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Archive for the ‘Crispr’ Category

Addgene: CRISPR Guide

Generating a Knockout Using CRISPR

You can use CRISPR to generate knockout cells or animals by co-expressing an endonuclease like Cas9 or Cpf1 and a gRNA specific to the gene to be targeted. The genomic target can be any 20 nucleotide DNA sequence, provided it meets two conditions:

The PAM sequence is essential for target binding, but the exact sequence depends on which Cas protein you use. We’ll use the popular S. pyogenes Cas9 (SpCas9) as an example, but check out our list of additional Cas proteins and PAM sequences. Once expressed, the Cas9 protein and the gRNA form a ribonucleoprotein complex through interactions between the gRNA scaffold and surface-exposed positively-charged grooves on Cas9. Cas9 undergoes a conformational change upon gRNA binding that shifts the molecule from an inactive, non-DNA binding conformation into an active DNA-binding conformation. Importantly, the spacer region of the gRNA remains free to interact with target DNA.

Cas9 will only cleave a given locus if the gRNA spacer sequence shares sufficient homology with the target DNA. Once the Cas9-gRNA complex binds a putative DNA target, the seed sequence (8-10 bases at the 3 end of the gRNA targeting sequence) will begin to anneal to the target DNA. If the seed and target DNA sequences match, the gRNA will continue to anneal to the target DNA in a 3 to 5 direction. The zipper-like annealing mechanics of Cas9 may explain why mismatches between the target sequence in the 3 seed sequence completely abolish target cleavage, whereas mismatches toward the 5 end distal to the PAM often still permit target cleavage.

The Cas9 nuclease has two functional endonuclease domains: RuvC and HNH. Cas9 undergoes a second conformational change upon target binding that positions the nuclease domains to cleave opposite strands of the target DNA. The end result of Cas9-mediated DNA cleavage is a double-strand break (DSB) within the target DNA (3-4 nucleotides upstream of the PAM sequence).

The resulting DSB is then repaired by one of two general repair pathways:

The NHEJ repair pathway is the most active repair mechanism, and it frequently causes small nucleotide insertions or deletions (indels) at the DSB site. The randomness of NHEJ-mediated DSB repair has important practical implications, because a population of cells expressing Cas9 and a gRNA will result in a diverse array of mutations (for more information, jump to Plan Your Experiment.) In most cases, NHEJ gives rise to small indels in the target DNA that result in amino acid deletions, insertions, or frameshift mutations leading to premature stop codons within the open reading frame (ORF) of the targeted gene. The ideal end result is a loss-of-function mutation within the targeted gene. However, the strength of the knockout phenotype for a given mutant cell must be validated experimentally. Learn more about non-homologous end joining (NHEJ).

Browse Plasmids: Double-Strand Break (Cut)

CRISPR specificity is partially determined by how specific the gRNA targeting sequence is for the genomic target compared to the rest of the genome. Ideally, a gRNA targeting sequence will have perfect homology to the target DNA with no homology elsewhere in the genome. Realistically, a given gRNA targeting sequence will have additional sites throughout the genome where partial homology exists. These sites are called off-targets and need to be considered when designing a gRNA for your experiment (see the Plan Your Experiment section below).

In addition to optimizing gRNA design, CRISPR specificity can also be increased through modifications to Cas9. As discussed previously, Cas9 generates double-strand breaks (DSBs) through the combined activity of two nuclease domains, RuvC and HNH. Cas9 nickase, a D10A mutant of SpCas9, retains one nuclease domain and generates a DNA nick rather than a DSB.

Thus, two nickases targeting opposite DNA strands are required to generate a DSB within the target DNA (often referred to as a double nick or dual nickase CRISPR system). This requirement dramatically increases target specificity, since it is unlikely that two off-target nicks will be generated within close enough proximity to cause a DSB. Therefore, if high specificity is crucial to your experiment, you might consider using the dual nickase approach to create a double nick-induced DSB. The nickase system can also be combined with HDR-mediated gene editing for specific gene edits.

In 2015, researchers used rational mutagenesis to develop two high fidelity Cas9s: eSpCas9(1.1) and SpCas9-HF1. eSpCas9(1.1) contains alanine substitutions that weaken the interactions between the HNH/RuvC groove and the non-target DNA strand, preventing strand separation and cutting at off-target sites. Similarly, SpCas9-HF1 lowers off-target editing through alanine substitutions that disrupt Cas9’s interactions with the DNA phosphate backbone. HypaCas9, developed in 2017, contains mutations in the REC3 domain that increase Cas9 proofreading and target discrimination. All three high fidelity enzymes generate less off-target editing than wildtype Cas9.

Browse Plasmids: Single-Strand Break (Nick)

While NHEJ-mediated DSB repair often disrupts the open reading frame of the gene, homology directed repair (HDR) can be used to generate specific nucleotide changes ranging from a single nucleotide change to large insertions like the addition of a fluorophore or tag.

In order to utilize HDR for gene editing, a DNA repair template containing the desired sequence must be delivered into the cell type of interest with the gRNA(s) and Cas9 or Cas9 nickase. The repair template must contain the desired edit as well as additional homologous sequence immediately upstream and downstream of the target (termed left & right homology arms.) The length of each homology arm is dependent on the size of the change being introduced, with larger insertions requiring longer homology arms.

Depending on the application, the repair template may be a single-stranded oligonucleotide, double-stranded oligonucleotide, or a double-stranded DNA plasmid. When designing the repair template, do not include the PAM sequence present in the genomic DNA. This step prevents the repair template from being a suitable target for Cas9 cleavage. For example, you could alter the DNA sequence of the PAM with a silent mutation that does not change the amino acid sequence.

The efficiency of HDR is generally low (

Since the efficiency of Cas9 cleavage is relatively high and the efficiency of HDR is relatively low, a large portion of the Cas9-induced DSBs will be repaired via NHEJ. In other words, the resulting population of cells will contain some combination of wild-type alleles, NHEJ-repaired alleles, and/or the desired HDR-edited allele. Therefore, it is important to confirm the presence of the desired edit experimentally and to isolate clones containing the desired edit (see the validation section in Plan Your Experiment). Learn more about homology directed repair (HDR).

Browse Plasmids: Endogenous Tagging

As discussed above, the efficiency of HDR is very low due to the number of DSBs repaired by NHEJ. To make point mutations without using HDR, researchers have developed CRISPR base editors that fuse Cas9 nickase or dCas9 to a cytidine deaminase like APOBEC1. Base editors are targeted to a specific locus by a gRNA, and they can convert cytidine to uridine within a small editing window near the PAM site. Uridine is subsequently converted to thymidine through base excision repair, creating a C->T change (or G->A on the opposite strand.) This class of base editors is available with multiple Cas9 variants and using high fidelity Cas9s. In addition, new base editors have been engineered to convert adenosine to inosine, which is treated like guanosine by the cell, creating an A->G (or T->C) change. Learn more about CRISPR DNA base editors.

Browse Plasmids: Base Edit

Type VI CRISPR systems, including the enzymes Cas13a/C2c2 and Cas13b, target RNA rather than DNA. Fusing an ADAR2(E488Q) adenosine deaminase to catalytically dead Cas13b creates a programmable RNA base editor that converts adenosine to inosine in RNA (termed REPAIR.) Since inosine is functionally equivalent to guanosine, the result is an A->G change in RNA. dPspCas13b does not appear to require a specific sequence adjacent to the RNA target, making this a very flexible editing system. Editors based on ADAR2(E488Q/T375G) display improved specificity, and editors carrying the delta-984-1090 ADAR truncation retain RNA editing capabilities and are small enough to be packaged in AAV particles.

Browse Plasmids: RNA Editing

CRISPR is a remarkably flexible tool for genome manipulation, as Cas enzymes bind target DNA independently of their ability to cleave target DNA. Specifically, both RuvC and HNH nuclease domains can be rendered inactive by point mutations (D10A and H840A in SpCas9), resulting in a nuclease dead Cas9 (dCas9) molecule that cannot cleave target DNA. The dCas9 molecule retains the ability to bind to target DNA based on the gRNA targeting sequence.

Early experiments demonstrated that targeting dCas9 to transcription start sites was sufficient to repress transcription by blocking initiation. dCas9 can also be tagged with transcriptional repressors or activators, and targeting these dCas9 fusion proteins to the promoter region results in robust transcriptional repression or activation of downstream target genes. The simplest dCas9-based activators and repressors consist of dCas9 fused directly to a single transcriptional activator, A (e.g. VP64) or transcriptional repressor, R (e.g. KRAB; see panel A to the right).

Additionally, more elaborate activation strategies have been developed for more potent activation of target genes in mammalian cells. These include: co-expression of epitope-tagged dCas9 and antibody-activator effector proteins (e.g. SunTag system, panel B), dCas9 fused to several different activation domains in series (e.g. dCas9-VPR, panel C) or co-expression of dCas9-VP64 with a modified scaffold gRNA and additional RNA-binding helper activators (e.g. SAM activators, panel D). Importantly, unlike the genome modifications induced by Cas9 or Cas9 nickase, dCas9-mediated gene activation or repression is reversible, since it does not permanently modify the genomic DNA.

Browse Plasmids: Activate, Repress/Interfere

Cas enzymes can be fused to epigenetic modifiers like p300 and TET1 to create programmable epigenome-engineering tools. Like CRISPR activators and repressors, these tools alter gene expression without inducing double-strand breaks. However, they are much more specific for particular chromatin and DNA modifications, allowing researchers to isolate the effects of a single epigenetic mark.

Another potential advantage of CRISPR epigenetic tools is their persistence and inheritance. CRISPR activators and repressors are thought to be reversible once the effector is inactivated/removed from the system. In contrast, epigenetic marks left by targeted epigenetic modifiers may be more frequently inherited by daughter cells. In certain cases, epigenetic modifiers may work better than activators/repressors in modulating transcription. However, since the effects of these tools are likely cell type- and context-dependent, it might be beneficial to try multiple CRISPR strategies when setting up your experimental system.

Browse Plasmids: Epigenetics

Expressing several gRNAs from the same plasmid ensures that each cell containing the plasmid will express all of the desired gRNAs, thus increasing the likelihood that all desired genomic edits will be carried out by Cas9. Such multiplex CRISPR applications include:

Current multiplex CRISPR systems enable researchers to target anywhere from 2 to 7 genetic loci by cloning multiple gRNAs into a single plasmid. These multiplex gRNA vectors can conceivably be combined with any of the aforementioned CRISPR derivatives to not only knock out target genes, but activate or repress target genes as well. Read more about Cas9 multiplexing and Cpf1 multiplexing.

Browse Plasmids: Multiplex gRNA vectors

The ease of gRNA design and synthesis, as well as the ability to target almost any genomic locus, make CRISPR the ideal genome engineering system for large-scale forward genetic screening. Forward genetic screens are particularly useful for studying diseases or phenotypes for which the underlying genetic cause is not known. In general, the goal of a genetic screen is to generate a large population of cells with mutations in a wide variety of genes and then use these mutant cells to identify the genetic perturbations that result in a desired phenotype.

Before CRISPR, genetic screens relied heavily on shRNA technology, which is prone to off-target effects and false negatives due to incomplete knockdown of target genes. In contrast, CRISPR is capable of making highly specific, permanent genetic modifications that are more likely to ablate target gene function. CRISPR has already been used extensively to screen for novel genes that regulate known phenotypes, including resistance to chemotherapy drugs, resistance to toxins, cell viability, and tumor metastasis. Currently, the most popular method for conducting genome-wide screens using CRISPR involves the use of pooled lentiviral CRISPR libraries.

Pooled lentiviral CRISPR libraries (often referred to as CRISPR libraries) are a heterogenous population of lentiviral transfer vectors, each containing an individual gRNA targeting a single gene in a given genome.

