically altering human embryos.

The research which has yet to be published was led by Shoukhrat Mitalipov of Oregon Health and Science University. It involved editing a large number of viable embryos and effectively correcting disease-causing genes, according to MIT Technology Review. (Its unclear exactly how many embryos were edited, or which genes.) The embryos were developed for only a few days and were not implanted. Without implantation, embryos cannot develop into babies.

Human embryos have been edited with CRISPR before, only in China. In the US, this kind of research is much more controversial: theres even a ban on using National Institutes of Health funding for research using gene-editing technologies in human embryos. In February, however, a committee created by the National Academy of Sciences and the National Academy of Medicine endorsed the use of genetic engineering on human embryos when there isnt a reasonable alternative available, and only to eliminate serious diseases.

There are many concerns around genetically engineering humans. CRISPR is a very precise gene-editing tool, but it can sometimes lead to editing errors. So some fear that small mistakes could lead to permanent problems in the human gene pool. There are also ethical concerns: bioethicists fear that gene-editing will lead to a world where parents will be able to customize their own designer baby, complete with specific traits.

These super-baby concerns could be worked out easily, says Arthur Caplan, a bioethicist at New York University. If you dont want eugenics, you just draw a line and stop there, Caplan tells The Verge. Scientists and bioethicists should agree on rules on what should and should not be done, and then make sure that editors of scientific journals enforce them. Research into how to create designer babies should not be published. Or you could have the National Academy of Sciences work with industry and Congress to lay out a review committee and permit funding.

If America were to take the lead both in terms of working with journals, working with private foundations, with patient groups, and working with state and federal government, I think youd get collaboration from the rest of the world, Caplan says.

Engineered humans are still far away into the future. But Mitalipovs research is getting us closer: he and his team were able to edit the embryos precisely, with very few editing errors, according to STAT. They also avoided another problem: in experiments in China, the desired DNA changes were picked up only by some cells, not all the cells of an embryo an effect called mosaicism. That makes gene-editing unsafe. But Mitalipov was able to significantly reduce mosaicism, according to MIT Technology Review.

Some in the field questioned just how groundbreaking the research is. Hank Greely, a law professor and bioethicist at Stanford University, tweeted that the real breakthrough will be when someone actually implants the human embryos, so they can develop into human beings.

Regardless, the research shows just how far gene editing has come and makes the prospect of engineered, disease-free humans more science fact than science fiction.

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Human embryos reportedly edited for first time in the US using CRISPR - The Verge

Mike Feibus/ Special for USA Today Published 9:00 a.m. ET July 24, 2017

Humans had better be ready to play God. Because weve now got the tools to do just that.

Credit the recent discovery of CRISPR-Cas9, a powerful gene-editing tool that gives scientists the ability to make precise edits of single strands of DNA. Other so-called molecular scissors had already been developed, but they were very costly and time-consuming to implement. The emergence of CRISPR has put genomics exploration into overdrive with quick, precise and cheap tools, sending science on a fast track to new discoveries.

CRISPR could be used to erase and replace mutations that make some susceptible to a wide range of conditions, from AIDS to the Zika virus. Healthier, more resilient farm animals, pets, fruits and vegetables are also in the hopper.

Billions of dollars are being poured into CRISPR research, precisely because the possibilities are seemingly endless. Start-ups have sprouted around CRISPR pioneers, including CRISPR Therapeutics, Editas Medicine, eGenesis, Intellia Therapeutics and Synthego. Last year, three of them went public, each IPO resulting in valuations in excess of $500 million.

Earlier this month, Harvard University researchers revealed that they actually used CRISPR to etch a motion GIF of a galloping horse into the DNA of living bacteria. Not exactly a cure for cancer, to be sure. Though it does raise some intriguing possibilities for using DNA to store non-genetic data, like a built-in human flash drive. As well, the demonstration does serve as a good illustration for just how much editing prowess CRISPR affords.

Laboratory fun aside, keeping a lid on CRISPR will be paramount, as it is just as potent a tool for evil as it is for good. CRISPR could potentially pave the way for bad actors on the world stage to develop, say, chemical weapons alongside super-soldiers resistant to them.

Such doomsday scenarios keep some scientists up at night, in much the same way that Albert Einstein fretted over the shape of our future in a nuclear world and former Intel CEO Andy Grove feared for our privacy and security in the early days of the Internet boom.

Indeed, with the global WannaCry ransomware attack and North Koreas ever-present march to intercontinental nuclear attack capability as a backdrop, effectively locking down CRISPR technology to prevent catastrophe could become as crucial to our own survival as the cures it spawns.

And we havent even touched on the ever-present fear of the unintended consequences of going where no man has gone before. What if, say, the Harvard researchers inadvertently created a deadly, drug-resistant, mother-of-all mutant bacteria with their artistic demonstration? That issue came to the fore in late May not with horses, but with mice.

Two blind mice, in fact. In 2015, researchers successfully restored the mices sight using CRISPR to repair a gene mutation that causes blindness. In a follow-up study, disclosed May 30in a letter to the editor of a health journal, researchers found hundreds of unintended mutations throughout the mices genome. The researchers noted that the mice did not exhibit any ill effects as a result.

The news spooked investors, who sent shares of the publicly-traded CRISPR stocks downward. As well, it also spurred some observers to wonder aloud whether we are ready to handle our newfound godlike powers.

The news didnt concern many scientists, however. Most of them understand the process of discovery is rarely a straight line. And bumps in the road like the errant mutations found in the follow-up study are all part of the journey. Some even assert that many of the mutations wouldnt occur today, because the circa-2015 CRISPR tools the researchers used are as outmoded as VCRs. They feel confident that, by the time you head to the doctor for some gene-editing to wipe away your ailments, theyll have it all ironed out.

Lets hope so. Because if not, Galloping Horse Syndrome would be the least of our problems.

Mike Feibus is principal analyst at FeibusTech, a Scottsdale, Ariz., market strategy and analysis firm focusing on mobile ecosystems and client technologies. Reach him atmikef@feibustech.com. Follow him on Twitter @MikeFeibus.

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CRISPR gene editing tool: Are we ready to play God? - USA TODAY

Those who keep track of current science news, scientists and nonscientists alike, have probably found themselves asking aloud very often is there anything CRISPR cant do? So far, it would seem the answer to that question is "no" as a team of investigators from Schepens Eye Research Institute of Massachusetts Eye and Ear have found a new area for CRISPR interventionangiogenesis of the retina. The scientists were able to prevent the development of angiogenesis in mice, which often causes vision loss and blindness and is a feature of several degenerative eye conditions, including proliferative diabetic retinopathy (PDR), wet age-related macular degeneration (AMD), and retinopathy of prematurity (ROP).

Findings from the new studypublished recently in Nature Communications in an article entitled Genome Editing Abrogates Angiogenesis In Vivocould potentially lead to the development of new therapies for eye conditions marked by pathological intraocular angiogenesis.

"We know that vascular endothelial growth factor receptor 2 (VEGFR2) plays an essential role in angiogenesis," explained senior study investigator Hetian Lei, Ph.D., assistant professor of ophthalmology at Harvard Medical School and assistant scientist at Schepens Eye Research Institute of Massachusetts Eye and Ear. "The CRISPR/Cas9 system can be utilized to edit the VEGFR2 gene, preventing intraocular pathological angiogenesis."

