Archive for the ‘Crispr’ Category

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nventing a nonsurgical way to zap away fat is probably not the first thing that comes to mind when one thinks about the revolutionary genome-editing technique CRISPR, but maybe it should be.

A Boston dermatologist credited with developing the novelapproach to fat loss is now the owner of aprized internet domain: crispr.com.

Though perhaps not as lucrative as the technology itself, thedomain could have been advantageousforCRISPR-focusedcompanies Editas Medicine, CRISPR Therapeutics, Intellia that might have seen a clever branding opportunity. Butuntil recently, crispr.com had languished in the electronic ether for a decade, under the control of a cybersquatting computer engineer.

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According tothe Internet Corporation for Assigned Names and Numbers (ICANN), the nonprofit organization that coordinates domain names, however, CRISPR.comis now owned by Dr. Dieter Manstein.

The German-born dermatologist, who is affiliated with Massachusetts General Hospital, is best known for inventing Coolsculpting, a controlled cooling way to remove body fat, and although he also does serious research on melanoma,he does not seem to be into genome-editing for, say, acne prevention.

University of California appeals CRISPR patent setback

Manstein did not reply to interview requests, but internet records show he is a prolific buyer of domain names, with 776 registered to his Gmail account. They include some related to his profession laserskintreatments.net, lasertattoo.org, bodysculpting.com, and germanskincare.com, for example and some not, such as iwantmyson.com.

No public records indicate what Manstein paid for crispr.com, but some domain names similar to crispr.com are currentlygoing for up to five figures.An auction for crisprcas9.co (Cas9 is the enzyme used in the most common CRISPR system) starts at $2,000, with bids due May 8, while genecrispr.com and genomecrispr.com were both asking a shade under $40,000.

Experts doubt the domain name purchased by Manstein commanded anything close to this years priciest so far. 01.com, for instance, would have set you back $1,820,000, while Refi.com sold for $500,000 and Physician.com for $179,000.

Nikolay Kolev was the previous owner of CRISPR.com. Kolev, who on Twitter describes himself as a father, husband, software developer, Orthodox Christian, and Bulgarian in California, wasnt prescient when he registered crispr.com in March 2006.

Rather, he credited the domains existence to the photo-sharing site Flickr, which was popular when he first registered CRISPR.com in 2006.

I registered (or won it on an auction, I cant recall) as a Flickr-like version of crisper, he told STAT via Twitter. Yes, Flickr was cool at the time.

Like many domain name owners, Kolev didnt build a website. He did not answer questions about whether he was approached by any of the biotech companies, and none of the likely suspectsreplied to questions from STAT as to whether they ever sought to purchase it.

Domain-name brokers, however, noticed that a transaction for crispr.com was in escrow as of March 31, meaning a buyer had deposited payment with a third party and was waiting for Kolev to transfer ownership. As of this month, according to ICANN, the new owner is Manstein.

Sharon Begley can be reached at sharon.begley@statnews.com Follow Sharon on Twitter @sxbegle

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CRISPR.com was for sale, and you won't guess who bought it - STAT

Even since Alexander Fleming stumbled across penicillinthe first antibiotic drugscientists knew our fight with evolution was on.

Most antibiotics work by blocking biological processes that allow bacteria to thrive and multiply. With prolonged, low-dosage use, however, antibiotics become a source of pressure that forces bacteria to evolveand because these microorganisms are extremely adept at swapping and sharing bits of their DNA, when one member becomes resistant, so does most of its population.

Even more terrifying is this: because the same family of antibiotics generally act on the same biological pathways, when bacteria generate a mutation that resists one type of drug, it often renders that entire family of drugs useless.

The arms race with increasing high rates of antibiotic resistance has forced scientists to think outside the box. Although still a work in progress, teams of scientists are now working on a truly creative strategy: a pill carrying the genome-editing power tool CRISPR that instructs harmful bacteria to shred their own genes to bits.

In essence, scientists are returning CRISPR to its roots. While best known as a handy way to manipulate DNA in mice and humans, CRISPR is actually a part of the bacterias immune defense system.

Just like our immune systems can turn against ourselves, scientists are now hoping to give harmful bacteria a destructive autoimmune disease.

When optimized, a CRISPR pill could have the ability to precisely target single strains of harmful bacteria, while leaving other typesincluding beneficial bacteria in the gutintact.

First, the bad news: were rapidly losing our war on microbugs, and if things dont change were heading full throttle into an antibiotic apocalypse.

Part of the bacterias survival prowess comes from their ability to rapidly multiply. Under the right conditionsa damp, nutrition-packed human cell, for examplethe common gut bug E. Coli multiplies exponentially, doubling every thirty minutes. This gives their DNA plenty of chances to mutate and for the species to adapt.

Whats more, bacteria arent stingy about sharing their DNA. Antibiotic-resistant genes are often carried on snippets of genetic material that floats around in the bacterias innards. Microbugs can literally extend a tube out to their neighbors to inject these genetic pieces, thus sharing their resistant genes far and wide.