Guide RNAs are designed in silico and synthesized (see panel A below), then cloned in a pooled format into lentiviral transfer vectors (panel B). CRISPR libraries have been designed for common CRISPR applications including genetic knockout, activation, and repression for human and mouse genes.

Each CRISPR library is different, as libraries can target anywhere from a single class of genes up to every gene in the genome. However, there are several features that are common across most CRISPR libraries. First, each library typically contains 3-6 gRNAs per gene to ensure modification of every target gene, so CRISPR libraries contain thousands of unique gRNAs targeting a wide variety of genes. Guide RNA design for CRISPR libraries is usually optimized to select for guide RNAs with high on-target activity and low off-target activity.

Keep in mind that the exact region of the gene to be targeted varies depending on the specific application. For example, knockout libraries often target 5 constitutively expressed exons, but activation and repression libraries will target promoter or enhancer regions. Be sure to check the library page/original publication to see if a library is suitable for your experiment. Libraries may be available in a 1-plasmid system, in which Cas9 is included on the gRNA-containing plasmid, or a 2-plasmid system in which Cas9 must be delivered separately.

CRISPR libraries from Addgene are available in two formats: as DNA, or in select cases, as pre-made lentivirus.

In the case of DNA libraries, the CRISPR library will be shipped at a concentration that is too low to be used in experiments. Thus, the first step in using your library is to amplify the library (panel C) to increase the total amount of DNA. When amplifying the library, it is important to maintain good representation of gRNAs so that the composition of your amplified library matches that of the original library. You’ll use next-generation sequencing (NGS) to verify that this is the case. Learn more about library verification.

Once the library has been amplified/verified, the next step is to generate lentivirus containing the entire CRISPR library (panel D). Then, you will transduce cells with the lentiviral library (panel E). Remember – if you are using a 2-vector system, you will transduce cells that are already expressing Cas9. After applying your screening conditions, you will look for relevant genes (hits) using NGS technology. For more detail on using CRISPR for both positive and negative screens, see our pooled library guide.

As noted above, forward genetic screens are most useful for situations in which the physiology or cell biology behind a particular phenotype or disease is well understood, but the underlying genetic causes are unknown. Therefore, genome-wide screens using CRISPR libraries are a great way to gather unbiased information regarding which genes play a causal role in a given phenotype. With any experiment, it is important to verify that the hits you identify are actually important for your phenotype of interest. You can individually test the gRNAs identified in your screen to ensure that they reproduce the phenotype of interest.

Find more information on factors to consider before starting your pooled library experiment in Practical Considerations for Using Pooled Lentiviral CRISPR Libraries (McDade et al., 2016).

Browse Libraries: CRISPR Pooled Libraries

Using catalytically inactive Cas9 (dCas9) fused to a fluorescent marker like GFP, researchers have turned dCas9 into a customizable DNA labeler compatible with fluorescence microscopy in living cells. Alternatively, gRNAs can be fused to protein-interacting RNA aptamers, which recruit specific RNA-binding proteins (RBPs) tagged with fluorescent proteins to visualize targeted genomic loci.

CRISPR imaging has numerous advantages over other imaging techniques, including that it is easy to implement due to the simplicity of gRNA design, programmable for different genomic loci, capable of detecting multiple genomic loci, and compatible with live cell imaging. Compared to techniques like fluorescence in situ hybridization (FISH), CRISPR imaging offers a unique method for detecting the chromatin dynamics in living cells.

Multicolor CRISPR imaging allows for simultaneous tracking of multiple genomic loci in living cells. One method uses orthogonal dCas9s (e.g., S. pyogenes dCas9 and S. aureus dCas9) tagged with different fluorescent proteins. Alternatively, one can fuse gRNAs to orthogonal protein-interacting RNA aptamers, which recruit specific orthogonal RNA-binding proteins (RBPs) tagged with different fluorescent proteins, as seen in the popular CRISPRainbow kit.

The fluorescent CRISPR system has been used for dynamic tracking of repetitive and non-repetitive genomic loci, as well as chromosome painting in living cells. Visualizing a specific genomic locus requires recruitment of many copies of labeled proteins to the given region. For example, chromosome-specific repetitive loci can be efficiently visualized in living cells using a single gRNA that has multiple targeted sequences in close proximity. A non-repetitive genomic locus can also be labeled by co-delivering multiple gRNAs that tile the locus. Chromosome painting requires delivery of hundreds of gRNAs with target sites throughout the chromosome.

Browse Plasmids: Label

Identifying molecules associated with a genomic region of interest in vivo is essential to understanding locus function. Using CRISPR, researchers have expanded chromatin immunoprecipitation (ChIP) to allow purification of any genomic sequence specified by a particular gRNA.

In the enChIP (engineered DNA-binding molecule-mediated ChIP) system, catalytically inactive dCas9 is used to purify genomic DNA bound by the gRNA. An epitope tag(s) can be fused to dCas9 or gRNA for efficient purification. Various epitope tags including 3xFLAG-tag, PA, and biotin tags, can be used for enChIP, as well as an anti-Cas9 antibody. Biotin tagging of dCas9 can be achieved by fusing a biotin acceptor site to dCas9 and co-expressing BirA biotin ligase, as seen in the CAPTURE system. The locus is subsequently isolated by affinity purification against the epitope tag.

After purification of the locus, molecules associated with the locus can be identified by mass spectrometry (proteins), RNA-sequencing (RNAs), and next-generation sequencing (NGS) (other genomic regions). Compared to conventional methods for genomic purification, CRISPR-based purification methods are more straightforward and enable direct identification of molecules associated with a genomic region of interest in vivo.

Browse Plasmids: Purify

In bacteria, type VI CRISPR systems recognize ssRNA rather than dsDNA. Many type VI enzymes also have the ability to process crRNA precursors to mature crRNAs. Upon ssRNA recognition by the crRNA, the target RNA is degraded. In bacteria, Cas13 enzymes can also cleave RNAs nonspecifically after the initial crRNA-guided cleavage. This promiscuous cleavage activity slows bacterial cell growth and may further protect bacteria from viral pathogens. Non-specific cleavage does not occur in mammalian cells. Similar to Cas9 and Cpf1, Cas13 can be converted to an RNA-binding protein through mutation of its catalytic domain. Learn more about Cas13a.

Browse Plasmids: RNA Targeting

While S. pyogenes Cas9 (SpCas9) is certainly the most commonly used CRISPR endonuclease for genome engineering, it may not be the best endonuclease for every application. For example, the PAM sequence for SpCas9 (5 NGG 3) is abundant throughout the human genome, but an NGG sequence may not be positioned correctly to target your desired genes for modification. This limitation is of particular concern when trying to edit a gene using homology directed repair (HDR), which requires PAM sequences in very close proximity to the region to be edited. Kleinstiver et al. generated synthetic SpCas9-derived variants with non-NGG PAM sequences. Gao et al. subsequently engineered Cpf1 PAM variants. The inclusion of these variants into the CRISPR arsenal effectively doubles the targeting range of CRISPR in the human genome. Read more about Cas9 variants.

Additional Cas9 orthologs from various species bind a variety of PAM sequences. These enzymes may have other characteristics that make them more useful than SpCas9 for specific applications. For example, the relatively large size of SpCas9 (4kb coding sequence) means that plasmids carrying the SpCas9 cDNA cannot be efficiently packaged into adeno-associated virus (AAV). Since the coding sequence for Staphylococcus aureus Cas9 (SaCas9) is 1 kilobase shorter than SpCas9, SaCas9 can be efficiently packaged into AAV. Similar to SpCas9, the SaCas9 endonuclease is capable of modifying target genes in mammalian cells in vitro and in mice in vivo.

Another limitation of SpCas9 is the low efficiency of making specific genetic edits via HDR. For specific point edits, CRISPR base editing is a useful alternative to HDR. For larger edits, Cpf1, first described by Zetsche et al., may be a better option. Unlike Cas9 nucleases, which create blunt DSBs, Cpf1-mediated DNA cleavage creates DSBs with a short 3 overhang. Cpf1s staggered cleavage pattern opens up the possibility of directional gene transfer, analogous to traditional restriction enzyme cloning, which may increase the efficiency of gene editing. Like the Cas9 variants and orthologs described above, Cpf1 also expands the range of sites that can be targeted by CRISPR to AT-rich regions or AT-rich genomes that lack the NGG PAM sites favored by SpCas9.

CRISPR is a powerful system that enables researchers to manipulate the genome like never before. This section will provide a general framework to get you started using CRISPR in your research. Although we will use the example of CRISPR/Cas9 in mammalian cells, many of these principles apply to using CRISPR in other organisms. First, consider the genetic manipulation that is necessary to model your specific disease or process of interest. Do you want to:

Once you have a clear understanding of your experimental goal, you are ready to start navigating the different reagents that are available for your particular experiment.

Different genetic manipulations require different CRISPR components. Selecting a specific genetic manipulation can be a good way to narrow down which reagents are appropriate for a given experiment. Make sure to check whether reagents are available to carry out your experiment in your particular model organism. There may not be a perfect plasmid for your specific application, and in such cases, it may be necessary to customize an existing reagent to suit your needs.

To use CRISPR, you will need both Cas9 and a gRNA expressed in your target cells. For easy-to-transfect cell types (e.g. HEK293 cells), transfection with standard transfection reagents may be sufficient to express the CRISPR machinery. For more difficult cells (e.g. primary cells), viral delivery of CRISPR reagents may be more appropriate. In cases where off-target editing is a major concern, Cas9-gRNA ribonucleoprotein (RNP) complexes are advantageous due to the transient Cas9 expression.

The table below summarizes the major expression systems and variables for using CRISPR in mammalian cells. Some of the variables include:

Once you have selected your CRISPR components and method of delivery, you are ready to select a target sequence and design your gRNA.

When possible, you should sequence the region you are planning to modify prior to designing your gRNA, as sequence variation between your gRNA targeting sequence and target DNA may result in reduced cleavage. The number of alleles for each gene may vary depending on the specific cell line or organism, which may affect the observed efficiency of CRISPR knockout or knockin.

In order to manipulate a given gene using CRISPR, you will have to identify the genomic sequence for the gene you are trying to target. However, the exact region of the gene you target will depend on your specific application. For example:

A PAM sequence is absolutely necessary for Cas9 to bind target DNA. As such, one can start by identifying all PAM sequences within the genetic region to be targeted. If there are no PAM sequences for your chosen enzyme within your desired sequence, you may want to consider alternative Cas enzymes (see Cas9 variants and PAM sequences). Once possible PAM sequences and putative target sites have been identified, it is time to choose which site is likely to result in the most efficient on-target cleavage.

The gRNA target sequence needs to match the target locus, but it is also critical to ensure that the gRNA target sequence does NOT match additional sites within the genome. In a perfect world, your gRNA target sequence would have perfect homology to your target with no homology elsewhere in the genome. Realistically, a given gRNA target sequence will have partial homology to additional sites throughout the genome. These sites are called off-targets and should be examined during gRNA design. In general, off-target sites are not cleaved as efficiently when mismatches occur near the PAM sequence, so gRNAs with no homology or those with mismatches close to the PAM sequence will have the highest specificity. To increase specificity, you can also consider using a high-fidelity Cas enzyme.

In addition to off-target activity, it is also important to consider factors that maximize cleavage of the desired target sequence or on-target activity. Two gRNA targeting sequences with 100% homology to their DNA targets may not result in equivalent cleavage efficiency. In fact, cleavage efficiency may increase or decrease depending upon the specific nucleotides within the selected target sequence. For example, gRNA targeting sequences containing a G nucleotide at position 20 (1 bp upstream of the PAM) may be more efficacious than gRNAs containing a C nucleotide at the same position in spite of being a perfect match for the target sequence.