Even with the success of several VEGF-inhibiting agents in reducing neovascular growth and lessening vascular leakage in retinal diseases such as PDR and AMD, several therapeutic challenges remainnamely a need for sustained treatment and a modality to treat the sizeable number of patients who do not respond to anti-VEGF therapies.

Clinically, many vision disorders present when blood vessels within the retina begin to grow new, abnormal blood vessels on the surface of the retina. As the damage progresses, these vessels can leak, rupture, or cause retinal detachment, leading to impaired vision. In the current study, the investigators decided to use the CRISPR/Cas9 system to target the VEGFR2 gene in mice, with the hope of preventing the start of angiogenesis.

...we report that a system of adeno-associated virus (AAV)-mediated clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease (Cas)9 from Streptococcus pyogenes (SpCas9) is used to deplete VEGFR2 in vascular endothelial cells (ECs), whereby the expression of SpCas9 is driven by an endothelial-specific promoter of intercellular adhesion molecule 2, the authors wrote. We further show that recombinant AAV serotype 1 (rAAV1) transduces ECs of pathologic vessels, and that editing of genomic VEGFR2 locus using rAAV1-mediated CRISPR/Cas9 abrogates angiogenesis in the mouse models of oxygen-induced retinopathy and laser-induced choroid neovascularization.

Amazingly, the research team was able to prevent retinal angiogenesis in the preclinical models using only a single injection of the AAV/CRISPR therapy. The investigators were excited by their findings and are optimistic that their study will lead to future strategies using genome-editing tools to vision loss disorders.

"As this genomic editing gains traction in virtually all medical fields, we are cautiously optimistic that this powerful tool may present a novel therapy to prevent vision loss in eye disease marked by intraocular pathological angiogenesis," Dr. Lei concluded. "While further study is needed to determine safety and efficacy of this approach, our work shows that the CRISPR/Cas9 system is a precise and efficient tool with the potential to treat angiogenesis-associated diseases."

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CRISPR Prevents Beginning Stage of Vision Loss - Genetic Engineering & Biotechnology News

I walked into Camp East Woods in Oyster Bay, Long Island, about twenty minutes before class started. Dozens of kids, from four years old to sophomores in high school, were trying to figure out where their friends were, checking different rooms to see who had arrived. It smelled like sunscreen and sweat.

I was there for the Serious Science program, where kids of all ages get to explore everything from biochemistry to engineering. The syllabus included CRISPR, the powerful gene editing technology that allows you to cut out and change specific sections of DNA. Researchers are using it to battle things like HIV, blindness, and malaria, just to name a few.

CRISPR is all the rage in the scientific community, and I was curious how Jane Powel, who leads the program, planned to teach this crucial subject to young kids. When new science makes its way into mainstream conversations, especially powerful science like CRISPR, those discussions can suffer when there's a significant gap in knowledge between researchers and the public. Without everyone at the table, conversations can become tainted with confusion, fear, and impulsive decisions. And that education has to start pretty early.

At the classroom that day, I expected such a complicated experiment and nuanced topic would require a very structured day, a really clear plan, and lots of guidance. I was wrong.

Students discussing the CRISPR experiment with Powel. Image: Michael Fairchild

Once class started, Powel quickly dove into a discussion of CRISPR, introducing it with a frequently used metaphor that compares it to the process of deleting and replacing a mistake that you've typed on the computer. There were a couple dozen or so kids in the room, all listening closely, and they jumped to answer any questions Powel posed to them.

While they named different things that you might want to cut from a genomelike genes that lead to higher risks of cancer or those that cause muscular dystrophyPowel asked the students if there were any potential issues with CRISPR that scientists might want to consider alongside all of the good that might come of it. A nine-year-old named Evan immediately raised his hand to point out that it's possible other parts of DNA could be damaged aside from the region you're trying to fix.

"Sometimes it sounds like a great idea to cut and paste and edit DNA, and other times it sounds like it might have a bad consequence that we weren't even thinking of," Powel agreed.

After the discussion, the classroom broke into groups and the students went off to do their activities. Some wanted to fly drones, helicopters, hovercrafts, and remote control airplanes. Others were going to drive an electric car that a student's uncle had built and lent to the camp. Another group went to pick flowers, dissect them, and look at their parts under a microscope.

I sat down with the group getting ready to perform the CRISPR experiment, which would involve them transforming a harmless bacteria's DNA to make it resistant to an antibiotic. Five girls were at the table. There was Despina, a soft-spoken sophomore in high school who got interested in genetics from a biology class in school. And three 11-year-oldsAvery, Cristabella, and Darshini. Nine-year-old Brinley was the youngest of the group.

A student mixes agar to be poured into plates. Image: Mallory Locklear

In the day's experiment, the campers would grow cultures of E. coli, bacteria that are usually susceptible to the antibiotic Streptomycin. And the following day, they would take that fresh bacteria and treat it with chemicals that would allow the CRISPR/Cas9 complex to enter the bacterial cells, and then cut out and replace the part of the E. coli DNA that binds to Streptomycin. If successful, the E.coli should then be able to grow on plates treated with the antibiotic instead of being killed, something it normally can't do.

As the students got into the nitty gritty of the day's work, Powel broached the ethics conversation again. "Everybody's excited about this, but people are worried about it too," she said, "Because just as Evan said, sometimes you can think you're doing a good thing and you're really not. Or there are some people who want to do bad things."

Some of the concerns with CRISPR tap into questions surrounding consent, reach, and unintended effects. For example, knocking malaria out of an entire mosquito population sounds like a net positive, but could also make those insects more susceptible to carrying other disease. Additionally, making changes to DNA with CRISPR impacts not only the organism or person, but its progeny as well.

That also brings up the issue of consent. Sure, someone may not have any issues with having their own disease-causing genes snipped out while they were in the womb, but going beyond that and making changes that aren't survival-related, what about the choices of the individual and their descendants?

Plates of bacteria. Image: Mallory Locklear

"Now you have this very powerful tool, so that's why it's so important that you guys learn about this and use it for good," Powel said. "And know what's going on when you hear news and be able to think critically."

Educators across the country are starting to incorporate CRISPR, and these lessons in genetic literacy, into their teachings. Michael Hirsch, who teaches science to 6th to 8th graders at the Acera School in Massachusetts, introduced CRISPR into his curriculum this past year. He also brought up its ethical aspects with his students.

"No one in the class seemed to have any objections to removing potentially hazardous and dangerous diseases from the genome," he said, "But it ran the gamut from, we shouldn't decide [whether parents will conceive a] boy or girl, to we can't decide [a baby's] hair color. Then again, some were like, well, I do want my baby to be born with a certain hair color so"

It seems to help that both Hirsch and Powel have unconventional teaching methods. "I've always wanted to cater my classroom science experience, and give students the same sort of struggles and highs and lows in doing research as I experienced in the lab," says Hirsch, who studied molecular biology in college and worked in the biotech industry before becoming a teacher.