In what is likely the most chilling demonstration of antibacterial resistance in action, you can now watch a strain of bacteria become impervious to increasingly higher doses of an antibioticup to 1,000 times higherin just 11 days.

Obviously, heaping larger and larger doses of drugs on already weak patients isnt the solution. What we need isnt stronger drugs, but smarter drugs.

Most of our current antibiotics work in one of few ways: interfering with the bacterias DNA repair system, stopping the bacterias ability to reproduce, or weakening the bacterias cell wallsomething our cells dont haveuntil it explodes.

The downside of antibiotics is they are a sledgehammer that depletes and destroys the gut microbial community, says Dr. Jan Peter van Pijkeren at the University of Madison-Wisconsin, who is working on CRISPR-based antibiotics. You want to instead use a scalpel in order to specifically eradicate the microbe of interest.

The new CRISPR pill eschews all traditional ideas, instead relying on the bacterias mortal enemy: a type of virus called bacteriophages (or, more endearingly, phages).

Like all viruses, phages cant reproduce on their own. Instead, they constantly invade bacteria and inject viral genomes into the hosts, hoping to co-opt bacterial machinery to make armies of phage replicas.

This onslaught of foreign genetic material has spurred bacteria into developing a sophisticated defense system. When bacteria detect viral DNA, they store bits and pieces of it into their own genome to form a genetic sequence that we call CRISPRa molecular memory of the phage, so to speak.

When the bacteria detect a matching viral DNA sequence, they activate CRISPR and, together with a pair of protein scissors called Cas-9, the system destroys the viral DNA. Voila, invasion blocked.

Scientists have found that the CRISPR system doesnt cut the bacterias own DNA under normal circumstances; when it does, the result is lethal.

This spurred an ingenious idea: scientists could use phages to inject custom Trojan horses that trick the bacteria into cutting its own genes.

The idea of CRISPR-based approaches is to enact sequence-specific antimicrobial activity, placing selective pressure against genes that are bad rather than conserved bacterial targets, explains Dr. Timothy Lu at MIT.

Previously, Lus team successfully manufactured phages that carry DNA similar to antibiotic-resistant genes. Because the phage DNA was misdeemed a foreign invader, it spurred the bacterias CRISPR system into action, snipping away at its own genome and committing suicide.

Bacteria cells without the resistant gene didnt sound their alarm bells, and in turn were spared and ended up dominating the population.

Similarly, van Pijkeren is working on a CRISPR pill that contains a phage harboring bits of genomic DNA of Clostridium difficile.

C. diff is an infection that is notoriously difficult to treat, causing long-term gastrointestinal distress in nearly half a million Americans in a single year, resulting in at least 15,000 deaths. The current best treatmentwhen antibiotics failis a fecal transplant from healthy donors, but the method is still considered experimental, and long-term effects are unclear (there is, of course, also the ick factor).

Because phages are readily chewed up in our stomach acid, van Pijkeren is working on packaging them up into Lactobacillus bacteriaa common probiotic often present in yogurt.

As an initial proof-of-concept step, the team has successfully engineered Lactobacillus bacteria to produce phages that target themselves. The next step, van Pijekeren explains, is to use these probiotics as motherships that travel the gut, dispensing phages along the way to infect any nearby C. diff, and tricking them into hacking up their own DNA.

Toexploit these microbes to deliver therapeutics is very appealing because we know humans have been safely consuming them for thousands of years, says van Pijkeren.

Promises aside, scientists already see several snags that might prevent the CRISPR pill from unleashing its full power.

Part of it is the delivery vehiclethe phage. Phages are rather particular about the types of bacteria they invade, and matching courier to target will require additional research.

Scientists also worry that if not all targeted bacteria are killed or if the process isnt fast enough, some resilient members may evade the attack. Bacteria are also known to develop resistance to phage invasionwhich means that if the treatment continues, selection pressure will push the population towards resistance.

But phages arent the only way to deliver CRISPR pills, and scientists are hopeful.

The way I view it is not that we will be able to make an evolution-proof therapy, but that the genetic engineering tools will become more robust so that as evolution happens, we can rapidly develop countermeasures, says Lu.

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CRISPR Pill May Be Key in Fight Against Antibiotic Resistance - Singularity Hub

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Intellia Therapeutics, Inc. (NASDAQ: NTLA) and CRISPR Therapeutics AG (NASDAQ: CRSP), two leading genome editing companies focused on the development of potentially curative therapies, announced that the United States Patent and Trademarks Office (USPTO) is expected to issue a CRISPR/Cas9 genome editing patent to Vilnius University (Vilnius). Intellia and CRISPR are nonexclusive sublicensees for a defined field of human therapeutic, prophylactic, and palliative uses (including companion diagnostics), excluding anti-fungal and anti-microbial applications.