Many gRNA design programs can locate potential PAM and target sequences and rank the associated gRNAs based on their predicted on-target and off-target activity (see gRNA design software). Additionally, many plasmids containing validated gRNAs are now available through Addgene. These plasmids contain gRNAs that have been used successfully in genome engineering experiments. Using validated gRNAs can save your lab valuable time and resources when carrying out CRISPR experiments. Read more about how to design your gRNA.

Browse Plasmids: Validated gRNAs

Once you have selected your target sequences it is time to design your gRNA oligos and clone these oligos into your desired vector. In many cases, targeting oligos are synthesized, annealed, and inserted into plasmids containing the gRNA scaffold using standard restriction-ligation cloning. However, the exact cloning strategy will depend on the gRNA vector you have chosen, so it is best to review the protocol associated with the specific plasmid in question (see CRISPR protocols from Addgene depositors).

Choose a delivery method that is compatible with your experimental system. CRISPR efficiency will vary based on the method of delivery and the cell type. Before proceeding with your experiment, it may be necessary to optimize your delivery conditions. Learn more about CRISPR delivery in mammalian systems.

Once you have successfully delivered the gRNA and Cas enzyme to your target cells, it is time to validate your genome edit. CRISPR editing produces several possible genotypes within the resulting cell population. Some cells may be wild-type due to either (1) a lack of gRNA and/or Cas9 expression or (2) a lack of efficient target cleavage in cells expressing both Cas9 and gRNA.

Edited cells may be homozygous or heterozygous for edits at your target locus. Furthermore, in cells containing two mutated alleles, each mutated allele may be different owing to the error-prone nature of NHEJ. In HDR gene editing experiments, most mutated alleles will not contain the desired edit, as a large percentage of DSBs are still repaired by NHEJ.

How do you determine that your desired edit has occurred? The exact method necessary to validate your edit will depend upon your specific application. However, there are several common ways to verify that your cells contain your desired edit, including but not limited to:

More information on each of these techniques can be found in our blog post CRISPR 101: Validating your Genome Edit.

The majority of the CRISPR plasmids in Addgenes collection are from S. pyogenes unless otherwise noted.

Engineered Cpf1 variants with altered PAM specificities. 2017. Gao L, Cox DBT, Yan WX, Manteiga JC, Schneider MW, Yamano T, Nishimasu H, Nureki O, Crosetto N, Zhang F. Nat Biotechnol. 35(8):789-792. PMID: 28581492

Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. 2017. Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, Harrington LB, Sternberg SH, Joung JK, Yildiz A, Doudna JA. Nature. 550(7676):407-410. PMID: 28931002

Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. 2017. Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, Harrington LB, Sternberg SH, Joung JK, Yildiz A, Doudna JA. Nature. 550(7676):407-410. PMID: 28931002

Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity. 2017. Komor AC, Zhao KT, Packer MS, Gaudelli NM, Waterbury AL, Koblan LW, Kim YB, Badran AH, Liu DR. Sci Adv. 3(8):eaao4774. PMID: 28875174

Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery. 2017. Rees HA, Komor AC, Yeh WH, Caetano-Lopes J, Warman M, Edge ASB, Liu DR. Nat Commun. 8:15790. PMID: 28585549

Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. 2017. Kim YB, Komor AC, Levy JM, Packer MS, Zhao KT, Liu DR. Nat Biotechnol. 35(4):371-376. PMID: 28191901

Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. 2017. Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, Wu WY, Scott DA, Severinov K, van der Oost J, Zhang F. Nat Biotechnol. 35(1):31-34. PMID: 27918548

Nucleic acid detection with CRISPR-Cas13a/C2c2. 2017. Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F. Science. 356(6336):438-442. PMID: 28408723

Programmable base editing of AT to GC in genomic DNA without DNA cleavage. 2017. Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR. Nature. 551(7681):464-471. PMID: 29160308

RNA editing with CRISPR-Cas13. 2017. Cox DBT, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ, Joung J, Zhang F. Science. pii: eaaq0180. PMID: 29070703

RNA targeting with CRISPR-Cas13. 2017. Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto JJ, Verdine V, Cox DBT, Kellner MJ, Regev A, Lander ES, Voytas DF, Ting AY, Zhang F. . 550(7675):280-284. PMID: 28976959

High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. 2016. Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, Joung JK. Nature. 529(7587):490-5. PMID: 26735016

Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. 2016. Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T. Nat Biotechnol. . PMID: 27088723

Naturally occurring off-switches for CRISPR-Cas9. 2016. Pawluk A, Amrani N, Zhang Y, Garcia B, Hidalgo-Reyes Y, Lee J, Edraki A, Shah M, Sontheimer EJ, Maxwell KL, Davidson AR. Cell. 167(7):1829-1838. PMID: 27984730

Practical Considerations for Using Pooled Lentiviral CRISPR Libraries. 2016. McDade JR, Waxmonsky NC, Swanson LE, Fan M. Curr Protoc Mol Biol. 115:31.5.1-31.5.13. PMID: 27366891

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. 2016. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Nature. 533(7603):420-4. PMID: 27096365

Rationally engineered Cas9 nucleases with improved specificity. 2016. Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F. Science. 351(6268):84-8. PMID: 26628643

A Scalable Genome-Editing-Based Approach for Mapping Multiprotein Complexes in Human Cells. 2015. Dalvai M, Loehr J, Jacquet K, Huard CC, Roques C, Herst P, Ct J, Doyon Y. Cell Rep. 13(3):621-33. PMID: 26456817

An updated evolutionary classification of CRISPR-Cas systems. 2015. Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJ, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV. Nat Rev Microbiol. 13(11):722-36. PMID: 26411297

Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo. 2015. Zuris JA, Thompson DB, Shu Y, Guilinger JP, Bessen JL, Hu JH, Maeder ML, Joung JK, Chen ZY, Liu DR. Nat Biotechnol. 33(1):73-80. PMID: 25357182

CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins. 2015. Savic D, Partridge EC, Newberry KM, Smith SB, Meadows SK, Roberts BS, Mackiewicz M, Mendenhall EM, Myers RM. Genome Res. 25(10):1581-9. PMID: 26355004

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Articles A CRISPR/Cas-GFP Vector for Rapid Expression Verification and Enrichment of Genome Edited Cells

In many genome editing experiments involving ZFNs and CRISPR/Cas nucleases, the first challenge is achieving successful delivery of plasmids and subsequent expression of the encoded nucleases. While …Keywords: Cloning, Gene expression, Sequencing, Transfection

This Product and its use are the subject of one or more of the following patents controlled by The Broad Institute, Inc. (BROAD), the Massachusetts Institute of Technology (MIT), or the President and…Keywords: Agriculture, Clinical, Diagnostic, Substitutions, Veterinary

Deciphering the genetics of neuroscience has always been challenging. Heterogeneous tissue microenvironments, complex genetic interactions and phenotypes, lack of model systems that accurately mimic …Keywords: Functional genomics, Gene expression, Genetic, Genetics, Genomics, Neuroscience, Sequencing

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While several genome editing tools have been developed in recent years, including zinc finger-based strategies and TALENs (transcription activator-like effector nucleases), none have been as efficien…Keywords: Amplification, Cell culture, Enzyme-linked immunosorbent assay, Gene expression, Genetic, Genetics, Immunohistochemistry, Immunology, Nutrition, Polymerase chain reaction, Recombination, Southern blot, Transcription, Transfection, Western blot

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CRISPR endonucleases have shown wide variation in their activity, even among multiple CRISPRs designed within close genomic proximity.1 For this reason, we highly recommend that you test 3 to 4 CRIS…Keywords: Cell culture, Cloning, DNA purification, Gene expression, Microscopy, Purification, Reductions, Sequencing, Transcription, Transfection

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F Ann Ran a, b, c, d, e , Patrick D Hsu a, b, c, d, e , Jason Wright a , Vineeta Agarwala a, f, g , David A Scott a, b, c, d , Feng Zhang a, b, c, dKeywords: Amplification, Antibiotics, Antivirals, Apoptosis, Catalysis, Cell culture, Cell dissociation, Central Nervous System, Chromatin immunoprecipitation, Cloning, Digestions, Electrophoresis, Gel electrophoresis, Gene expression, Genetic, Genetics, Growth factors, Melting, Nucleic acid annealing, PAGE, Peptide synthesis, Polymerase chain reaction, Polymorphisms, Purification, Rearrangements, Recombination, Sample preparations, Sequencing, Transcription, Transfection, transformation

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FACS Analysis of CFU FACS (Fluorescence-Activated Cell Sorting) provides a method for sorting a mixed population of cells into two or more groups, one cell at a time, based on the specific light scat…Keywords: Enzyme-linked immunosorbent assay, Flow cytometry, Gene expression, Titrations, Transduction

Successful targeting relies on optimizing key sensitive steps in the process, including lentiviral transduction. Below are some helpful handling and titration tips from our R&D lentiviral experts. As…Keywords: Antibiotics, Enzyme-linked immunosorbent assay, Gene expression, PAGE, Polymerase chain reaction, Titrations, Transduction

CRISPR-Cas9 nucleases have revolutionized genome editing enabling unprecedented efficiency of targeted mutagenesis. The ability to perform large-scale, whole genome loss-of-function screens has allow…Keywords: Antibiotics, Cell culture, Cloning, Functional genomics, Gene expression, Genetic, Genomics, Molecular biology, Polymorphisms, Sequencing, Transfection

Caroline Beckett, the global CRISPR product manager for MilliporeSigma, discusses reagent solutions for creating predictive models for neuroscience research. She notes that many neuroscientists want …Keywords: Cell culture, Diseases, Neurodegenerative Diseases, Neuroscience

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Custom CRISPR Products | Sigma-Aldrich

What Is CRISPR? – CB Insights

CRISPR. What is it? And why is the scientific community so fascinated by its potential applications? Starting with its definition, we explain how this technology harnesses an ancient bacteria-based defense system and how it will impact the world around us today.

Imagine a future where parents can create bespoke babies, selecting the height and eye color of their yet unborn children.In fact, all traits can be customized to ones preferences: the size of domestic pets, the longevity of plants, etc.

It soundslike the backdrop of a dystopian science fiction novel. Yet some of this isalready happening.

Since its initial discovery in 2012, scientists have marveled at the applications of CRISPR (also known as Cas9 orCRISPR-Cas9).

And with a Jennifer Lopez-produced bio-terror TV drama called C.R.I.S.P.R. on the horizon, CRISPR has reached a new peak in interest from outside the scientific community.

CRISPR may revolutionize howwe tackle some of the worlds biggest problems, like cancer, food shortages, and organ transplant needs.Recent reports even examineits useasa highly efficient disease diagnostics tool. But, as with any new technology, it may also cause new unintended problems.

Changing DNA the code of life will inevitably come with a host ofimportant consequences. But society and industry cant have this conversation without understanding the basics of CRISPR.

In this explainer, we dive into CRISPR, from a simple explanation of what exactly it is to its applications and limitations.

CRISPR is adefining feature of the bacterial genetic code andits immune system,functioningas a defense system that bacteria use to protect themselves against attacks from viruses. Its also used by organisms in the Archaea kingdom (single-celled microorganisms).

The acronym CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. Essentially, it is a series ofshort repeating DNA sequences withspacers sitting in between them.

In short,bacteria usethese geneticsequences to remember each specific virus that attacks them.

They do this byincorporatingthe virus DNA into their own bacterial genome. Thisviral DNA ends up as the spacers in the CRISPR sequence.This method then gives thebacteria protection or immunity when a specific virus tries to attack again.

Accompanying CRISPR are genes that are always located nearby, called Cas (CRISPR-associated) genes.

Once activated, these genes make special proteins known as enzymes that seem to have co-evolved with CRISPR. The significance of these Cas enzymes is their ability to act as molecular scissors that can cut into DNA.