When he teaches, he sets students up as they would be if they were scientists in a lab. "There's some sort of problem and there has to be either mystery in how you get to the solution or mystery in the starting materials and what you end up with. It can't all be cookbook," he says, "Give them as little information as possible to keep them going."

A student's CRISPR notes at the camp. Image: Mallory Locklear

Back on Long Island, the CRISPR group was joined by two boys discussing how getting negatively charged DNA through the bacteria's negatively charged cell wall is a problem they would have to surmount in order to transform their bacteria's DNA. One of the boys, John Michael, jumped up and grabbed two magnets from a drawer to give a visual.

As they talked about what helps solve this particular problema buffer with three chemicals that will neutralize the negative DNA charge and make the bacteria's cell wall permeablethey began setting up their bacterial cultures and then expertly streaked their sample across a number of plates they'd put together earlier in the day. Their culture would have to sit overnight before they could do the next steps.

Throughout the day, some students showed hesitation when working through some of the steps, always short-lived. They mixed and poured agar, labeled plates, and pipetted reagents with very little help from Powel.

Teaching CRISPR to kids is about bringing science to the public and bringing the public into discussions about how to implement it. It's hard to have meaningful conversations about CRISPR or the ethics of using it if people don't understand what it is. So, the only way to implement safeguards or boundaries that aren't driven by misunderstanding or fear is to make CRISPR accessible to everyonescientists, non-scientists, even kids.

At the very beginning of class, one student summed up something Powel has been instilling in her students all summer and what scientific understanding and education is so often about, "It's about seeing things in a new way."

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These Kids Are Learning CRISPR At Summer Camp - Motherboard

Researchers in Portland, Oregon have, for the first time, edited a human embryo in the US.

This work adds to the promise of CRISPR, and it stands as an important step toward the birth of the first genetically modified humans.

By now, most of us know what CRISPR gene editing is. At the very least, we have heard of this revolutionary technology that allows us to alter DNA - the source code of life itself.

One day, CRISPR could allow us to delete genes in order to eradicate genetic diseases, add in new genes in order to vastly improve various biological functions, or even genetically modify human embryos in order to create an entirely new class of humans of super humans.

But first, we have a lot of research to do.

And that brings us to today. Reports from MIT were just released which assert that the very first attempt at creating genetically modified human embryos in the United States has been carried out by a team of researchers in Portland, Oregon.

"So far as I know this will be the first study reported in the US," Jun Wu, who played a role in the project and is a collaborator at the Salk Institute, said to MIT.

According to MIT, the work was led by Shoukhrat Mitalipov, who comes from the Oregon Health and Science University.

Although details are scarce at this point, sources familiar with the work assert that the research involved changing the DNA of one-cell embryos using CRISPR gene-editing.

Further, Mitalipov is believed to have broken records in two notable ways:

This is notable because, despite the fact that it has been around for several years now, CRISPR is still an incredibly new tool - one that could have unintended consequences.

As previous work published in the journal Nature Methods revealed, CRISPR-Cas9 could lead to unintended mutations in a genome.

However, the work was later reviewed by researchers at another institution and the findings were brought into question.

It remains to be seen whether the original study will be corrected or retracted, but this development highlights the importance of peer review in science.

In this regard, Mitalipov's work brings us further down the path to understanding exactly how CRISPR works in humans, and reveals that is it possible to avoid both mosaicism (changes that are taken up not by only some of the cells of an embryo, as opposed to all of them) and ;off-target' effects.

It is important to note that none of the embryos were allowed to develop for more than a few days, and that the team never had any intention of implanting them into a womb.

However, it seems that this is largely due to ongoing regulatory issues, as opposed to issues with the technology itself.

In the United States, all efforts to turn edited embryos into a baby - to bring the embryo to full term - have been blocked by Congress, which added language to the Department of Health and Human Services funding bill that forbids it from approving any such clinical trials.

Yet, the potential of the CRISPR-Cas9 system as a gene editing technology is undeniable.As previously mentioned, it has seen success in developing possible cancer treatments, in making animals disease-resistant, and it has even shown promise in replacing antibiotics altogether.

This new work adds to the promise of CRISPR, and stands as an important step toward the birth of the first genetically modified humans.

This article was originally published by Futurism. Read the original article.

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Scientists Have Used CRISPR to Edit a Human Embryo in The US For The First Time - ScienceAlert

Internet users have a variety of format options in which to store their movies, and biologists have now joined the party. Researchers have usedthe microbial immune system CRISPRCasto encode a movie into the genome of the bacteriumEscherichia coli.

The technical achievement, reported on July 12 inNature, is a step towards creating cellular recording systems that are capable of encoding a series of events, says Seth Shipman, a synthetic biologist at Harvard Medical School in Boston, Massachusetts. While studying brain development, Shipman became frustrated by the lack of a technique to capture how cells in the brain take on distinct identities. This inspired him to explore the possibility of making cellular recorders.

Cells have this privileged access to all sorts of information, he says. I would like to have these molecular recordings functioning in the developing nervous system and recording information.

To develop such a system, however, his team would need to establish a method for recording hundreds of events in a cell. Shipman and his colleagues, including Harvard geneticist George Church, harnessed the CRISPRCas immune system best known for enabling researchers to alter genomes with relative ease and accuracy.

Shipmans team exploited the ability tocapture snippets of DNA from invading virusesand store them in an organized array in the host genome. In nature, those snippets then target an enzyme to slice up the invaders DNA. (It is typically this targeted DNA cutting that geneticists harness for gene editing.)

The team designed its system so that these snippets corresponded to pixels in an image. The researchers encoded the shading of each pixelalong with a barcode that indicated its position in the imageinto 33 DNA letters. Each frame of the movie consisted of 104 of these DNA fragments.

The movie that the researchers selected consisted of five frames adapted from British photographer Eadweard MuybridgesHuman and Animal Locomotionseries. The photos show a mare named Annie G. galloping in 1887.

The team introduced the DNA intoE. coliat a rate of one frame per day for five days. The researchers then sequenced the CRISPR regions in a population of bacteria to recover the image. Because the CRISPR system adds DNA snippets sequentially, the position of each snippet in the array could be used to determine the original frame to which the snippet belonged.

The system is a long way from becoming the recorder of which Shipman dreamt while studying the brain. Substantial technological advances are needed to reach that point, notes bioengineer Randall Platt at the Swiss Federal Institute of Technology (ETH) Zurich in Basel. Because no single cell takes up more than one DNA snippet from each frame, the information for the movie is stored across populations of cells. And no one has yet transferred the CRISPR arrays into mammalian cells. Its full of limitations, but this is pioneering work that theyre doing, he says. Its elegant.

Other CRISPRCas systems can convert RNA into DNA that is then inserted into the CRISPR array[2]. This could open up the door to using the arrays to track gene expression without cracking cells open to remove their RNA, Platt notes.

Victor Zhirnov, chief scientist at the Semiconductor Research Corporation in Durham, North Carolina, calls the work revolutionary, and hopes to start tinkering with the technique at his research foundation. Its like this is the first aeroplane flown in 1903: it was just a curiosity, says Zhirnov. But ten years from that, we had aeroplanes almost like what we have today.

This article is reproduced with permission and wasfirst publishedon July 12, 2017.