The Vilnius patent claims are directed to CRISPR/Cas9 complexes assembled in vitro and used for site-specific modification of target DNA sequences. CRISPR/Cas9 complexes, referred to as CRISPR ribonucleoproteins or RNPs, are contemplated for use in a number of ex vivo applications in which cells, such as blood cells, may be corrected or edited outside of the body before being returned to a patient as a potential therapeutic. The patent is expected to issue on May 2, 2017 as U.S. Patent No. 9,637,739.

This new patent, together with the companies respective rights to foundational CRISPR/Cas9 intellectual property co-owned by The Regents of the University of California, University of Vienna and Dr. Emmanuelle Charpentier, provide CRISPR and Intellia with complementary rights to inventions claimed by the earliest developers in the discovery and application of CRISPR/Cas9 technology.

Intellia has a non-exclusive, royalty-free, worldwide sublicense to the Vilnius intellectual property through a 2014 license agreement with Caribou Biosciences, Inc., under which Intellia has an exclusive, worldwide sublicense to certain of Caribous developed or in-licensed CRISPR/Cas9 technology intellectual property for a defined field of human therapeutic, prophylactic, and palliative uses (including companion diagnostics), excluding anti-fungal and anti-microbial applications. Caribou has certain rights to Vilnius Universitys intellectual property through a cross-license agreement with the DuPont Company.

CRISPR acquired rights to this patent as a result of a cross-option and license agreement with Intellia which was completed in connection with the global agreement on foundational intellectual property for CRISPR/Cas9 gene editing that both companies jointly announced with the co-owners and licensors, as well as another licensee, on December 16, 2016. Under the cross-option and license agreement, CRISPR has a royalty-free worldwide sublicense to Intellias rights to the Vilnius intellectual property.

Link:

Intellia (NTLA), CRISPR Therapeutics (CRSP) Receive U.S. Patent for CRISPR/Cas9 Ribonucleoprotein Complexes - StreetInsider.com

LSIPR and law firm HGF held a webinar yesterday focusing on CRISPR and how to navigate the IP landscape.

The two presenters from HGF, Dr Claire Irvine and Catherine Coombes, covered multiple angles on this groundbreaking technology, including the science behind it and the named inventors for the technology.

The panellists also spoke in detail about licensingin European countries, among other issues.

In the US, a CRISPR patent dispute is continuing with an appeal from the University of California (UC), Berkeley in a case against the Broad Institute of Harvard and MITs patents concerning the technology.

The Patent Trial and Appeal Board ruled in February that the Broads patents concerning CRISPR do not interfere with patent claims filed by UC.

The case was referred to in the presentation as potentially being the biggest patentability mess ever.

To watch the webinar, click here. The full presentation is also available on demand.

See the rest here:

CRISPR webinar: HGF discusses IP landscape - Life Sciences Intellectual Property Review (subscription)

CRISPR technology is a simple yet powerful tool for editing genomes. It allows researchers to easily alter DNA sequences and modify gene function. Its many potential applications include correcting genetic defects, treating and preventing the spread of diseases and improving crops. However, its promise also raises ethical concerns.

In popular usage, "CRISPR" (pronounced "crisper") is shorthand for "CRISPR-Cas9." CRISPRs are specialized stretches of DNA. The protein Cas9 (or "CRISPR-associated") is an enzyme that acts like a pair of molecular scissors, capable of cutting strands of DNA.

CRISPR technology was adapted from the natural defense mechanisms of bacteria and archaea (the domain of single-celled microorganisms). These organisms use CRISPR-derived RNA and various Cas proteins, including Cas9, to foil attacks by viruses and other foreign bodies. They do so primarily by chopping up and destroying the DNA of a foreign invader. When these components are transferred into other, more complex, organisms, it allows for the manipulation of genes, or "editing."

CRISPRs:"CRISPR" stands for "clusters of regularly interspaced short palindromic repeats." It is a specialized region of DNA with two distinct characteristics: the presence of nucleotide repeats and spacers. Repeated sequences of nucleotides the building blocks of DNA are distributed throughout a CRISPR region. Spacers are bits of DNA that are interspersed among these repeated sequences.

In the case of bacteria, the spacers are taken from viruses that previously attacked the organism. They serve as a bank of memories, which enables bacteria to recognize the viruses and fight off future attacks.

This was first demonstrated experimentally by Rodolphe Barrangou and a team of researchers at Danisco, a food ingredients company. In a2007 paperpublished in the journal Science, the researchers usedStreptococcus thermophilusbacteria, which are commonly found in yogurt and other dairy cultures, as their model. They observed that after a virus attack, new spacers were incorporated into the CRISPR region. Moreover, the DNA sequence of these spacers was identical to parts of the virusgenome. They also manipulated the spacers by taking them out or putting in new viral DNA sequences. In this way, they were able to alter the bacteria's resistance to an attack by a specific virus. Thus, the researchers confirmed that CRISPRs play a role in regulating bacterial immunity.