To recap: in nature,when a virus invades bacteria, its unique DNA is integrated into a CRISPR sequence in the bacterial genome. This means that the next time the virus attacks, the bacteria will remember it and sendRNA and Cas to locate and destroy the virus.

While there are other Cas enzymes derived from bacteria that cut out viruses when they attack bacteria, Cas9 is the best enzyme at doing this in animals. The widely-known term CRISPR-Cas9 refers to a Cas variety beingused to cut animal (and human) DNA.

Inharnessing this technology, researchers have added a new step: after DNA is cut by CRISPR-Cas9, a new DNA sequence carrying a fixed version of a gene can nestle into the new space. Alternatively, the cut can altogether knock out ofa particular unwanted gene for example, a gene that causes diseases.

Oneway to think about CRISPR-Cas9 isto compare it to theFind & Replace function in Word: itfinds thegenetic data (or word)you want to correct and replaces it with new material. Or, as CRISPR pioneer Jennifer Doudna puts it in her book A Crack In Creation: Gene Editing and the Unthinkable Power to Control Evolution, CRISPR is likea Swiss army knife, with different functions depending on how we want to use it.

CRISPR research has moved so fast that its already gone beyond basic DNA editing. In December 2017, the Salk Institute designed a handicapped version of the CRISPR-Cas9 system, capable of turninga targeted gene on or off without editing the genome at all. Going forward, this kind of process could ease the concerns surrounding the permanent nature of gene editing.

These are the 3 key players that help theCRISPR-Cas9 tech do its work:

Below, we illustrate how these parts come together to create a potential therapy.

Please click to enlarge.

The guide RNAserves as the GPS coordinates for finding the piece of DNA you want toedit and zeroes in on the targeted part of the gene. Once located, Cas9, the scissors, makes a double stranded break in the DNA, and the DNAyou want to insert takes its place.

The implications for this are vast.

Yes, this technology will disrupt medical treatment. But beyond that, it could also transform everything from the food we eat to the chemicals we use as fuel, since these may be engineered through gene technology as well.

Feng Zhang, PhD, from the Broad Institute of MIT and Harvard, describedCRISPR using a helpful nursery rhyme. We can imagine a certainDNA sequence that is fixed in this way:

Twinkle Twinkle Big Star Twinkle Twinkle Little Star

In this process:

The CRISPR sequence was first discovered in 1987. But its function would not be discovered until 2012.

Keypeople involved in the initial discovery of the bacterial CRISPR-Cas9 systems function include Jennifer Doudna, PhD at University of California, Berkeley, and French scientist Emmanuelle Charpentier, PhD. Through their strategic collaboration, they ushered in a new era of biotechnology.

Another important figure is Feng Zhang, PhD, who was instrumental in figuring out CRISPRs therapeutic applications using mice and human cells in 2013.Harvard geneticist George Church, PhDalso contributed to early CRISPR research with Zhang.

All four researchers went on to play crucial roles in setting up someof the most well-funded CRISPR therapeutic startups, includingEditas Medicine, CRISPR Therapeutics, and Intellia Therapeutics.All 3 of these companiesIPOed in 2016 and are in the drug discovery/pre-clinical stage of testing their respective CRISPR therapeutic candidates for various human diseases.

Before CRISPR was heralded asthegene editing method, two other gene-editing techniques dominated the field: Zinc Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs). Research efforts using these tools are still ongoing.

Like CRISPR, these toolscan each cut DNA. Thought they are generally more difficult to make and use, these tools do offer their own advantages:

Each also has vital therapeutic applications.

Biotech companyCellectis uses the TALEN gene editing technology to make CAR-T therapies for leukemia, whileSangamo BioSciencesmakes ZFNs that can disable a gene known to be key in HIV infection.Notably, each of these companies hold key IP rights to these specific gene-editing methods, which could make it difficult for other biotech companiesto use these tools.

Meanwhile, CRISPR has certainly stolen the spotlight as of late, due to its efficiency, flexibility, and cheap price tag. Itsplausible that CRISPR could face similar IP issues and there are already some IP controversies going on but with such vast applications for this system, research on multiple fronts seems to be moving forward fast.

Every industry can harnessCRISPR as a tool: itcan create new drug therapies for human diseases, help farmers grow pathogen-resistant crops, create new species of plants and animals and maybe even bring back old ones.

Since the initial discovery of CRISPR as a gene-editing mechanism, the list of applications has grown rapidly. Though still in early stages, animal models (i.e. lab animals) have provided key insights into how we may be able to manipulate CRISPR.

Mice have been especially telling when it comes to CRISPRs therapeutic potential. As mammals sharing more than 90% of our human genes, mice have been used as ideal test subjects.

Experiments on mice haveshown that CRISPR can disable a defective gene associated with Duchenne muscular dystrophy (DMD), inhibit the formation of deadly proteins involved in Huntingtons disease, and eliminate HIV infection.

In 2015, Chinese scientists created two super muscular beagles by disabling the myostatin gene, which directs normal muscle development. In the absence of thegene, the beagles displayed muscular hypertrophy, creating dogs which were visibly much more muscular than non-genetically modified ones.

Other CRISPR animal trials haveranged from genetically engineering long-haired goats for higher production of cashmere to breeding hornless cows to avoid the painful process of shearing horns off.

Compared to research involving animals, CRISPR trialsthat edit human DNA have movedmore slowly, largely due to the ethical and regulatory issues at play.

Given the permanent nature of altering a humans genome, the FDA is approaching CRISPR cautiously. Some scientists have even proposed a moratorium on CRISPR trials untilwe have more information on the potentialimpact on humans.

In the US and Europe, 2018 will be the year for CRISPR human trials.

Currently (as of 2/13/18),the University of Pennsylvania is awaiting the FDAs final approval to start a study that would evaluate the safety of using CRISPR for patients with multiple myeloma, melanoma, and sarcoma.

Europe may also see its first human CRISPR study in 2018 withCRISPR Therapeutics study focused on a blood disorder known as beta-thalassemia,which results in abnormal red blood cell production.

While clinical trials involving patient participation are still awaiting regulatory approval, CRISPR has already been applied to both viable and non-viable human embryos.

For example, in August 2017, a team lead by reproductive biologist Shoukhrat Mitalipov of Oregon Health and Science University received private funding to use CRISPR-Cas9 to target a mutation in viable human embryos that causes the thickening of heart muscles. The altered embryos came back 72% mutation-free in the lab (higher than theusual 50% chance of inheritance).

Some critics say the gene editing of embryos is unethical, even if the edited embryos are not destined for transfer and implantation. This type of testing currently does not receive federal funding, but instead relies on private donor funding.

On the other side of the world, Chinese researchersoperate under a different regulatory framework. Some hospital ethics committees can approve studies in as little as one day, with no need to seek approval from a federal agency.

Since 2015, China has been conductinghuman trials using CRISPRto combat various cancers, HIV, and HPV. It is the only country in the world toconduct human trials thus far.

According to ClinicalTrials.Gov, there are 10 active or upcoming CRISPR therapy trials in China, targeting advanced cancers like stage 4 gastric and nasopharyngeal carcinomas. So far results are only anecdotal, and while some participants tumors shrank, no formal results have been made available.

Although possible long-term side effectsarent fully understood,CRISPR is already an option for some patients in China who have exhausted all of the conventional treatments.

Potential high impact industries for CRISPR include medicine, food, agriculture, and the industrial biotech space. BecausetheCRISPR-Cas9 gene-editing system issoeasy to make and use, researchers from a range of scientific disciplines can access it to genetically engineer the organism of their choice.

The future of medicine will be written with CRISPR.

The current drug discovery process is long, given the need to ensure patientsafety and gain a thorough understanding of unintended effects.Moreover, current US regulatory policies often result in a decades-long development process.

However, teamsusing CRISPR can bringcustomized therapies to market more quickly than was previously dreamed, speeding upthe traditional drug discovery process.

Timeline of drug development. Credit: PhRMA

CRISPRscheap price tag and flexibilityallows accurate and fast identification of potential gene targets for efficient pre-clinical testing. Because itcan be used to knock out different genes, CRISPR givesresearchers a faster and more affordableway to study hundreds of thousands of genes to see which ones are affected by a particular disease.

Of course, alongwith providing a more streamlined drug development process, CRISPR offers the possibility of new ways to treat patients.

For example,monogenic diseasesdiseases caused by a mutation ina single gene present an attractive starting point for CRISPR trials. The nature of these illnesses provides an exact target for the treatment: the problematic mutation on a single gene.

Blood-based, single-gene diseases like beta-thalassemia or sickle cell are alsogreat candidates for CRISPR therapy, because of their ability to be treated outside of the body (known as ex-vivo therapy). A patients blood cells can be taken out, treated with the CRISPR system, then put back into the body.

An earlyapplication of CRISPR was pioneered by yogurt company Danisco in the 2000s, when scientists used an early version of CRISPR to combat a key bacterium found inmilk and yogurt cultures (streptococcus thermophilus) that kept getting infected by viruses. At that point, the ins and outs of CRISPRwere still unclear.

Fast forward to today, when climate change will further increasethe need to use CRISPR to protect the food and agriculture industries against new bacteria.For example, cacao is becoming difficult to farm as growing regions get hotter and drier. This environmental change will further exacerbate the damage done by pathogens.

If youve eaten yogurt or cheese, chances are youve eaten CRISPR-ized cells.

Rodolphe Barrangou, former Daniscoscientist & Editor-in-Chief of The CRISPR Journal

To combat this issue, the Innovative Genomics Institute (IGI) at UC Berkeley is applying CRISPR to create disease-resistant cacao. Leading chocolate supplier MARS Inc. is supporting this effort.Gene editing can make farming more efficient. It can curb global food shortages for staple crops like potatoes and tomatoes. And it can create resilient crops, impervious to droughts and other environmental impacts.Regulators have shown little resistanceto gene-edited crops, and the United States Department of Agriculture (USDA) in particular is not regulating the space. This is largely because when CRISPR is applied to crops, theres no foreign DNA being added: CRISPR is simply used to edit a crops own genetics to select for desirable traits.In 2016, the white button mushroom, modified to beresistant to browning, became the first CRISPR-edited organism to bypass USDA. In October 2017, it was announced that agriculture company DuPont Pioneer and the Broad Institute would collaborate for agriculture researchusing their CRISPR-Cas9 intellectual property.

InSeptember 2017, biotech company Yield10 Bioscience got approval for its CRISPR-edited plantCamelina sativa (false flax), which hasenhanced omega-3 oil and is used to make vegetable oil and animal feed.

These are indicationsthat newbreeds of crops could reachmarketsmuch faster than previously thought. Without USDA oversight, these items and other food products could go into production relatively quickly.

This will impact the food we eat, as food items are edited tocarry more nutrients or to last longer on grocery shelves.

Another area currently generating buzz isthe production of leaner livestock.

In October 2017, scientists at the Chinese Academy of Sciences in Beijing used CRISPR to genetically engineer pig meat that had 24% less body fat.

Researchersdid this by inserting a mouse gene into pig cellsin order tobetter regulate body temperature.Although this example technically makes the result a GMO product, it may not be too long before pigs genes are used for the same purpose.

Future versionsof this technology applied to human nutrition will be one area to look out for.

Another key, but less obvious, use of CRISPR lies is in the industrial biotech space. By re-engineering microbes using CRISPR,researcher can create new materials.

How is this relevant to society at large?

From an industrial standpoint, this is big for modifying and creating new chemical products. We can alter microbes to increase diversity, create new bio-based materials, and make more efficient biofuels.From active chemicals in fragrances to those involved in industrial cleaning, CRISPR could have agreat impact here by creating new and more efficientbiological materials.