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Lights, Cameras, CRISPR: Biologists Use Gene Editing to Store Movies in DNA - Scientific American

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What happened

Shares ofCRISPR Therapeutics(NASDAQ: CRSP), a leaderin the field ofgenetic engineering, rose more than 11% in June, according to data fromS&P Global Market Intelligence.

Investors can largely thank two news items for the jump. First, CRISPR and MaSTherCell SA announced that they have signed a development and manufacturing agreement related to allogeneic CAR-T therapies. The deal calls forMaSTherCell to handle the development and manufacturing of CRISPR's compound CTX101 in clinical studies aimed at treating a number of diseases.

Image Source: Getty Images.

Second, the company announced that ithas been awarded a patent for its CRISPR/Cas9 technology in China. The company believes that this patent covers the company's technology in very broad terms, which should help to protect it from competition down the road.

Given the upbeat news flow, it isn't hard to figure out why the share price was lifted last month.

It's great to see that the company continues to partner with others in an effort to move its pipeline forward. CRISPR has already succeeded at landing industry giants like Vertex Pharmaceuticalsand Bayeraspartners, so addingMaSTherCell to the list is certainly a positive. The collaboration deal with Vertex is especiallyexciting since it included a hefty upfront payment, and also required Vertex to make an investment in the company.

On the other hand, CRISPR'sproducts are still highly experimental, so shareholders will have a lot of waiting to do before they learn how these products perform in the clinic. For that reason, potential investors must approach this stock with an ultra long-term mindset if they're interested in getting in.

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Why CRISPR Therapeutics AG Jumped 11.7% in June - Madison.com

In BriefA study published earlier this year warned scientists ofpotential complications with CRISPR/Cas9, but after review byresearchers at another institution, the findings of that study arebeing brought into question. It remains to be seen whether theoriginal study will be corrected or retracted, but this developmenthighlights the importance of peer review in science. Wrongfully Accused?

A study published earlier this year warned scientists of potential complications in their work with CRISPR/Cas9, but after review by researchers at another institution, the findings of that study are being brought into question. The original paper was publishedby a team at Columbia University Medical Center (CUMC) in May of this year in the journal Nature Methods.

In the studys original press release, co-author Stephen Tsang said: We feel its critical that the scientific community consider the potential hazards of all off-target mutations caused by CRISPR, including single nucleotide mutations and mutations in non-coding regions of the genome. The researchers had sequenced the genomes of mice whose genes had previously been editing using CRISPR in an attempt to cure their blindness. The genomes revealed there were 1,500 single-nucleotide mutations and over 100 larger deletions,= and/or insertions in two of the mice which had been modified using the gene-editing technique.

In their study, the researchers attributed these genetic anomalies to the use of CRISPR but a team of researchers from Harvard University and MIT have reviewed the paper and are challenging that attribution. In a paper published in bioRxiv a pre-print server for biology research which is not a peer reviewed journal the researchers pointed out the CUMC study had several serious problems. The most glaring of which, the Harvard and MIT researchers argue, is that the mutations found in the mice that were attributed to CRISPR were more likely than not already present in those mice before they were exposed to the gene-editing technique.

The third mouse whose genome had been edited with CRISPR did not demonstrate the mutations, and was also not as genetically similar as the two mice who did. The Harvard and MIT research team argue that this supports the theory that the mutations in the pair of mice were not caused by CRISPR. It should be noted that this criticism comes from a small study that was not peer reviewed.

The teams goal in refuting the research is to make sure the rest of the scientific community is reminded of the lasting impact claims that are not well supported by data can have. Given these substantial issues, we urge the authors to revise or re-state the original conclusions of their published work so as to avoid leaving misleading and unsupported statements to persist in the literature, the team explained in their paper.

The peer review process is essential to scientific disciplines other than biology and genetics, of course. Whether researchers are making claims about climate change, artificial intelligence, or medical treatments, rigorous review of their methods, data, and analysis by other scientists who are doing similar work is essential. This process ensures that the research and the way it is presented is accurate, of high quality, and will be useful not only to the scientific community, but to the general public.

For teams who have spent months if not years heavily focused on a single study, trial, or data set, it can be very easy to lose sight of the bigger picture. Peer review offers research teams the chance to address inconsistencies, data that doesnt add up, and conclusions that make assumptions or inferences that arent supported by the data.

While there have certainly been instances where teams have intentionally fabricated data in order to mislead their peers and the public, most members of the scientific community do not mislead intentionally. But thats why the peer review process is so important. It remains to be seen if the team at CUMC plans to revisit, or possible retract, their paper in light of the response.

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Researchers Refute Study That Claims CRISPR Causes Unexpected Mutations - Futurism

The Broad Institute of MIT and Harvard said today they have joined discussions to create a nonexclusive CRISPR/Cas9 joint licensing pool being coordinated by MPEG LA, which operates patent pool licensing programs across institutions and countries.

The patent pool would facilitate the licensing of patents covering CRISPRwhich stands for clustered regularly interspaced short palindromic repeatsby creating a one-stop shop for commercial users without forcing licensees to pursue agreements with several entities, the Broad said.

The Broad disclosed today that it responded June 28, two days before the deadline set in April by MPEG LA, a provider of one-stop licenses for standards and other technology platforms. MPEG LA requested submissions by CRISPR/Cas9 patent holders to join in creating a global joint licensing platform related to the technology.

The Broad submitted for evaluation 22 patents13 U.S. patents and 10 European patentscontained within 10 patent families. That submission, the Broad said, was also being made on behalf of joint patent owners Harvard University, the Massachusetts Institute of Technology, and The Rockefeller University.

We strongly support making CRISPR technology broadly available, Issi Rozen, CBO of the Broad Institute, said in a statement. We look forward to working with others to ensure the widest possible access to all key CRISPR intellectual property.

The Broad says it joins with MIT, Harvard, and Rockefeller to make CRISPR tools freely available to the academic and nonprofit communities and issue nonexclusive licenses for most types of commercial research, including agriculture. The exception is human therapeutics, where the Broad limits exclusivity through its Inclusive Innovation model, which offers one licensee exclusive use for a defined two-year period, followed by an open call for applications by other groups. The two-year exclusive period has already ended for CRISPR applications.

According to the Institute, the patents it submitted for discussion include not only those related to CRISPR/Cas9, but more broadly relevant CRISPR patents and application related to the technology.

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Broad Institute Joins CRISPR Patent Pool Talks | GEN - Genetic Engineering & Biotechnology News (blog)

Its been a good week for Neon: After posting positive cancer vaccine data a few days ago, the Fierce 15 winner has signed a new R&D pact with gene-editing biotech CRISPR Therapeutics.

In a brief update, the pair said that the research collaboration [will] explore the combination of each companys proprietary technologies to develop novel T cell therapies.

CRISPR, which went public last year, is currently working on early-stage CRISPR/Cas9 technology that could change the way many diseases, from cancer to sickle cell disease are treated, while Neon is working on neoantigen vaccines a new form of personalized immunotherapy in which antigens that are found in diseased tissues but not normally in healthy patients are used to develop targeted vaccines.