CRISPR RNA (crRNA):Once a spacer is incorporated and the virus attacks again, a portion of the CRISPR istranscribedand processed intoCRISPR RNA, or "crRNA." The nucleotide sequence of the CRISPR acts as a template to produce a complementary sequence of single-stranded RNA.Each crRNA consists of a nucleotide repeatand a spacer portion, according to a 2014 review by Jennifer Doudna and Emmanuelle Charpentier, published in the journal Science.

Cas9:The Cas9 protein is an enzyme that cuts foreign DNA.

The protein typically binds to two RNA molecules: crRNA and another called tracrRNA (or "trans-activating crRNA"). The two then guide Cas9 to the target site where it will make its cut. This expanse of DNA is complementary to a 20-nucleotide stretch of the crRNA.

Using two separate regions, or "domains" on its structure, Cas9 cuts both strands of the DNA double helix, making what is known as a "double-stranded break," according to the 2014 Science article.

There is a built-in safety mechanism, which ensures that Cas9 doesn't just cut anywhere in a genome. Short DNA sequences known as PAMs ("protospacer adjacent motifs") serve as tags and sit adjacent to the target DNA sequence. If the Cas9 complex doesn't see a PAM next to its target DNA sequence, it won't cut. This is one possible reason thatCas9 doesn't ever attack the CRISPRregion in bacteria, according to a 2014 review published in Nature Biotechnology.

The genomes of various organisms encode a series of messages and instructions within their DNA sequences. Genome editing involves changing those sequences, thereby changing the messages. This can be done by inserting a cut or break in the DNA and tricking a cell's natural DNA repair mechanisms into introducing the changes one wants. CRISPR-Cas9 provides a means to do so.

In 2012, two pivotal research papers were published in the journalsScienceandPNAS, which helped transform bacterial CRISPR-Cas9 into a simple, programmable genome-editing tool.

The studies, conducted by separate groups, concluded that Cas9 could be directed to cut any region of DNA. This could be done by simply changing the nucleotide sequence of crRNA, which binds to a complementary DNA target. In the 2012 Science article, Martin Jinek and colleagues further simplified the system by fusing crRNA and tracrRNA to create a single "guide RNA." Thus, genome editing requires only two components: a guide RNA and the Cas9 protein.

"Operationally, you design a stretch of 20 [nucleotide] base pairs that match a gene that you want to edit," saidGeorge Church, Robert Winthrop Professor of Genetics at Harvard Medical School. An RNA molecule complementary to those 20 base pairs is constructed. Church emphasized the importance of making sure that the nucleotide sequence is found only in the target gene and nowhere else in the genome. "Then the RNA plus the protein [Cas9] will cut like a pair of scissors the DNA at that site, and ideally nowhere else," he explained.

Once the DNA is cut, the cell's natural repair mechanisms kick in and work to introduce mutations or other changes to the genome. There are two ways this can happen. According to theHuntington's Outreach Project at Stanford (University), one repair method involves gluing the two cuts back together. This method, known as "non-homologous end joining," tends to introduce errors. Nucleotides are accidentally inserted or deleted, resulting inmutations, which could disrupt a gene. In the second method, the break is fixed by filling in the gap with a sequence of nucleotides. In order to do so, the cell uses a short strand of DNA as a template. Scientists can supply the DNA template of their choosing, thereby writing-in any gene they want, or correcting a mutation.

CRISPR-Cas9 has become popular in recent years. Church notes that the technology is easy to use and is about four times more efficient than the previous best genome-editing tool (calledTALENS).

In 2013, the first reports of using CRISPR-Cas9 to edit human cells in an experimental setting were published by researchers from the laboratories ofChurchandFeng Zhangof the Broad Institute of the Massachusetts Institute of Technology and Harvard. Studies using in vitro(laboratory) and animal models of human disease have demonstrated that the technology can be effective in correcting genetic defects. Examples of such diseases includecystic fibrosis, cataracts and Fanconi anemia, according to a 2016 review article published in the journal Nature Biotechnology. These studies pave the way for therapeutic applications in humans.

CRISPR technology has also been applied in the food and agricultural industries to engineer probiotic cultures and to vaccinate industrial cultures (for yogurt, for example) against viruses. It is also being used in crops to improve yield, drought tolerance and nutritional properties.

One other potential application is to create gene drives. These are genetic systems, which increase the chances of a particular trait passing on from parent to offspring. Eventually, over the course of generations, the trait spreads through entire populations, according to theWyss Institute. Gene drives can aid in controlling the spread of diseases such as malaria by enhancing sterility among the disease vector femaleAnopheles gambiaemosquitoes according to the 2016 Nature Biotechnology article. In addition, gene drives could also be usedto eradicate invasive species and reverse pesticide and herbicide resistance,according to a 2014 article by Kenneth Oye and colleagues, published in the journal Science.

However, CRISPR-Cas9 is not without its drawbacks.