Jennifer Doudnas first CRISPR startup, Caribou Biosciences, was founded in 2011 for non-therapeutic research purposes across industries. It is one of the key companies providing various industries with the tools to use CRISPR fora range of purposes.

CRISPRs list of potential benefits is a long one. But the technology also brings with it a number of limitations.

Possible unintended effects and all the unknown variables are some of the drawbacks to this newtechnology, while newethicalquestions and controversies are also emerging as human trials near.

When using CRISPRfor human therapies, safety is the biggest issue. As with any new form of technology, researchers are unsure of the entire range of CRISPRs effects.Off-target activity is the main concern here. A single gene editcould cause unintended activity somewhere else in the genome. A possible consequence of this is abnormal growth of tissues, leading to cancer. As more research uncovers new details, this could result in more refined, precise gene targeting.

Another issue is the possibility of mosaic generation.After a CRISPR treatment, a patient could have a mix of both edited and unedited cells a mosaic. As cells continue to divide and replicate, some cells may get repaired, while others wont.

Finally, immune systemcomplications mean that these interventions and therapies may trigger an undesired response froma patients immune system.Early research shows theimmune system may dispose of Cas enzymes before they achieve their purpose, or may have an averse reaction resulting in side effects like inflammation. (In 1999, a patient in the US died of a severe immune reaction, instilling more caution in researchers when it comes to CRISPR trials.)

However, all three of these limitations have some possible solutions.

Different enzymes (molecular scissors) or more precise delivery vehicles can reduce off-target activity. If modified stem cells in egg or sperm (i.e. cells that can become every cell in the human body) are edited, mosaics can be avoided.

With the immune system issue, researchers can isolate different Cas proteins from more obscure bacterial strains that humans dont already have an adaptive immunity to in order to circumvent an unwanted immune response. Meanwhile, ex-vivo therapies, wherescientists take a patients blood cells out of the body and treat them before infusing them back in, can also helpbypass the immune system.

One potential big limitation for CRISPR isthat CRISPR-Cas9 system lacks surgical precision. The Cas enzyme cuts both strands of the DNA double helix, and this double-stranded breakcreates worries over the precision of the cut.

Repairing a defective gene would be like finding a needle in a haystack and then removing that needle without disturbing a single strand of hay in the process.-Jennifer Doudna

While currently the Cas9 enzyme gets the most attentionas the enzyme doing the cutting, scientists are actively pursuing alternatives to find better candidates.

Alternative options include asmaller version of Cas9, or a different enzyme entirely: Cpf1, whichhas become popular due to its easy transport to the targeted DNA location.

Besides using other Cas enzymes, alternate delivery vehiclesfor therapeutic genes are another option. Harmless engineered viruses can carry therapeutic genes to the site of mutation, while lipid nanoparticles can avoid immune system detection, avoiding an immune reaction. Both options present promising avenues of research.

Whentechnology can alter the code of life, its implications are far-reaching as are its controversies. Here we outlinea few of the main controversies surroundingCRISPR.

Originally posted here:
What Is CRISPR? – CB Insights

Crisprs Epic Patent Fight Changed the Course of Biology | WIRED

After three bitter years and tens of millions of dollars in legal fees, the epic battle over who owns one of the most common methods for editing the DNA in any living thing is finally drawing to a close. On Monday, the US Court of Appeals for the Federal Circuit issued a decisive ruling on the rights to Crispr-Cas9 gene editingawarding crucial intellectual property spoils to scientists at the Broad Institute of Cambridge, Massachusetts.

The fight for Crispr-Cas9which divided the research community and triggered an uncomfortable discussion about science for personal profit versus public goodhas dramatically shaped how biology research turns into real-world products. But its long-term legacy is not what happened in the courtroom, but what took place in the labs: A wealth of innovation that is now threatening to make Cas9 obsolete.

This latest legal decision, which upholds a 2017 ruling by the US Patent and Trademark Office, was an expected one, given how rarely such rulings are overturned. And it more or less seals defeat for researchers at the University of California Berkeley, who also have claims to invention of the world-remaking technology.

The Broad celebrated the win while calling for a cease-fire, saying it was time to work together to ensure wide, open access to this transformative technology. UCs general counsel, Charles F. Robinson, struck a less conciliatory note, saying in a statement that the university was evaluating further litigation options. Those could include a rehearing from the same court or appeal to the Supreme Court.

But legal experts say the chances of either happening are vanishingly slim. It is very possible that there is no path forward for Berkeley in regards to broad patents covering Crispr-Cas9 at this point , says Jacob Sherkow a scholar of patent law at New York Law School who has closely followed the case. In addition to the Broad Institutes claims, UC-Berkeley also has to contend with another foundational patent for Crispr-Cas9 gene editing filed before anyone else in March 2012, by Virginijus iknys, a Lithuanian scientist who shares the prestigious Kavli Prize with Berkeleys Jennifer Doudna and The University of Viennas Emmanuelle Charpentier for their early work on Crispr. The USPTO has since granted his patent. UC didnt know about it at the time of its own filing because of an 18-month secrecy statute surrounding new applications. If this was a choose-your-own-adventure book, they just turned all the wrong pages, says Sherkow.

The University of California isnt the only loser here; the companies that already placed bets on it being the patent victor must now tread a difficult though not impassable IP landscape. That includes Intellia and Crispr Therapeuticscompanies cofounded by Doudna and Charpentier respectivelywhich are both developing Crispr treatments for human disease. The two firms released a joint statement Monday afternoon underscoring their faith in the strength and scope of UCs foundational IP. A spokesperson for Intellia also said in an email that the Federal Circuit decision will not impact the companys freedom to operate going forward.

For all the ferocity that fueled the fight from its outset, Mondays decision was met with muted interest from inside the halls of science to the crowded trading floors of Wall Street. Thats because a lot has changed since the first gene editing pioneers filed the original Crispr-Cas9 patents. In 2012, Cas9 was the entire Crispr universe. That little enzyme powered all the promise of Crispr gene editing, and the stakes for owning it couldnt have been higher. Scientists didnt yet know that biology would prove to be more creative than patent lawyers. They still had no notion of the vast constellations of constructs and enzymes that could be engineered, evolved in a lab, or harvested from the wild to replace Cas9.

Since then though, the fast-moving field of Crispr biology has yielded more than just alternative pairs of molecular scissors. Researchers have updated the Crispr system to manipulate the code of life in myriad novel waysfrom swapping out individual DNA letters to temporarily flipping genes on and off to detecting dangerous infections. And theyve unearthed dozens of Crispr enzymes of still unknown functions that might one day solve problems scientists havent even thought of yet.

The rush of discoveries and inventions has led to a full-blown patent race, says Sherkow, with anyone who found any new variation racing to file IP protections. The irony is that as the universe of Crispr expands, owning a part of it becomes less and less valuable. Twenty years from now, when the umpteenth drug gets approved using Crispr and some nuclease named Cas132013, people are going to look back on this patent battle and think, what a godawful waste of money, says Sherkow.

He expects that the field will eventually reach a point where the value of each new Crispr patent is so low that researchers dont bother going through all the paperwork and spending the thousands of dollars necessary to file an application. Already, biotechnologists are beginning to learn this lesson in adjacent fields; a land grab for patents is not the only way to go.

The Biobricks Foundation is a nonprofit dedicated to supporting the development of an open-source biotechnology commons. In 2015, it created a legal framework for scientists to put their discoveries in the public domain, safeguarding them from being patented elsewhere, and ensuring that anyone can access them. So far, the organization has begun to stockpile gene sequences for useful tools like fluorescent proteins. Linda Kahl, Biobricks senior counsel and a director there, says theyre still waiting for a group to design an open-source Crispr system. Thats a gauntlet thats in front of researchers, she says. With the ashes of the patent fight still glowing, it might be too soon to expect anyone to give a Crispr tool away for free just yet. But it probably wont take long.

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Crisprs Epic Patent Fight Changed the Course of Biology | WIRED

CRISPR, one of the biggest science stories of the decade …

One of the biggest and most important science stories of the past few years will probably also be one of the biggest science stories of the next few years. So this is as good a time as any to get acquainted with the powerful new gene editing technology known as CRISPR.

If you havent heard of CRISPR yet, the short explanation goes like this: In the past six years, scientists have figured out how to exploit a quirk in the immune systems of bacteria to edit genes in other organisms plants, mice, even humans. With CRISPR, they can now make these edits quickly and cheaply, in days rather than weeks or months. (The technology is often known as CRISPR/Cas9, but well stick with CRISPR, pronounced crisper.)

Let that sink in. Were talking about a powerful new tool to control which genes get expressed in plants, animals, and even humans; the ability to delete undesirable traits and, potentially, add desirable traits with more precision than ever before.

In 2017 alone, researchers reported in Nature that theyd successfully used CRISPR in human embryos to fix a mutation that causes a terrible heart muscle disorder called hypertrophic cardiomyopathy. (Other researchers have since called some of the conclusions into question.) Another team used it to reduce the severity of genetic deafness in mice, suggesting it could one day be used to treat the same type of hearing loss in people.

Meanwhile, researchers at the Broad Institute of MIT and Harvard launched a coordinated blitz with two big studies that move CRISPR in that safer and more precise direction. A paper published in Science describes an entirely new CRISPR-based gene editing tool that targets RNA, DNAs sister, allowing for transient changes to genetic material. In Nature, scientists published on a more refined type of CRISPR gene editing that can alter a single bit of DNA without cutting it increasing the tools precision and efficiency.

And these are just a few of the astounding things researchers have recently shown CRISPR can do. Weve already learned that it can help us create mushrooms that dont brown easily and edit bone marrow cells in mice to treat sickle-cell anemia. Down the road, CRISPR might help us develop drought-tolerant crops and create powerful new antibiotics. CRISPR could one day even allow us to wipe out entire populations of malaria-spreading mosquitoes or resurrect once-extinct species like the passenger pigeon.

But there are real limits to what CRISPR can do, at least right now. Scientists have recently learned that the approach to gene editing can inadvertently wipe out and rearrange large swaths of DNA in ways that may imperil human health. That follows recent studies showing that CRISPR-edited cells can inadvertently trigger cancer.

As scientists work to overcome these limitations, much of the hype around CRISPR has focused on whether we might engineer humans with specific genetic traits (like heightened intelligence). But in some ways, thats a sideshow. Designer babies are still far off, and there are enormous obstacles to making those sorts of complex genetic modifications. The stuff thats closer at hand from new therapies to fighting malaria is whats most exciting. So heres a basic guide to what CRISPR is and what it can do.

If we want to understand CRISPR, we should go back to 1987, when Japanese scientists studying E. coli first came across some unusual repeating sequences in the bacterias DNA. The biological significance of these sequences, they wrote, is unknown. Over time, other researchers found similar clusters in the DNA of other bacteria (and archaea). They gave these sequences a name: Clustered Regularly Interspaced Short Palindromic Repeats or CRISPR.

Yet these CRISPR sequences were mostly a mystery until 2007, when food scientists studying the Streptococcus bacteria used to make yogurt showed how these odd clusters actually served a vital function: Theyre part of the bacterias immune system.

See, bacteria are under constant assault from viruses and produce enzymes to fight off viral infections. Whenever the bacterias enzymes manage to kill off an invading virus, other little enzymes will come along, scoop up the remains of the viruss genetic code, cut it into little bits, and then store it in those CRISPR spaces.

Now comes the clever part: The bacteria use the genetic information stored in these CRISPR spaces to fend off future attacks. When a new infection occurs, the bacteria produce special attack enzymes, known as Cas9, that carry around those stored bits of viral genetic code like a mug shot. When these Cas9 enzymes come across a virus, they see if the viruss RNA matches whats in the mug shot. If theres a match, the Cas9 enzyme starts chopping up the viruss DNA to neutralize the threat. It looks a little like this:

So thats what CRISPR/Cas9 does. For a while, these discoveries werent of much interest to anyone except microbiologists until a series of further breakthroughs occurred.