Neon's peptide-based vaccine (NEO-PV-01) is made from up to 20 antigens harvested from patients' own tumor cells, and last week it posted data from a small study of six patients with melanoma who were given the vaccine at around the same time as they underwent surgery to remove the tumor in a bid to prevent recurrence.

More than 70% of the peptides successfully generated measurable immune responses, and after over two years of followup, four of the six patients were recurrence-free.

Cancer vaccines have largely failed to deliver on their early promise in the clinic, but these data, coupled with positive results also coming from an RNA-based vaccine developed by BioNTech last week, has boosted confidence in this research area.

RELATED: Fierce 15 winner Neon Therapeutics

Neon Therapeutics is committed to employ leading technologies, including CRISPR/Cas9, to improve the quality of our cell therapy approaches, said Richard Gaynor, M.D., president of research and development at Neon.

This collaboration will explore gene-based technologies from CRISPR Therapeutics with our expertise in neoantigen science and T cell biology.

Back in January, the company also said it raised a chunky $70 million in its series B round, and has also combined its candidate with Bristol-Myers Squibb's checkpoint inhibitor Opdivo (nivolumab); data from that early test should be out before the years end.

Samarth Kulkarni, president and chief business officer of CRISPR Therapeutics, added: We look forward to applying our proprietary CRISPR/Cas9 technologies in a variety of ways to generate potent T cell therapies directed against neoantigens. This collaboration with Neon Therapeutics supplements our internal efforts in immuno-oncology and broadens the spectrum of approaches we are able to explore.

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Neon partners up with CRISPR Therapeutics for IO work - FierceBiotech

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CRISPR: 5 ways it will save your life - Red Bull Red Bull How bioengineering is becoming a game of Ctrl-X, C and V, and saving countless lives along the way. Microsoft-founder Bill Gates told Wired magazine in 2010 ... and more »

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Representation of the Cpf1 protein in complex with its target RNA and target DNA. The determination of its structure at high resolution has allowed to reveal the modus operandi of this genetic engineering tool. / University of Copenhagen

A scientific team from in the Novo Nordisk Foundation Center for Protein Research (NNF-CPR), at the University of Copenhagen, has succeeded in visualizing and describing how a new system for genome editing, known as Cpf1, works. This protein belongs to the Cas family and enables the cleavage of double stranded DNA, thus allowing the initiation of the genome modification process. The results of the study have been published in the journal Nature.

Guillermo Montoya, a researcher in the fields of biochemistry and molecular biology who led the study, explains to SINC that the new molecular scissors will enable us to more safely modify and edit the instructions written in the genome, due to the utmost precision of the target DNA sequence recognition.

The CRISPR Cas9 system for cutting and paste genome sequences is already being used to modify animal and plant genomes. Also to treat illnesses, such as cancer and retinal diseases, in humans and its applications are growing very fast.

X-Ray Crystallography Technique

Researchers across the world are trying to perfect this genome editing technique with the aim of making it yet more precise and efficient. To achieve this, they have also focused on other proteins that specifically cut DNA, such as Cpf1, whose manipulation can direct them to specific locations in the genome. Montoyas team has achieved this using an X-ray Crystallography to decipher the molecular mechanisms controlling this process.

We radiated the crystals of the Cpf1 protein using X-rays to be able to observe its structure at atomic resolution, enabling us to see all its components, points out the co-author of this study. X-ray diffraction is one of the main biophysical techniques used to elucidate biomolecular structures, he continues.

In his opinion, the main advantage of Cpf1 lies in its high specificity and the cleaving mode of the DNA, since it is possible to create staggered ends with the new molecular scissors, instead of blunt-ended breaks as is the case with Cas9, which facilitates the insertion of a DNA sequence.

The high precision of this protein recognising the DNA sequence on which it is going to act functions like a GPS, directing the Cpf1 system within the intricate map of the genome to identify its destination. In comparison with other proteins used for this purpose, it is also very versatile and easy to be reprogrammed, Montoya adds.

Genetic diseases and tumours

These properties make this system particularly suitable for its use in the treatment of genetic diseases and tumours, he affirms.

The team has previously worked with the French biotechnology company Celletics on the use of meganucleases other proteins that can be redesigned to cut the genome in a specific location to treat certain types of leukemia.

The new technology can also be used to modify microorganisms, with the aim of synthesising the metabolites required in the production of drugs and biofuels, adds Montoya.

This researcher, from Getxo (Biscay, Spain), says that there are many companies interested in this new technology. They are mostly from the biotechnology sector in the field of microorganism manipulation, but cannot be named due to confidentiality agreements.

This article has been republished frommaterialsprovided by SINC. Note: material may have been edited for length and content. For further information, please contact the cited source.

Reference

Stella, S., Alcn, P., & Montoya, G. (2017). Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage. Nature.

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Improving Genome Editing: CRISPR Cpf1 mechanism visualized - Technology Networks

Researchers have revealed the structure and action of a new type of 'molecular scissors' known as Cpf1, which may improve CRISPR genome editing.

Using X-ray crystallography, the team were able to view the three-dimensional structure of Cpf1, a bacterial protein from the CRISPR-Cas family of molecules. Like CRISPR/Cas9, the CRISPR-Cpf1 tool has potentially widespread applications in biotechnology.

They were also able to visualise exactly how Cpf1 unzips and cuts double-stranded DNA, saying that Cpf1 'acts like a GPS' across the genome to recognise and cleave DNA (genetic) sequences with high precision.

The new CRISPR-Cpf1 technique has therapeutic potential fortreating cancers and genetic diseases, and could also 'be used to modify microorganisms, with the aim of synthesising the metabolites required in the production of drugs and biofuels', according to lead researcher, Professor Guillermo Montoya, from the Novo Nordisk Foundation Center for Protein Research (NNF-CPR) at the University of Copenhagen, Denmark.

The researchers, who published their study in Nature, first created Cpf1 gene constructs and inserted these into Escherichia coli bacteria to trigger Cpf1 gene expression which they observed. 'We radiated the crystals of the Cpf1 protein using X-rays to be able to observe its structure at atomic resolution, enabling us to see all its components. X-ray diffraction is one of the main biophysical techniques used to elucidate biomolecular structures,' said Professor Montoya.

While cutting DNA using Cas9 results in blunt ended strands, the study showed that Cpf1 cleaves DNA in a staggered fashion leaving 'sticky ends', which makes insertion of a DNA sequence easier. Furthermore, in comparison to Cas9, thestructural component for DNA recognition and binding for CRISPR-Cpf1 (called the Protospacer Adjacent Motif or PAM) is located far from the DNA cleavage site. The resulting physical separation may prevent damage of PAM site and offer new possibilities for DNA cleavage.

Professor Montoya said: 'The high precision of this protein recognising the DNA sequence on which it is going to act functions like a GPS, directing the Cpf1 system within the intricate map of the genome to identify its destination. In comparison with other proteins used for this purpose, it is also very versatile and easy to be reprogrammed.'