"I think the biggest limitation of CRISPR is it is not a hundred percent efficient," Church told Live Science. Moreover, the genome-editing efficiencies can vary. According to the 2014 Science article by Doudna and Charpentier, in a study conducted in rice, gene editing occurred in nearly 50 percent of the cells that received the Cas9-RNA complex. Whereas, other analyses have shown that depending on the target, editing efficiencies can reach as high as 80 percent or more.

There is also the phenomenon of "off-target effects," where DNA is cut at sites other than the intended target. This can lead to the introduction of unintended mutations. Furthermore, Church noted that even when the system cuts on target, there is a chance of not getting a precise edit. He called this "genome vandalism."

The many potential applications of CRISPR technology raise questions about the ethical merits and consequences of tampering with genomes.

In the 2014 Science article, Oye and colleagues point to the potential ecological impact of using gene drives. An introduced trait could spread beyond the target population to other organisms through crossbreeding. Gene drives could also reduce the genetic diversity of the target population.

Making genetic modifications to human embryos and reproductive cells such as sperm and eggs is known as germline editing. Since changes to these cells can be passed on to subsequent generations, using CRISPR technology to make germline edits has raised a number of ethical concerns.

Variable efficacy, off-target effects and imprecise edits all pose safety risks. In addition, there is much that is still unknown to the scientific community. In a 2015 article published in Science, David Baltimore and a group of scientists, ethicists and legal experts note thatgermline editing raises the possibility of unintended consequences for future generations"because there are limits to our knowledge of human genetics, gene-environment interactions, and the pathways of disease (including the interplay between one disease and other conditions or diseases in the same patient)."

Other ethical concerns are more nuanced. Should we make changes that could fundamentally affect future generations without having their consent? What if the use of germline editing veers from being a therapeutic tool to an enhancement tool for various human characteristics?

To address these concerns, the National Academies of Sciences, Engineering and Medicine put together acomprehensive report with guidelines and recommendationsfor genome editing.

Although the National Academies urge caution in pursuing germline editing, they emphasize "caution does not mean prohibition." They recommend that germline editing be done only on genes that lead to serious diseases and only when there are no other reasonable treatment alternatives. Among other criteria, they stress the need to have data on the health risks and benefits and the need for continuous oversight during clinical trials. They also recommend following up on families for multiple generations.

Additional resources

Broad Institute: A timeline of pivotal work on CRISPR

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What Is CRISPR? - livescience.com

Researchers at the Wellcome Trust Sanger Institute and their colleagues at the University of British Columbia have developed a novel method for studying how the bacterium Chlamydia trachomatis interacts with the human immune system. Theyused a combination of gene-editing and stem cell technologies to make the model that helped lead to the discovery of two genes from our immune system, interferon regulatory factor 5 (IRF5) and interleukin-10 receptor subunit alpha (IL-10RA), as key players in fighting a Chlamydia infection.

The results, reported inNature Communications ("Exploiting Induced Pluripotent Stem Cell-Derived Macrophages to Unravel Host factor Influencing Chlamydia trachomatis Pathogenesis"), identify novel drug targets for the sexually transmitted disease.

In this study, scientists created macrophages from human induced pluripotent stem cells to study Chlamydia infection. Macrophages have a crucial role in killing Chlamydia to limit the infection. The macrophages produced responded to the disease in a similar way to those taken from human blood, meaning they are more human-like than those produced by previous methods.

This new model will enable scientists to study how Chlamydia interacts with the human immune system to avoid antibiotics and spread, according toAmy Yeung, Ph.D., first author from the Wellcome Trust Sanger Institute.

"Chlamydia is tricky to study because it can permeate and hide in macrophages where it is difficult to reach with antibiotics. Inside the macrophage, one or two Chlamydia cells can replicate into hundreds in just a day or two, before bursting out to spread the infection," she said. "This new system will allow us to understand how Chlamydia can survive and replicate in human macrophages and could have major implications for the development of new drugs."

The new model has advantages over previous methods that used macrophages either derived from mice, which differ from humans in their immune response, or immortalized human macrophage cell lines, which are genetically different from normal macrophages, she added.

In the study, scientists used CRISPR/Cas9 to genetically edit the human induced pluripotent stem cells, and then see the effects of the genetic manipulation on the resulting macrophages' ability to fight infection.

Robert Hancock, Ph.D., lead author from the University of British Columbia and associate faculty member at the Wellcome Trust Sanger Institute, noted that, "We can knock out specific genes in stem cells and look at how the gene editing influences the resulting macrophages and their interaction with Chlamydia. We're effectively sieving through the genome to find key players and can now easily see genes that weren't previously thought to be involved in fighting the infection."

The team discovered two macrophage genes in particular that were key to limiting Chlamydia infectionIRF5 and IL-10RA. When these genes were switched off, the macrophages were more susceptible to Chlamydia infection. The results suggest these genes could be drug targets for new chlamydia treatments.