In 2011, Jennifer Doudna of the University of California Berkeley and Emmanuelle Charpentier of Ume University in Sweden were puzzling over how the CRISPR/Cas9 system actually worked. How did the Cas9 enzyme match the RNA in the mug shots with that in the viruses? How did the enzymes know when to start chopping?

The scientists soon discovered they could fool the Cas9 protein by feeding it artificial RNA a fake mug shot. When they did that, the enzyme would search for anything with that same code, not just viruses, and start chopping. In a landmark 2012 paper, Doudna, Charpentier, and Martin Jinek showed they could use this CRISPR/Cas9 system to cut up any genome at any place they wanted.

While the technique had only been demonstrated on molecules in test tubes at that point, the implications were breathtaking.

Further advances followed. Feng Zhang, a scientist at the Broad Institute in Boston, co-authored a paper in Science in February 2013 showing that CRISPR/Cas9 could be used to edit the genomes of cultured mouse cells or human cells. In the same issue of Science, Harvards George Church and his team showed how a different CRISPR technique could be used to edit human cells.

Since then, researchers have found that CRISPR/Cas9 is ridiculously versatile. Not only can scientists use CRISPR to silence genes by snipping them out, they can also harness repair enzymes to substitute desired genes into the hole left by the snippers (though this latter technique is trickier to pull off). So, for instance, scientists could tell the Cas9 enzyme to snip out a gene that causes Huntingtons disease and insert a good gene to replace it.

Gene editing itself isnt new. Various techniques to knock out genes have been around for years. What makes CRISPR so revolutionary is that its incredibly precise: The Cas9 enzyme mostly goes wherever you tell it to. And its incredibly cheap and easy: In the past, it might have cost thousands of dollars and weeks or months of fiddling to alter a gene. Now it might cost just $75 and only take a few hours. And this technique has worked on every organism its been tried on.

This has become one of the hottest fields around. In 2011, there were fewer than 100 published papers on CRISPR. In 2017, there were more than 14,000 and counting, with new refinements to CRISPR, new techniques for manipulating genes, improvements in precision, and more. This has become such a fast-moving field that I even have trouble keeping up now, says Doudna. Were getting to the point where the efficiencies of gene editing are at levels that are clearly going to be useful therapeutically as well as a vast number of other applications.

Theres been an intense legal battle over who exactly should get credit for this CRISPR technology was Doudnas 2012 paper the breakthrough, or was Zhangs 2013 paper the key advance? Ultimately, a court ruled in February that the patent should go to Zhang and the Broad Institute, Harvard, and MIT. In the July, the University of California and others on Doudnas side said they were launching an appeal of the decision. But the important thing is that CRISPR has arrived.

So many things. Paul Knoepfler, an associate professor at UC Davis School of Medicine, told Vox that CRISPR makes him feel like a kid in a candy store.

At the most basic level, CRISPR can make it much easier for researchers to figure out what different genes in different organisms actually do by, for instance, knocking out individual genes and seeing which traits are affected. This is important: While weve had a complete map of the human genome since 2003, we dont really know what function all those genes serve. CRISPR can help speed up genome screening, and genetics research could advance massively as a result.

Researchers have also discovered there are numerous CRISPRs. So CRISPR is actually a pretty broad term. Its like the term fruit it describes a whole category, said the Broads Zhang. When people talk about CRISPR, they are usually referring to the CRISPR/Cas9 system weve been talking about here. But in recent years, researchers like Zhang have found other types of CRISPR proteins that also work as gene editors. Cas13, for example, can edit DNAs sister, RNA. Cas9 and Cas13 are like apples and bananas, Zhang added.

The real fun and, potentially, the real risks could come from using CRISPRs to edit various plants and animals. A recent paper in Nature Biotechnology by Rodolphe Barrangou and Doudna listed a flurry of potential future applications:

1) Edit crops to be more nutritious: Crop scientists are already looking to use CRISPR to edit the genes of various crops to make them tastier or more nutritious or better survivors of heat and stress. They could potentially use CRISPR to snip out the allergens in peanuts. Korean researchers are looking to see if CRISPR could help bananas survive a deadly fungal disease. Some scientists have shown that CRISPR can create hornless dairy cows a huge advance for animal welfare.

Recently, major companies like Monsanto and DuPont have begun licensing CRISPR technology, hoping to develop valuable new crop varieties. While this technique wont entirely replace traditional GMO techniques, which can transplant genes from one organism to another, CRISPR is a versatile new tool that can help identify genes associated with desired crop traits much more quickly. It could also allow scientists to insert desired traits into crops more precisely than traditional breeding, which is a much messier way of swapping in genes.

With genome editing, we can absolutely do things we couldnt do before, says Pamela Ronald, a plant geneticist at the University of California Davis. That said, she cautions that its only one of many tools for crop modification out there and successfully breeding new varieties could still take years of testing.

Its also possible that these new tools could attract controversy. Foods that have had a few genes knocked out via CRISPR are currently regulated more lightly than traditional GMOs. Policymakers in Washington, DC, are currently debating whether it might make sense to rethink regulations here. This piece for Ensia by Maywa Montenegro delves into some of the debates CRISPR raises in agriculture.

2) New tools to stop genetic diseases: As the new Nature paper shows, scientists are now using CRISPR/Cas9 to edit the human genome and try to knock out genetic diseases like hypertrophic cardiomyopathy. Theyre also looking at using it on mutations that cause Huntingtons disease or cystic fibrosis, and are talking about trying it on the BRCA-1 and 2 mutations linked to breast and ovarian cancers. Scientists have even shown that CRISPR can knock HIV infections out of T cells.

So far, however, scientists have only tested this on cells in the lab. There are still a few hurdles to overcome before anyone starts clinical trials on actual humans. For example, the Cas9 enzymes can occasionally misfire and edit DNA in unexpected places, which in human cells might lead to cancer or even create new diseases. As geneticist Allan Bradley, of Englands Wellcome Sanger Institute, told STAT, CRISPRs ability to wreak havoc on DNA has been seriously underestimated.

And while there have also been major advances in improving CRISPR precision and reducing these off-target effects, scientists are urging caution on human testing. Theres also plenty of work to be done on actually delivering the editing molecules to particular cells a major challenge going forward.

3) Powerful new antibiotics and antivirals: One of the most frightening public health facts around is that we are running low on effective antibiotics as bacteria evolve resistance to them. Currently, its difficult and costly to develop fresh antibiotics for deadly infections. But CRISPR/Cas9 systems could, in theory, be developed to eradicate certain bacteria more precisely than ever (though, again, figuring out delivery mechanisms will be a challenge). Other researchers are working on CRISPR systems that target viruses such as HIV and herpes.

4) Gene drives that could alter entire species: Scientists have also demonstrated that CRISPR could be used, in theory, to modify not just a single organism but an entire species. Its an unnerving concept called gene drive.

It works like this: Normally, whenever an organism like a fruit fly mates, theres a 50-50 chance that it will pass on any given gene to its offspring. But using CRISPR, scientists can alter these odds so that theres a nearly 100 percent chance that a particular gene gets passed on. Using this gene drive, scientists could ensure that an altered gene propagates throughout an entire population in short order:

By harnessing this technique, scientists could, say, genetically modify mosquitoes to only produce male offspring and then use a gene drive to push that trait through an entire population. Over time, the population would go extinct. Or you could just add a gene making them resistant to the malaria parasite, preventing its transmission to humans, Voxs Dylan Matthews explains in his story on CRISPR gene drives for malaria.

Suffice to say, there are also hurdles to overcome before this technology is rolled out en masse and not necessarily the ones youd expect. The problem of malaria gene drives is rapidly becoming a problem of politics and governance more than it is a problem of biology, Matthews writes. Regulators will need to figure out how to handle this technology, and ethicists will need to grapple with knotty questions about its fairness.

5) Creating designer babies: This is the one that gets the most attention. Its not entirely far-fetched to think we might one day use CRISPR to edit the human genome to eliminate disease, or to select for athleticism or superior intelligence.

That said, scientists arent even close to being able to do this. Were not even close to the point where scientists could safely make the complex changes needed to, for instance, improve intelligence, in part because it involves so many genes. So dont go dreaming of Gattaca just yet.

I think the reality is we dont understand enough yet about the human genome, how genes interact, which genes give rise to certain traits, in most cases, to enable editing for enhancement today, Doudna said in 2015. Still, she added: Thatll change over time.

Given all the fraught issues associated with gene editing, many scientists are advocating a slow approach here. They are also trying to keep the conversation about this technology open and transparent, build public trust, and avoid some of the mistakes that were made with GMOs.

In February 2017, a report from the National Academy of Sciences said that clinical trials could be greenlit in the future for serious conditions under stringent oversight. But it also made clear that genome editing for enhancement should not be allowed at this time.

Society still needs to grapple with all the ethical considerations at play here. For example, if we edited a germline, future generations wouldnt be able to opt out. Genetic changes might be difficult to undo. Even this stance has worried some researchers, like Francis Collins of the National Institutes of Health, who has said the US government will not fund any genomic editing of human embryos.

In the meantime, researchers in the US who can drum up their own funding, along with others in the UK, Sweden, and China, are moving forward with their own experiments.

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CRISPR, one of the biggest science stories of the decade …

CRISPR safety calls for cautious approach – washingtonpost.com

In the movie Rampage, the character played by Dwayne Johnson uses a genetic engineering technology called CRISPR to transform a gorilla into a flying dragon-monster with gigantic teeth. Although this is science fiction, not to mention impossible, the movie captures the recent interest and fascination with one of the newest scientific technologies.

CRISPR which stands for clustered regularly interspaced short palindromic repeats was originally seen as part of a bacterial defense system that evolved to destroy foreign DNA that entered a bacterium. But this system is also capable of editing DNA and now geneticists have honed the technology to alter DNA sequences that we specify.

This has generated enormous excitement and great expectations about the possibility of using CRISPR to alter genetic sequences to improve our health, to treat diseases, to improve the quality and quantity of our food supplies, and to tackle environmental pollution.

Using genome editing to treat human diseases is very tantalizing. Correcting inherited genetic defects that cause human disease just as one edits a sentence is the obvious application. This strategy has been successful in tests on animals.

But a few recent scientific papers suggest that CRISPR is not without its problems. The research reveals that CRISPR can damage DNA located far from the target DNA we are trying to correct. As a cancer biologist at the University of Pittsburgh School of Medicine, I use CRISPR in my lab to study human cancers and develop ways to kill cancer cells.

Although the new findings appear significant, I dont think that these revelations rule out using the technology in a clinical setting; rather, they suggest we take additional cautionary measures as we implement these strategies.

Treating human diseases

In the United States and Europe, clinical trials have been planned for several human diseases. Most notably, a gene-editing Phase I/II trial is planned in Europe for beta-thalassemia, a hereditary blood disorder that causes anemia that requires lifelong blood transfusions. This year, a CRISPR trial for sickle cell anemia, another inherited blood disorder caused by a mutation that deforms the red blood cells, is planned in the United States.

For both of these trials, the gene editing is done ex vivo meaning outside the patients body. Hematopoietic blood cells the stem cells that generate red blood cells are taken from the patient and edited in the lab. The cells are then reintroduced into the same patients after the mutations have been corrected. The expectation is that by correcting the stem cells, the cells they produce will be normal, curing the disease.