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How new 'molecular scissors' may give crisper CRISPR - BioNews

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5 ways CRISPR will save your life Red Bull Past tense, because of Clustered Regularly Interspaced Short Palindromic Repeats, or CRISPR for short. CRISPR works much like a DNA-level pair of scissors and glue stick. It dramatically lowers the bar for biotech innovation, making it 99 percent ... and more »

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5 ways CRISPR will save your life - Red Bull

Wall Street Journal (subscription)

Crispr Patent-Holders Move Toward Easing Access to Gene-Editing Technology Wall Street Journal (subscription) A holder of key patents to the Crispr gene-editing technology is willing to join a world-wide joint patent poola development that medical and legal experts think could hasten the development of new human therapies. The Broad Institute of MIT and ...

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Crispr Patent-Holders Move Toward Easing Access to Gene-Editing Technology - Wall Street Journal (subscription)

After CRISPR, theres a new genetic technique with a tongue-in-cheek name in town: LASSO cloning.

Researchersfrom four institutions, including the US-based John Hopkins, Rutgers and Harvard, and the University of Trento in Italy, have developed a new technology tostudy large chunks of DNA and their function. The work behind it was recently published inNature Biomedical Engineering,and a patent was filed earlier this month.

This molecular tool is called long adapter single-stranded oligonucleotide, or LASSO for short. The lasso rope metaphor applies to the tools mechanism, which can capture and clone long sequences of DNA fragments. Fragment length had so far been the main challenge for cloning probes and the genome sequencing field at large. Next generation sequencing (NGS), which has gained a lot of attention in medical research, relies on sequencing short fragments that are then put together, like a puzzle, by bioinformatics tools. However, this method falls short for certain types of samples. Short reads capture only about 100 basepairs, or DNA letters, at a time, while LASSO can read more than1000 base pairs.

As a proof of concept, the researchers set out to test LASSO probes in biotechs favorite microorganism,E. coli. The tool managed to simultaneously clone over 3000 DNA fragments of the genome ofE. coli, capturing around 75% of the targets and leaving almost all of the non-targeted DNA alone, and the studys authors say theres still certainly room for improvement.

LASSO cloning should enable the scientific community to build libraries of a given organisms protein in a much faster and cheaper way, democratizing research that was so far only within the reach of big research consortia. The usefulness of such studies ranges from a better understanding of organisms to the ability to screen large libraries of natural enzymes and compounds that could be valuable leads in drug discovery,as it has been done before for some species likePenicilliumfungistrains, for example.

One of the organisms to be better studied is, of course, human beings. Researchers already tested LASSO cloning with human DNA, something has the potential to yield new biomarkers for a range of diseases. Another focus of interest is the human microbiome. As described in the same paper, LASSO was used to build the first protein library of the microbiome, and the research team hopes that it can improve precision medicine strategies that takeinto account the microbes living within us.

Images by DWilliam/Pixabay and Jennifer E. Fairman/John Hopkins University

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Better than CRISPR? LASSO Cloning ropes in Long-Read DNA - Labiotech.eu (blog)

How many mutations?

By Michael Le Page

As you were. In May, a study claimed that the revolutionary CRISPR gene editing technique can cause thousands of unwanted and potentially dangerous mutations. The authors called for regulators to reassess the safety of the technique.

But doubts were raised about these claims from the very beginning, not least because it was a tiny study involving just three mice. Some critics have called for the paper to be withdrawn. Now a paper posted online on 5 July has proposed a simple and more plausible explanation for the controversial results. If its right, the authors of the original study were wrong.

We strongly encourage the authors to restate the title and conclusions of their originalpaper or provide properly controlled experiments that can adequately support their claims, write the team behind the new study. Not doing so does a disservice to the field and leaves the misleading impression that the strong statements and recommendations found in their paper are adequately supported by the data presented.

The aim of gene editing is to make a precise change in a DNA sequence while leaving the rest of the genome untouched. Gene editing can be used to introduce desirable changes into plants and animals (and perhaps people too one day), and to treat a range of disorders in people.

Gene editing has been around for decades but it remained extremely difficult and expensive until the revolutionary CRISPR technique was discovered in 2013. CRISPR is so cheap and easy that it is already widely used by researchers around the world, and nearly 20 clinical trials in people are already getting underway. The rapid pace of development has been unprecedented.

But have doctors been rushing to use it too soon? When Stephen Tsang of Columbia University Medical Center and colleagues compared the entire genomes of two CRISPR-edited mice with a third one, they found thousands of shared mutations in the two edited mice.

Tsang and co attributed to these mutations to CRISPR, and issued a widely-covered press release that suggested CRISPR is far riskier than dozens of other studies had suggested.

It has always been clear that CRISPR, like other gene-editing techniques, can sometimes make alterations other than the intended one. These off-target changes are most likely to occur when the CRISPR machinery binds to DNA sequences very similar to the target one.

For this reason, studies on the safety of CRISPR have usually looked to see if any sequences resembling the target sequences have been altered. Most have found few unwanted changes, suggesting CRISPR is safe. And some teams have already tweaked the CRISPR machinery to reduce these off-targets effects even more.

Tsang and colleagues claimed that by sequencing the entire genome, they found off-target mutations missed by studies that only looked at sites resembling the target sequence. But there is a much simpler explanation, says the latest study: the two CRISPR-edited mice just happened to be more closely related and thus shared more mutations.

Tsang and colleagues assumed the three mice they studied were essentially genetically identical because their parents were very closely related, but the way the colony of mice was maintained means this was probably not the case, the team, which includes Luca Pinello of Harvard University, say.

This explanation makes sense for another reason, too. The shared mutations in the edited mice were nowhere near DNA sequences resembling the one were targeted for editing, Pinello and colleagues point out, so its far from clear why CRISPR would cause mutations in these same sites in two different mice.

I agree the two mice are indeed more likely to be closely related, says geneticist Gaetan Burgio of the Australian National University, one of the many critics of the original paper. He says its publication in a prominent journal was a failure of peer review.

Journal reference: bioRxiv, DOI: 10.1101/159707

Read more: CRISPR causes many unwanted mutations, small study suggests

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CRISPR gene editing technique is probably safe, study confirms ... - New Scientist

CRIPSR-Cas is one tool that could help keep pace with the growing demand for more sustainable agricultural solutions.

DuPont Pioneer

When Carmen and I were young, we made our home at the foot of the Sandia Mountains east of Albuquerque. Back then, for a weekend outing on a pleasant summers day, we would avoid Interstate 25 and travel the Turquoise Trail National Scenic Byway, the picturesque backroad that links Albuquerque with Santa Fe through the high country. The Byway is named for the semi-precious, blue-green mineral deposits of hydrated copper and aluminum phosphatesought after by Native Americans for more than a millenniumwhich are found near the northern stretches of the road. Once bustling mining towns, scattered along the way like nuggets of the wild west, may also be discovered and explored; ghost towns such as Golden and Madrid (pronounced MAD-rid, not Ma-DRID).

During one of these trips, we stopped at the Golden General Merchandise Store and struck up a conversation with the proprietors, Vera and Bill Henderson. We learned that in 1962, Bill and Vera purchased the store from her parents. Together they turned the failing store into a thriving arts and crafts trading post featuring Native American jewelry, rugs, Kachina dolls, and pottery for sale.