"This system can be extended to study other pathogens and advance our understanding of the interactions between human hosts and infections," explainedGordon Dougan, Ph.D., senior author from the Wellcome Trust Sanger Institute. "Weare starting to unravel the role our genetics play in battling infections, such as Chlamydia, and these results could go toward designing more effective treatments in the future."

See the rest here:

CRISPR and Stem Cells Identify Novel Chlamydia Drug Targets - Genetic Engineering & Biotechnology News

Cross-Species Transplantation

One application benefiting from CRISPR/Cas9 technology is xenotransplantation, or cross-species transplantation. It offers the prospect of an unlimited supply of organs and cells, and it could resolve the critical shortage of human tissues.

For ethical and compatibility reasons, xenotransplantation shifted away from nonhuman primates as a potential source of donor tissues. Instead, the discipline began to focus on porcine organs. Nonetheless, in 1997, pig-to-human transplants were banned worldwide due to concerns about the transmission to humans of porcine endogenous retroviruses (PERVs), which are integrated into the genome of all pigs.

According to George Church, Ph.D., professor of genetics, Harvard Medical School, work was undertaken in his laboratory on PK15 porcine kidney epithelial cells to determine if PERVs could be eradicated. It was crucial to avoid disrupting the envelope gene and the terminal regulatory elements, as both of these could be important during normal pig fetal growth. In addition, a highly conserved target in the viral polymerase gene was desired for the guide RNA (gRNA) to bind.

First, the copy number of PK15 PERV was determined to be 62. Then, when CRISPR/Cas9 was used along with two gRNAs, one which did the bulk of the work, all 62 copies of the PERV pol gene were disrupted, demonstrating the possibility that PERVs could be inactivated for potential clinical pig-to-human xenotransplantation. The repeats were well separated, and not clustered, which could have meant higher toxicity.

After two weeks of cell culture, about 8% of clones were 100% altered, and no rearrangements were found. Although a few off-target effects and point mutations were expected, they were deemed unlikely to have an impact on pig fetal development. As with conventional breeding, PERV-free clones were empirically selected as they were the healthiest.

In addition to disrupting dozens of endogenous viral elements, Dr. Churchs group altered dozens of genes involved in immune and blood-clotting functions to increase human compatibility. Some of the changes were so extensive that more powerful DNA recombination tools, and not CRISPR, were utilized.

This work may benefit eGenesis, a Cambridge biotech focused on leveraging CRISPR technology to deliver safe and effective human transplantable cells, tissues, and organs. eGenesis was cofounded by Dr. Church and Luhan Yang, Ph.D., in early 2015 and is based on their research.

Continued here:

More Tooth, More Tail in CRISPR Operations | GEN - Genetic Engineering & Biotechnology News (press release)

The ability to quickly and cheaply detect minute amounts of specific nucleic acid (DNA and RNA) sequences could bring significant public health benefits. For example, it could be used to detect viral or bacterial infections in a population during outbreaks. Other possible uses include finding antibiotic-resistance genes in bacteria or tumor mutations in the body. Current methods for detecting nucleic acids involve trade-offs in sensitivity, specificity, simplicity, cost, and speed.

Drs. James J. Collins and Feng Zhang of the Broad Institute of MIT and Harvard developed a new approach by adapting the CRISPR system, which bacteria use to defend themselves from other microbes. CRISPR enzymes use short guide RNAs to identify specific target sequences to cleave. Zhangs group previously discovered that one CRISPR enzyme, called Cas13a, has an interesting collateral effect. After being activated by its target RNA sequence, Cas13a goes on to indiscriminately slice other non-targeted RNA nearby.

The researchers took advantage of this property to design a CRISPR-based nucleic acid detection platform. To detect when a target sequence was present, they added reporter RNA designed to emit a signal when cut. Whenever Cas13a was activated, it would go on to cut the reporter RNA and emit a signal. The study was funded in part by NIHs National Institute of Allergy and Infectious Diseases (NIAID) and National Institute of Mental Health (NIMH). The team described their approach online in Science on April 13, 2017.

The scientists first tested Cas13a enzymes from different bacteria to identify which had the best RNA-guided cutting activity. As amounts of DNA and RNA in samples can be minute, the researchers applied a technique called recombinase polymerase amplification, which can amplify nucleic acids without special equipment. Another enzyme could also be added to the reaction to convert DNA to RNA for Cas13a detection.

The team called this system SHERLOCK. Tests showed that SHERLOCK could detect RNA or DNA molecules at minute levels called attomolar levels. Established nucleic acid detection approaches can be similarly sensitive, but SHERLOCK gave more consistent results.

The researchers demonstrated several potential uses. SHERLOCK was able to detect specific strains of Zika and Dengue virus. It could detect Zika virus in serum, urine, and saliva from patients. It could distinguish pathogenic strains of bacteria. It could distinguish single base differences in DNA extracted from human saliva. Finally, it could detect cancer mutations among DNA fragments at levels like that found in patient blood.