The ex vivo approach has also been used in China to test treatments against an array of human cancers. There, researchers take immune cells called T cells from cancer patients and use CRISPR to stop these cells from producing a protein called PD-1 (program cell death-1). Normally, PD-1 prevents T cells from attacking ones own tissues. However, cancer cells exploit this protective mechanism to evade the bodys defense system. Removing PD-1 allows T cells to attack cancer cells vigorously. The initial results from clinical trials using gene-edited T cells appear mixed.

In my lab, we have recently been focusing on chromosome rearrangement, a genetic defect where a segment of chromosome skips and joins distant parts of the same or a different chromosome. A scrambled chromosome is a defining characteristic of most cancers. The most famous example of such an alteration is the Philadelphia Chromosome in which Chromosome 9 is connected to Chromosome 22 which causes acute myeloid leukemia.

My team has used CRISPR in animal models to insert a suicide gene to specifically target liver and prostate cancer cells that harbor such rearrangements. Since these chromosome rearrangements occur only in cancer cells but not normal cells, we can target the cancer without collateral damage to healthy cells.

CRISPR concerns

Despite all the excitement surrounding CRISPR editing, researchers have urged caution about moving too fast. Two recent studies have raised concerns that CRISPR may not be as effective as previously thought, and in some cases it may produce unwanted side effects.

The first study showed that when the Cas9 protein part of the CRISPR system that snips the DNA before correcting the mutation cuts the DNA of stem cells, it causes them to become stressed and stops them from being edited. While some cells can recover after their DNA has been corrected, other cells could die.

The second study showed that a protein called p53, which is well known for guarding against tumors, is activated by cellular stress. The protein then inhibits CRISPR from editing. Since CRISPR activity causes stress, the editing process may be thwarted before it even accomplishes its task.

Another study over the past year has revealed an additional potential issue with using CRISPR in humans. Because CRISPR is a bacterial protein, a significant portion of the human population may have been exposed to it during common bacterial infections. In these cases, the immune systems of these people may have developed immune defense against the protein, which means a persons body could attack the CRISPR machinery, just as it would attack an invading bacterium or virus, preventing the cell from the benefits of CRISPR-based therapy.

Additionally, like most technologies, not all editing is accurate. Occasionally, CRISPR targets the wrong sites in the DNA and makes changes that researchers fear could cause disease. A recent study showed that CRISPR caused large chunks of the chromosome to rearrange near the site of genome editing in mouse embryonic stem cells, although this effect isnt always observed in the other cell systems. Most published results indicate that off-target rates range from 1 to 5 percent. Even if the off-target rate is relatively low, we dont yet understand the long-term consequences.

Dangers have been hyped

The studies referenced above have led to a glut of media reports about the potential negative effect of CRISPR, many citing potential cancer risk. More often than not, these involve a far-fetched extrapolation of actual results. As far as I am aware, no animals treated with the CRISPR-Cas9 system have been shown to develop cancers.

Studies have shown CRISPR-based genome editing works more efficiently in cancer cells than normal cells. Indeed, the resistance of normal cells to CRISPR editing actually makes it more appealing for cancer treatment since there would be less potential collateral damage to normal tissues, a conclusion that is supported by research in our lab.

Looking forward, it is obvious that the technology has great potential to treat human diseases. The recent studies have revealed new aspects of how CRISPR works that may have implications for the ways in which these therapies are developed. However, the long-term effect of genome editing can only be assessed after CRISPR has been used widely to treat human diseases.

health-science@washpost.com

Luo is a professor of pathology at the University of Pittsburgh. This article was originally published on theconversation.com.

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CRISPR safety calls for cautious approach – washingtonpost.com

What is CRISPR? – YouTube

In this video Paul Andersen explains how the CRISPR/Cas immune system was identified in bacteria and how the CRISPR/Cas9 system was developed to edit genomes.

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All of the images are licensed under creative commons and public domain licensing:Adenosine. (2009). English: Artistic rendering of a T4 bacteriophage. The colours grey and orange do not signify anything, they are just used to illustrate structure. Created for Wikipedia. Retrieved from https://commons.wikimedia.org/wiki/Fi…E. coli Bacteria. (n.d.). Retrieved February 17, 2016, from https://www.flickr.com/photos/niaid/1…Fioretti, B. F. Hallbauer &. (2015). English: Director, Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology. Visiting professor The Laboratory for Molecular Infection Medicine Sweden MIMS; http://www.mpiib-berlin.mpg.de/resear…. Retrieved from https://commons.wikimedia.org/wiki/Fi…Foresman, P. S. ([object HTMLTableCellElement]). English: Line art drawing of a chimera. Retrieved from https://commons.wikimedia.org/wiki/Fi…Magladem96. (2014). English: Picture of DNA Base Flipping. Retrieved from https://commons.wikimedia.org/wiki/Fi…project, C. wiki. (2014). English: Crystal Structure of Cas9 bound to DNA based on the Anders et al 2014 Nature paper. Rendition was performed using UCSFs chimera software. Retrieved from https://commons.wikimedia.org/wiki/Fi…Providers, P. C. (1979). English: Photomicrograph of Streptococcus pyogenes bacteria, 900x Mag. A pus specimen, viewed using Pappenheims stain. Last century, infections by S. pyogenes claimed many lives especially since the organism was the most important cause of puerperal fever and scarlet fever. Streptococci. Retrieved from https://commons.wikimedia.org/wiki/Fi…RRZEicons. (2010). English: zipper, open, close. Retrieved from https://commons.wikimedia.org/wiki/Fi…UC Berkeley. (n.d.). Gene editing with CRISPR-Cas9. Retrieved from https://www.youtube.com/watch?v=avM1Y…

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What is CRISPR? – YouTube

With Embryo Base Editing, China Gets Another Crispr First

Scientists in the US may be out in front developing the next generation of Crispr-based genetic tools, but its China thats pushing those techniques toward human therapies the fastest. Chinese researchers were the first to Crispr monkeys, and non-viable embryos, and to stick Crisprd cells into a real live human. And now, a team of scientists in China have used a cutting-edge Crispr technique, known as base editing, to repair a disease-causing mutation in viable human embryos.

Published last week in the journal Molecular Therapy, and reported first by Stat, the study represents significant progress over previous attempts to remodel the DNA of human embryos. Thats in part because the editing worked so well, and in part because that editing took place in embryos created by a standard in-vitro fertilization technique.

So-called germline editing, the contentious technology that can permanently change the code in every cell in the human body, has been gaining acceptance in the last few years as research has pushed forward, illuminating the possibilities of Crispr. Immediately following those first reports of embryonic gene-editing in China in 2015, an international summit convened by the US National Academy of Sciences concluded that actually trying to produce a human pregnancy from such modified germlines was irresponsible, given ongoing safety concerns and lack of societal consensus. Two years later, a report from the NAS and the National Academy of Medicine stated that clinical trials for editing out heritable diseases could be permitted in the future, but only for serious conditions under stringent oversight.

Attitudes may be slowly changing: Last month, the United Kingdoms Nuffield Council on Bioethics went so far as to say that heritable genome editing could be ethically acceptable in some circumstances. A Pew Research Council study released at the end of July found that 72 percent of Americans think changing an unborn babys DNA to treat a serious disease would be an appropriate use of gene-editing technology.

In the study published in Molecular Therapy, the Chinese scientists corrected a mutation that causes Marfan syndrome, an incurable connective tissue disorder that affects about 1 in 5,000 people. A single letter mistake in the gene for FBN1, which codes for the fibrillin protein, can cause a ripple effect of problemsfrom loose joints to weak vision to life-threatening tears in the hearts walls. Starting with healthy eggs and sperm donated by a Marfan syndrome patient, the team of researchers from Shanghai Tech University and Guangzhou Medical University used an IVF technique to make viable human embryos. Then they injected the embryos with a Crispr construct known as a base editor, which swaps out a single DNA nucleotide for anotherin this case, removing a C and replacing it with a T.1 They kept the embryos alive for another two days in the lab, long enough to run tests to see how well the editing worked.

Sequencing revealed that all 18 embryos had been edited, with 16 of the embryos bearing only the corrected version of the FBN1 gene. In two of the embryos, additional unwanted edits had also taken place. Previously, the most successful demonstration of gene editing in the human germline was the correction of a mutation that causes a hereditary heart condition in 42 out of 58 embryos. That study, which was published last year, used standard Crispr cut-and-paste technology.

Its a nice demonstration of the use of base editors to correct a well-known point mutation that causes a human genetic disease in a setting that may become therapeutically relevant, says David Liu, whose lab at Harvard developed the base editor used to correct the Marfan mutation, though he was not involved in the study.

Rather than breaking the double-stranded DNA molecule and allowing the cell to repair itself with a healthy gene template, these newer versions of Crispr change just a single letter. If Crispr is a pair of molecular scissors, Lius base editors are more like a pencil with a squeaky new eraser. While the hope is that such precise gene-writing implements wont cause the kind of sloppy chaos that Crispr 1.0 is capable of, Liu says its too early to make any general statements about their relative risks as a therapeutic. Despite more than 50 publications using base editors from laboratories around the world, the entire field of base editing is only about two years old, and additional studies are needed to assess as many possible consequences of base editing as can be reasonably detected.

Some of those studies are being conducted at Beam Therapeutics, the startup that Liu co-founded earlier this year with fellow Crispr pioneer Feng Zhang. Beams first license agreement with Harvard covers Lius C base editor, which makes programmable G-to-A or C-to-T edits, like the one used to correct the Marfan mutation. The second is the A base editor, which can do T-to-C as well as A-to-G edits. But dont expect Beam to be erasing genetic diseases from the germline any time soon. The company is focused on using base editing to treat serious diseases in children and adults only, not on embryo editing, says CEO John Evans. More consideration would be needed before society is ready to consider embryo editing, and we look forward to participating in the discussion.

In the meantime, Beam will be just one of many US companies looking at an increasingly streamlined path for genetic medicines. In July, FDA Commissioner Scott Gottlieb announced a new regulatory framework for gene therapies to treat rare diseases. The agency issued a suite of six guidance documents updating the approval process. And on August 17, the FDA along with the National Institutes of Health proposed changes in the way the agencies together assess the safety of gene-therapy human trials.

Specifically, the proposals will eliminate review by the NIHs Recombinant DNA Advisory Committee, which was established in 1974 to advise on emerging genetic technologies. In a New England Journal of Medicine editorial describing the changes, Gottlieb and NIH Director Francis Collins wrote it was their view that there is no longer sufficient evidence to claim that the risks of gene therapy are entirely unique and unpredictableor that the field still requires special oversight that falls outside our existing framework for ensuring safety. A more streamlined approval process may help the US move faster in the long-run, though probably not enough to catch Chinas head start. But when it comes to gene editing’s most controversial applications, theres nothing wrong with being slow.

1Correction appended 8-27-2018, 10:45 EDT. The researchers changed a cytosine to a thymine, not an adenine to guanine, as previously stated.

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With Embryo Base Editing, China Gets Another Crispr First

CRISPR | Genome Editing, DNA Repair

Cas9 and Cpf1 can be reprogrammed to different sites or multiple sites using multiple gRNAs. The availability of the different engineered variants of Cas9 and Cpf1 allows for different types of cuts for genome editing, which include the following:

Cut & Revise and Cut & Remove typically result in disruption of a problematic gene or elimination of a mutation. These approaches leverage the cell’s natural DNA repair mechanisms known as non-homologous end joining, or NHEJ, to complete the edit.

When a cell repairs a DNA cut by NHEJ, it leaves small insertions and deletions at the cut site, collectively referred to as indels. NHEJ can be used to either cut and revise the targeted gene or to cut and remove a segment of DNA. In the ”cut and revise” process, a single cut is made. In the ”cut and remove” process, two cuts are made, which results in the removal of the intervening segment of DNA. This approach could be used to delete either a small or a large segment of DNA depending on the type of repair desired.