The Hendersons (both of these dear friends have passed away) were true and devoted connoisseurs and patrons of local and regional artisans. Vera especially wanted customers to share her passion in these handicrafts. If a potential patron showed lackadaisical interest in the artistic qualities of a piece or the artist who made it, she would send them on their way, telling them to take their business to Santa Fe!

I admired Veras spunk and forthrightness. She cared deeply, and she stood up for what she believed. She inspired me to learn the stories told about everyday Pueblo Indian life by silversmiths such as the Kewa Pueblo artist Vidal Aragon.

For example, a silver bracelet we purchased depicted a Pueblo village around which grew stalks of corn. As a kid growing up in the D.C. suburbs, about all I knew of corn was corn flakes. The Hendersons passion for Native American traditions encouraged me to deepen my cultural appreciation of food and agriculture.

The Keresan-speaking tribes of the American Southwest believed in a female corn goddess, whom they called Iyatiku. It is she who led the first people to the surface of the earth from Shipap, her underground realm. To provide for their sustenance and wellbeing, Iyatiku planted pieces of her heart in the fields surrounding their village. These tiny tokens of her body grew into lush fields of life-sustaining corn!

This worldviewthat seeds and plants are sacred gifts available to and shared by allis common among native peoples around the world. This ancient perspective stands in stark contrast to the modern view corporate ag-science offers us. To illustrate, I will use DuPont Pioneers CRISPR-Cas waxy corn as an example.

DuPont Pioneer has recently announced its intentions to commercialize waxy corn hybrids developed in the laboratory using a new and powerful gene editing technique called CRISPR-Cas: clustered regularly interspaced short palindromic repeats-CRISPR-associated system. (Thats not a typo. This two-part acronym incorporates its own acronym!)

Waxy corn produces a high amylopectin starch content, which is milled for a number of everyday consumer food and non-food uses including processed foods, adhesives and high-gloss paper. DuPont Pioneer created this hybrid using CRISPR-Cas advanced gene editing technology to program the plants molecular machinery to synthesize amylopectin starch in abnormally high levels.

According to DuPont Pioneers website and their September 2016 webinar, CRISPR-Cas is a more efficient and targeted plant breeding technology. In the past, genetic engineering of plants often has relied upon transgenic techniques, which modifies the host species by adding genetic material from different species (i.e., GMOs). CRISPR-Cas does not incorporate foreign DNA from other species. Its a continuation of what people have been doing since plants were first domesticatedselecting plants for their desired characteristics like higher yields, disease resistance, longer shelf life or better nutrition.

CRISPR-Cas gene editing technology is likened to word processing, by which scientist delete, edit, or search and replace specific portions of a plants genetic code. CRISPR-Cas uses molecular scissors to cut a specific section of DNA. After the DNA is cut, either a piece is removed and the loose ends are spliced back together eliminating an undesired trait; or a desired trait is inserted into the gap and the DNA is stitched together again.

DuPont Pioneer seeks to further the science and expand the adoption of CRISPR-Cas across all crops, including soybeans, rice, wheat, canola, sunflowers, fruits and vegetables. Agricultural products developed with CRISPR-Cas will be like the ones that we have been producing through conventional plant breeding for generations and will be subject to extensive testing prior to commercialization. As with every technology we apply, we hold ourselves accountable to our core values, to our customers and to consumers.

According to DuPont Pioneer, current Food and Drug Administration law will not require labelling of CRISPR-Cas waxy corn. Even under the newly enacted National Bioengineered Food Disclosure Law of 2016, their genetically edited waxy corn will not meet the definition of bioengineered as written in the law, and would therefore not require disclosure as a bioengineered food.

For much of human history, edible plants were cherished as gifts from the gods. Now, they are becoming high-tech, commercial products of industry. Once seeds were available to all. Now they are becoming proprietary, patented, intellectual property, licensed through end-user agreements.

Are these trends truly more sustainable agricultural solutions as industry claims they are? Are they empowering farmers? Or are corporate monopolies of engineered seeds leading to bondage and dependency for farmers who are getting trapped in debt to pay royalties in the words of Vandana Shiva, philosopher and eco-feminist.

On a personal level, I relish the smell of a freshly picked ear of corn. For me, summer would not be complete without a picnic lunch serving up hot corn-on-the-cob. I wonder, would my body and soul feel as nourished if I knew I was biting into kernels of CRISPR-Cas corn? If not, should I adapt my aesthetic sensibilities to these new agricultural realities by adopting the attitude CRISPR-Cas corn, and I dont care (sung to the antebellum minstrel tune Jimmy Crack Corn)?

J. Dirk Nies

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Science to Live By: CRISPR-Cas Corn - The Crozet Gazette

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The gene-editing tool CRISPR may cause thousands of unintended mutations, but critics say its way too soon to accuse it of infidelity1.

A two-page study, published 30 May in Nature Methods, put biologys hottest technique in the crosshairs, questioning its ability to rewrite DNA with the precision necessary for medicine. The papers findings quickly dominated social media conversations on biology. And the stocks of biotech companies with CRISPR-based projects dipped by as much as 15 percent.

But some researchers are loath to end their love affair with CRISPR. Reports of the methods infidelity, they say, are greatly exaggerated. One reason, they note, is that the study is small just two mice for CRISPR and a single control mouse.

I think its an important finding that we really need to follow up, but its really hard to judge why there are so many [mutations], says Guoping Feng, professor of brain and cognitive sciences at the Massachusetts Institute of Technology. He says another enzyme the team used may in fact have caused the errant mutations.

Two weeks after the papers publication, Nature Methods editors added a note to the paper, saying they are considering the criticism of the results and plan to respond soon.

CRISPR is a molecular scalpel that cuts DNA. It can home in on a specific spot on the molecule using a piece of RNA as a guide. The tool holds significant medical promise because it could help modify or fix genes that cause medical conditions.

In 2016, Alexander Bassuks team reported injecting mouse embryos with CRISPR fused to its usual protein partner, CAS9, which binds to DNA. The researchers targeted a gene called PDE6B that is involved in vision. The experiment was designed to correct a mutation that causes blindness in the mice2. It did.

For the new study, Bassuk and his collaborators looked for off-target effects of the treatment. They sequenced the whole genomes of the two mice and the control mouse. They compared the results from the edited mice against a database that includes genomes of 36 mouse strains.

CRISPR-CAS9 introduced more than 100 unintended mutations and more than 1,600 one-letter swaps in the code of DNA, the researchers found.

None of these changes had any obvious consequences. As far as we can tell, it hasnt affected the mice, says Bassuk, professor of pediatric neurology at the University of Iowa in Iowa City. But the researchers tested only the mices vision and do not know if the mutations affected the animals behavior or perception.

This was not the first time that CRISPR had caused accidental mutations, though previous reports found far fewer mutations3.

Its always been a concern for everyone in the field that this is not a completely clean method, says Anis Contractor, associate professor of physiology at Northwestern University in Chicago. Contractor was not involved in the research but uses CRISPR to make mouse models. This is a big red flag.

Contractor and others say the findings may prompt a change in best practices when using the method. Scientists may need to sequence the genomes of their models an expensive task to uncover any unexpected mutations.

Others, however, are downplaying the results.