Notably, SHERLOCK yielded comparable results when its components were freeze-dried, reconstituted, and tested on glass fiber paper. The scientists calculated that a paper test could be designed and created in a matter of days for as little as $0.61 per test. These qualities highlight the potential of this system for diagnostic field applications.

We can now effectively and readily make sensors for any nucleic acid, which is incredibly powerful when you think of diagnostics and research applications, Collins says. The scientific possibilities get very exciting very quickly.

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

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Quick, Sensitive Diagnostic Tests with CRISPR - Technology Networks

DENVER--(BUSINESS WIRE)--

World licensing leader MPEG LA, LLC today invited holders of CRISPR-Cas9 patents to participate in the creation of a global CRISPR-Cas9 Joint Licensing Platform that will make their groundbreaking technologies widely accessible.

Pooling the foundational CRISPR patent rights under a single nonexclusive, cost-effective, transparent license will allow the market to focus on the creation of new products and therapies that accelerate and expand CRISPRs deployment, said Larry Horn, MPEG LA President and CEO. Just as MPEG LAs pioneering efforts to manage licensing overhead and mitigate litigation risk helped assure the success of digital video in the consumer electronics industry, the CRISPR-Cas9 Joint Licensing Platform can do the same for healthcare and other biotechnology industries but with an impact far more profound.

At the same time, both foundational and other patent owners would be rewarded for their inventions from their fair share of reasonable royalties from the pool and incentivized to develop more, added Kristin Neuman, Executive Director, Biotechnology Licensing at MPEG LA. As a voluntary market-based business solution that balances access with incentive, an independently managed pool offers the best hope for addressing market and public interests in a way that will unleash CRISPRs full potential for the benefit of humanity.

MPEG LA welcomes CRISPR-Cas9 patent holders who would like to participate in this ground floor opportunity to create a Joint Licensing Platform to visit http://www.mpegla.com/main/pid/CRISPR/default.aspx for more information, including terms and procedures governing patent submissions and eligibility. At least one eligible patent is necessary to participate in the license development process, and eligibility will be determined by MPEG LA at no cost to submitters. Interested parties are asked to make their initial patent submissions by June 30, 2017. Although submissions will continue to be accepted in order to assure that the joint license includes as much relevant intellectual property as possible for the benefit of the market, those who submit patents by that date and are found eligible will be invited to attend an initial meeting with other eligible patent rights holders to explore the potential for joint terms on which the CRISPR-Cas9 Joint Licensing Platform may be offered. Except for confidentiality, participation is without obligation or commitment, including attendance at future meetings, until such time as an eligible patent holder may decide to join the Joint Licensing Platform.

MPEG LA, LLC

MPEG LA is the worlds leading provider of one-stop licenses for standards and other technology platforms. Starting in the 1990s, it pioneered the modern-day patent pool helping to produce the most widely used standards in consumer electronics history. MPEG LA has operated licensing programs for a variety of technologies consisting of more than 14,000 patents in 84 countries with some 230 patent holders and more than 6,000 licensees. By assisting users with implementation of their technology choices, MPEG LA offers licensing solutions that provide access to fundamental intellectual property, freedom to operate, reduced litigation risk and predictability in the business planning process. In turn, this enables inventors, research institutions and other technology owners to monetize and speed market adoption of their assets to a worldwide market while substantially reducing the cost of licensing. In addition to consumer electronics, MPEG LA is developing advanced Li-Ion battery and other gene editing patent pools and has conceived licensing ventures for molecular diagnostics and oligonucleotide therapeutics. For more information, go to http://www.mpegla.com.

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MPEG LA Invites CRISPR-Cas9 Patents to be Pooled in a One-Stop License - Yahoo Finance

Source: American Association of Swine VeterinariansAs resistance to antibiotics grows in the United States, researchers are looking for new ways to fight germs like Clostridium difficile, a bacterium that can cause fatal infections in hospitals and nursing homes.

One way to do that: a CRISPR pill that instructs harmful bacteria to self-destruct. CRISPR is the powerful gene-editing technology already being explored as a way to precisely edit human genes to cure diseases. But the technologys versatility is such that its being studied for a huge range of other uses. Just last week scientists in Boston showed they could craft CRISPR into cheap, simple diagnostic tests.

Now scientists want to turn it into ultra-precise antimicrobial treatments to specifically kill your bacteria of choice, says food scientist Jan-Peter Van Pijkeren of the University of Wisconsin-Madison.

While not a household name, Clostridium difficile tops the U.S. Centers for Disease Control and Preventions list of urgent drug-resistant threats. A 2015 study by the agency found that the bug caused nearly half a million infections in Americans, including 15,000 deaths.

CRISPR was actually discovered in bacteria. In fact, the system is an immune defense bacteria use to fend off invading viruses called bacteriophage.

The way it works is that bacteria store memories of viral DNA in their own genomes as clustered regularly interspaced short palindromic repeats or CRISPRs. They use this memory, plus a DNA-slicing enzyme known as a Cas to recognize and chop up the genes of invading bacteriophage.

Van Pijkerens idea is to use bacteriophage to send a false message to C. difficile, one that instead causes the bacteria to make lethal cuts to its own DNA.

To do it, Van Pijkeren lab is developing bacteriophage capable of carrying a customized CRISPR message. On their own, the bacteriophage would quickly get broken down by stomach acid. So to get the viruses into a person, Van Pijkeren plans to add them to a cocktail of innocuous bacteria, or probiotic, that a person could swallow as a pill or a liquid.

Van Pijkeren compares the probiotic to a mothership. As the probiotic bacteria pass through a persons intestinal tract, the bacteriophage would burst forth and infect any nearby C. difficile, causing them to hack up their own DNA.

Van Pijkeren says the probiotic is still in early stages of development and hasnt been tested in animals. However, researchers have previously shown that using bacteriophages to trigger CRISPR can efficiently kill skin bacteria and might also help combat Shigella sonnei, a diarrheal infection common in the developing world.

A few companies, including Eligo Bioscience in Paris and Locus Biosciences, a spinout from North Carolina State University, have started to pursue CRISPR-based antibiotics commercially.

The appeal of using CRISPR is that such drugs would be very specific theoretically, they would kill a single species of germ while leaving beneficial bacteria intact. Broad-spectrum antibiotics, by contrast, kill off large swaths of both good and bad bacteria. In fact, the overuse and abuse of conventional antibiotics is what leads to resistance in the first place.

As long as we house patients together in a hospital or in a nursing home and we give a lot of them antibiotics were going to have a problem with C. difficile, says Herbert DuPont, director of the Center for Infectious Diseases at the University of Texas.

Thats why alternatives like the one Van Pijkerens is developing are greatly needed. However, Peter Fineran, a microbiologist at the University of Otago in New Zealand, says there is still quite a long way to go before this replaces our current antibiotics.

He says one challenge in deploying the approach against more types of bacteria will be finding suitable bacteriophage. Thats because each type tends to infect only specific bacteria. Fineran predicts CRISPR will become a complementary tool in the arsenal against the rise in antibiotic resistant and pathogenic bacteria.

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'CRISPR pill' instructs harmful bacteria to self-destruct - National Hog Farmer

A new highly sensitive diagnostic system for diseases has been adapted from CRISPR.

Named SHERLOCK (Specific High-sensitivity Enzymatic Reporter UnLOCKing), the diagnostic systemcould detect miniscule amounts of RNA or DNA from samples and offer rapid, accurate results without the need for sophisticated lab equipment.

'This tool offers the sensitivity that could detect an extremely small amount of cancer DNA in a patient's blood sample, for example, which would help researchers understand how cancer mutates over time,' said Professor James Collins at MIT and Harvard University, who co-led the team behind the system. 'For public health, it could help researchers monitor the frequency of antibiotic-resistant bacteria in a population. The scientific possibilities get very exciting very quickly.'

The team led by Professor Collins and Professor Feng Zhang at MIT and Harvard University combined novel methods with established techniques to amplify genetic material in a sample, find a target sequence and then create a visible result.

The system uses an enzyme called Cas13a which targets RNA, and which was discovered by Professor Zhang of MIT and colleagues last year. By attaching a sequence tag, Cas13a can be guided to find and cut a specific RNA target. Once it has done this it will randomly cut any nearby pieces of 'collateral' RNA, regardless of their sequence.

The system adds so-called fluorescent reporter RNA to the samples, which emits a fluorescent signal only when cut. So if Cas13a finds its target sequence, its subsequent cutting of the reporter RNA produces a fluorescence which can be easily detected without the use of sophisticated equipment.

The precision of the enzyme is such that even a difference ofone base-pair- such as between the genetic codes of the African and American strains of Zika - will affect whether or not activation occurs. It is also able to detect concentrations as low as two molecules in a quintillion.

The system can be run in a standard test tube or on glass fibre paper, and requires no high-tech lab equipment or temperatures higher than body heat. The authors say the molecules for the test can be designed and made for as little as US $0.61.

'One thing that's especially powerful about SHERLOCK is its ability to start testing without a lot of complicated and time-consuming upstream experimental work,' said Professor Pardis Sabeti of Harvard University, a co-author of the paper. 'This ability to take raw samples and immediately start processing could transform the diagnosis of Zika and a boundless number of other infectious diseases.'

Dr Alexander McAdam, a medical microbiologist at Boston Children's Hospital who was not involved in the project, said to STAT: 'They've developed a promising method of detecting extremely low concentrations of [genetic material], but the key word is "promising".It's going to be a long walk from hopeful to clinically useful, and there is a lot to do to demonstrate practicality.'

The study was published in Science.

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Highly sensitive CRISPR diagnostic tool created - BioNews