I dont think this paper has any merit for CRISPR research, says George Church, professor of genetics at Harvard University. I think its a negative example that we can use as a cautionary tale. Church is co-founder of Editas Medicine, a biotechnology company that is using the technique to develop gene-editing therapies. The company lost 12 percent of its value the day the study was published. (Its stock has since gone up, surpassing its previous value.)

Church and the companys other executives wrote to Nature Methods with a laundry list of concerns about the paper. Their biggest beef, says Church: The studys control mouse likely wasnt genetically identical to the ones that had been edited with CRISPR, so its impossible to know whether the mutations resulted from the method.

Instead, Church argues, its possible that the mutations represent natural genetic variance between the animals. Church stops short of saying the paper should be retracted but calls it a rushed job. Another gene-editing company, Intellia Therapeutics, voiced similar complaints.

The team also used an unusual version of the editing system, says Feng, who is using CRISPR to create animal models of autism. He says the use of extra nickase, an enzyme that can cause breaks in a strand of DNA, could have caused the mutations.

I couldnt figure out what reason youd need to do it this way, he says.

Bassuk points out that the team did the editing work in 2015, early in CRISPRs use.

We used what was available at the time, Bassuk says. Its obviously not what people are using in 2017. He says he is not sure whether the editing system made a difference in the results.

In the past three months, researchers have debuted the first two mouse models of autism created using CRISPR. No one has yet published work on using CRISPR to correct genes in animal models of the condition.

In the short term, the findings will definitely temper the enthusiasm for CRISPR models, says J. Tiago Gonalves, assistant professor of neuroscience at Albert Einstein College of Medicine in New York, who was not involved in the research. But in the end, Im confident the problems will be solved and well figure out whats happening.

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CRISPR goes wild, and scientists debate its fidelity | Spectrum ... - Spectrum

CRISPR-Cas3 is a subtype of the CRISPR-Cas system, a widely adopted molecular tool for precision gene editing in biomedical research. Aspects of its mechanism of action, however, particularly how it searches for its DNA targets, were unclear, and concerns about unintended off-target effects have raised questions about the safety of CRISPR-Cas for treating human diseases.

Harvard Medical School and Cornell University scientists have nowgenerated near-atomic resolution snapshots of CRISPR that reveal key steps in its mechanism of action. The findings, published in Cell on June 29, provide the structural data necessary for efforts to improve the efficiency and accuracy of CRISPR for biomedical applications.

Through cryo-electron microscopy, the researchers describe for the first time the exact chain of events as the CRISPR complex loads target DNA and prepares it for cutting by the Cas3 enzyme. These structures reveal a process with multiple layers of error detectiona molecular redundancy that prevents unintended genomic damage, the researchers say.

High-resolution details of these structures shed light on ways to ensure accuracy and avert off-target effects when using CRISPR for gene editing.

To solve problems of specificity, we need to understand every step of CRISPR complex formation, said Maofu Liao, assistant professor of cell biology at Harvard Medical School and co-senior author of the study. Our study now shows the precise mechanism for how invading DNA is captured by CRISPR, from initial recognition of target DNA and through a process of conformational changes that make DNA accessible for final cleavage by Cas3.

Discovered less than a decade ago, CRISPR-Cas is an adaptive defense mechanism that bacteria use to fend off viral invaders. This process involves bacteria capturing snippets of viral DNA, which are then integrated into its genome and which produce short RNA sequences known as crRNA (CRISPR RNA). These crRNA snippets are used to spot enemy presence.

Acting like a barcode, crRNA is loaded onto members of the CRISPR family of enzymes, which perform the function of sentries that roam the bacteria and monitor for foreign code. If these riboprotein complexes encounter genetic material that matches its crRNA, they chop up that DNA to render it harmless. CRISPR-Cas subtypes, notably Cas9, can be programmed with synthetic RNA in order to cut genomes at precise locations, allowing researchers to edit genes with unprecedented ease.

To better understand how CRISPR-Cas functions, Liao partnered with Ailong Ke of Cornell University. Their teams focused on type 1 CRISPR, the most common subtype in bacteria, which utilizes a riboprotein complex known as CRISPR Cascade for DNA capture and the enzyme Cas3 for cutting foreign DNA.

Through a combination of biochemical techniques and cryo-electron microscopy, they reconstituted stable Cascade in different functional states, and further generated snapshots of Cascade as it captured and processed DNA at a resolution of up to 3.3 angstromsor roughly three times the diameter of a carbon atom.

In CRISPR-Cas3, crRNA is loaded onto CRISPR Cascade, which searches for a very short DNA sequence known as PAM that indicates the presence of foreign viral DNA.

Liao, Ke and their colleagues discovered that as Cascade detects PAM, it bends DNA at a sharp angle, forcing a small portion of the DNA to unwind. This allows an 11-nucleotide stretch of crRNA to bind with one strand of target DNA, forming a seed bubble.

The seed bubble acts as a fail-safe mechanism to check whether the target DNA matches the crRNA. If they match correctly, the bubble is enlarged and the remainder of the crRNA binds with its corresponding target DNA, forming what is known as an R-loop structure.

Once the R-loop is completely formed, the CRISPR Cascade complex undergoes a conformational change that locks the DNA into place. It also creates a bulge in the second, non-target strand of DNA, which is run through a separate location on the Cascade complex.

Only when a full R-loop state is formed does the Cas3 enzyme bind and cut the DNA at the bulge created in the non-target DNA strand.

The findings reveal an elaborate redundancy to ensure precision and avoid mistakenly chopping up the bacterias own DNA.

To apply CRISPR in human medicine, we must be sure the system is accurate and that it does not target the wrong genes, said Ke, who is co-senior author of the study. Our argument is that the CRISPR-Cas3 subtype has evolved to be a precise system that carries the potential to be a more accurate system to use for gene editing. If there is mistargeting, we know how to manipulate the system because we know the steps involved and where we might need to intervene.

Structures of CRISPR Cascade without target DNA and in its post-R-loop conformational states have been described, but this study is the first to reveal the full sequence of events from seed bubble formation to R-loop formation at high resolution.

In contrast to the scalpel-like Cas9, CRISPR-Cas3 acts like a shredder that chews DNA up beyond repair. While CRISPR-Cas3 has, thus far, limited utility for precision gene editing, it is being developed as a tool to combat antibiotic-resistant strains of bacteria. A better understanding of its mechanisms may broaden the range of potential applications for CRISPR-Cas3.

In addition, all CRISPR-Cas subtypes utilize some version of an R-loop formation to detect and prepare target DNA for cleavage. The improved structural understanding of this process can now enable researchers to work toward modifying multiple types of CRISPR-Cas systems to improve their accuracy and reduce the chance of off-target effects in biomedical applications.

Scientists hypothesized that these states existed but they were lacking the visual proof of their existence, said co-first author Min Luo, postdoctoral fellow in the Liao lab at HMS. The main obstacles came from stable biochemical reconstitution of these states and high-resolution structural visualization. Now, seeing really is believing.

Weve found that these steps must occur in a precise order, Luo said. Evolutionarily, this mechanism is very stringent and has triple redundancy, to ensure that this complex degrades only invading DNA.

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Bringing CRISPR into Focus - Bioscience Technology