The second mechanism our Cut & Replace approach leverages a different DNA repair mechanism known as homology directed repair, or HDR. In this approach, a DNA template is also provided, one that is similar to the DNA that has been cut. The cell can use the template to construct reparative DNA, resulting in the replacement of a defective genetic sequence with the correct one.

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CRISPR | Genome Editing, DNA Repair

Addgene: CRISPR References and Information

This table lists gRNA sequences that have been experimentally validated for use in CRISPR experiments.

gRNA design tool with extensive selection of eukaryotic pathogen genomes (200+) that can predict gRNA targets in gene families, HDR oligonucleotide design, and batch processing for designing genome-wide gRNA libraries. PubMed PMID 28348817.

This tool helps design (10 different prediction scores), clone (primer design), and evaluate gRNAs, as well as predict off-targets, for CRISPR in 180+ genomes. PubMed PMID: 27380939.

sgRNA Scorer 2.0From the Church Lab: a tool that identifies putative target sites for S. pyogenes Cas9, S. thermophilus Cas9, or Cpf from your input sequence or list of sequences.

Quilt Universal guide RNA designerSearch for gRNAs via gene name or by genomic location. Database includes gRNAs from popular CRISPR libraries and from more than two million DNAse hypersensitive sites for intergenic guide RNAs in hg19, filtered for off-target effects.

From the Kim Lab, Cas-OFFinder identifies gRNA target sequences from an input sequence and checks for off-target binding. Currently supports: Drosophila, Arabidopsis, zebrafish, C. elegans, mouse, human, rat, cow, dog, pig, Thale cress, rice (Oryza sativa), tomato, corn, monkey (macaca mulatta).

Cas-Designer searches for targets that maximize knockout efficiency while having a a low probability of off-target effects. Cas-Designer integrates information from the Kim Lab’s Cas-OFFinder and Microhomology predictor.

From the Qi Lab, a sgRNA design tool for genome editing, as well as gene regulation (repression and activation). Genome support for bacteria (E. coli, B. subtilis), yeast (S. cerevisiae), worm (C. elegans), fruit fly, zebrafish, mouse, rat, and human.

Identifies candidate sgRNA target sites by off-target quality. Validated for gene inactivation, NHEJ, and HDR. Reference genomes include Arabidopsis, C. elegans , sea squirt, cavefish, Chinese hamster, fruit fly, human, rice fish, mouse, silk worm, stickleback, tobacco, tomato, frog (X. laevis and X. tropicalis), and zebrafish.

Program for designing optimal gRNAs. Provides feedback on number of potential off-targets, target’s genomic location, and genome annotation. Available genomes are human (hg19 & hg38), mouse (mm10), and yeast (strain w303).

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Addgene: CRISPR References and Information

Here’s Why CRISPR Therapeutics Lost 18.8% in July — The …

What happened

Shares of CRISPR Therapeutics (NASDAQ:CRSP) fell nearly 19% last month, according to data provided by S&P Global Market Intelligence, after yet another study reminded Wall Street and investors that there’s still much for scientists to understand about the use of CRISPR gene-editing tools in human cells. Previously, in June, two studies surfaced that suggested certain uses of CRISPR could trigger faulty DNA repair mechanisms to activate and turn a cell cancerous.

That was followed up last month by a new study suggesting that certain uses of CRISPR tools “seriously underestimated” the number of off-target changes made to a genome. CRISPR Therapeuticssaid to Reutersthat “[w]e do not use the methods described in this Nature Biotech paper … nevertheless, in our work, we do not see similar findings.” While that wasn’t enough to appease Wall Street in July, shareholders have still enjoyed a year-to-date gain of 103%.

Image source: Getty Images.

The study published last month came from researchers at the prestigious Wellcome Sanger Institute, an affiliation that helped the results to be taken more seriously. But considering CRISPR Therapeutics says it doesn’t use the specific techniques identified, investors may be wondering why the company’s shares were impacted at all. Well, it has to do with increasing uncertainty over an important part of using certain gene-editing tools.

More specifically, the most recent study detailing off-target changes to DNA and those identifying the potential to activate cancerous mutations already present in cells all seem to imply the same thing: Scientists may have gotten a little ahead of themselves by assuming DNA repair mechanisms would work in a simple fashion. While CRISPR tools intend to fix genetic defects by cutting one or both strands of human DNA, all rely on DNA repair mechanisms already present in a cell to stitch the genome back together. If those fail, then CRISPR tools might be less effective or could even end up having significant unintended effects.

Right now, it appears that the most troubling side effects are observed when CRISPR tools cut both strands of DNA (a “double-strand break”). The lead drug candidates of all three major CRISPR companies deploying the technology for medical applications avoid that headache, although all companies are exploring preclinical therapeutics that will have to navigate that obstacle eventually.

Investors can likely expect gene-editing stocks such as CRISPR Therapeutics to experience a higher-than-normal amount of volatility. The technology has received an incredible amount of attention in the media and even popular culture, and the potential to cure diseases has Wall Street understandably excited. Those forces have combined to hand the pioneering companies premium market valuations, but it’s important to remember that CRISPR is a relatively new technology. Investors in it for the long haul will simply need to buckle up and remain patient as results from the first clinical trials (yet to get started) begin to trickle in within the next few years.

Maxx Chatsko has no position in any of the stocks mentioned. The Motley Fool owns shares of CRISPR Therapeutics. The Motley Fool has a disclosure policy.

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Here’s Why CRISPR Therapeutics Lost 18.8% in July — The …

Here’s Why CRISPR Stocks Are Down as Much as 11.4% Today …

What happened

Shares of the three leading companies developing human therapeutics based on CRISPR gene-editing technology fell as much as 11.4% today. There was no new news that could be interpreted as detrimental to CRISPR Therapeutics (NASDAQ:CRSP), Editas Medicine (NASDAQ:EDIT), or Intellia Therapeutics (NASDAQ:NTLA). But on July 23, many media outlets published stories commenting on a study released one week earlier.

While the stock moves may seem to be based on the rehashing of old news, there are good reasons investors shouldn’t be too quick to dismiss the concerns. As of 2:44 p.m. EDT, CRISPR Therapeutics stock had settled to a 9.5% loss, while Editas Medicine shares were down 10.4%, and Intellia Therapeutics stock had sunk by 7.2%.

Image source: Getty Images.

On July 16, scientists published a study in Nature Biotechnology demonstrating that using CRISPR tools to edit faulty DNA sequences can lead to unintended deletions and rearrangements of genetic material. The lead author, Dr. Allan Bradley, issued a cautious summary of the study:

This is the first systematic assessment of unexpected events resulting from CRISPR/Cas9 editing in therapeutically relevant cells, and we found that changes in the DNA have been seriously underestimated before now. It is important that anyone thinking of using this technology for gene therapy proceeds with caution, and looks very carefully to check for possible harmful effects.

The researchers, who hail from the prestigious Wellcome Sanger Institute, found that some of the genetic changes occurred far away from where CRISPR tools cut a genome, locations which would elude existing diagnostic tools used to gauge off-target effects. In other words, the field has “seriously underestimated” the potential for unintended genetic alterations because it hasn’t been looking in the right places.

All three companies made statements to Reuters last week regarding the study. CRISPR Therapeutics commented: “We do not use the methods described in this Nature Biotech paper … nevertheless, in our work, we do not see similar findings.” Editas Medicine said it was “not specifically concerned.” Intellia Therapeutics said it didn’t think the findings would affect the future of CRISPR-based therapies.

While it’s important for investors not to panic over the latest study showing potentially unintended consequences of using gene-editing tools, it is worth noting that most of the recent uncertainty injected into CRISPR stocks has come from observations of DNA repair mechanisms — one thing gene-editing tools have little to no control over. While companies focus on developing safe and effective ways to cut a genome, they must rely on natural cellular processes to stitch up the genome afterwards.

For instance, in June, investors worried over two studies showing that CRISPR tools could activate a faulty DNA repair mechanism and result in cancerous cells. The latest study from the Wellcome Sanger Institute was not concerned with the same question, but demonstrated that researchers may be overlooking the details of how genomes get stitched back up.

An open-minded approach to investing in CRISPR Therapeutics, Editas Medicine, and Intellia Therapeutics would nod to the awesome potential of the technology while acknowledging the risks of an early-stage investment. Recent stock moves hint that the hype may need to come back down to earth, as there’s much left to understand about using CRISPR tools in human cells. To date researchers have focused mostly on the ability to cut DNA, but it may be time to start paying closer attention to what happens after that.

Maxx Chatsko has no position in any of the stocks mentioned. The Motley Fool owns shares of CRISPR Therapeutics. The Motley Fool recommends Editas Medicine. The Motley Fool has a disclosure policy.

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Here’s Why CRISPR Stocks Are Down as Much as 11.4% Today …

Our Programs – CRISPR

Gene Editing to Treat Disease

The majority of medical therapies available today are directed at managing disease processes, the pathogenic or mis-regulated proteins or molecules associated with disease. However, these pathogenic molecules themselves are typically encoded in or affected by changes in genes or other sequences in the human genome, which encompasses the DNA in all our cells. Gene editing technologies, including CRISPR/Cas9, now offer us the ability to directly modify or correct the underlying disease-associated changes in our genome. Successfully editing or correcting a gene that encodes the dysfunctional or missing protein can in principle result in the expression of a fully normal protein and full correction of the disease.

Gene therapy and other technologies to modify the genome have been in development for many years, and a small number of gene therapies have been approved to treat patients. However, these older approaches have been burdened by challenges to their safety and efficacy and have not yet provided the ability to precisely control a range of different genetic changes.

We believe that CRISPR/Cas9 offers just such an opportunity, particularly to correct DNA changes in somatic (non germ line) cells in patients with serious disease.

CRISPR/Cas9 is a rapid and easy to use gene editing technology that can selectively delete, modify or correct a disease causing abnormality in a specific DNA segment. CRISPR refers to Clustered Regularly Interspaced Short Palindromic Repeats occurring in the genome of certain bacteria, from which the system was discovered; Cas9 is a CRISPR-associated endonuclease (an enzyme), the molecular scissors that are easily programmed to cut and edit, or correct, disease-associated DNA in a patients cell. The location at which the Cas9 molecular scissors cut the DNA to be edited is specified by guide RNA, which is comprised of a crRNA component and a tracrRNA component, either individually or combined together as a single guide RNA (sgRNA). For example, a guide RNA can direct the molecular scissors to cut the DNA at the exact site of the mutation present in the genome of patients with a particular genetic disease. Once the molecular scissors make a cut in the DNA, additional cellular mechanisms and exogenously added DNA will use the cells own machinery and other elements to specifically repair the cut DNA.

There are more than 10,000 known single-gene (or monogenic) diseases, occurring in about 1 out of every 100 births1. Scientists and clinicians are now conducting pioneering research using CRISPR/Cas9 to address both recessive and dominant genetic defects, opening up the potential of gene editing to provide novel transformative gene-based medicines for patients with a large number of both rare and common diseases.

Dr. Emmanuelle Charpentier, one of CRISPR Therapeutics scientific founders, co-invented the CRISPR/Cas9 technology.

The clustered repeats of CRISPR were discovered in 1987 in bacteria2, but their function was unknown. In 2000, these clustered repeat elements were found to be relatively common in bacteria3 hinting to an important role of these elements. The clustered repeats were given the name CRISPR in 2002 and multiple CRISPR-associated (Cas) genes were discovered adjacent to the repeat elements in that same year4.

CRISPR/Cas9 is a rapid and easy to use gene editing technology that can selectively delete, modify or correct a disease causing abnormality in a specific DNA segment. CRISPR refers to Clustered Regularly Interspaced Short Palindromic Repeats occurring in the genome of certain bacteria, from which the system was discovered; Cas9 is a CRISPR-associated endonuclease (an enzyme), the molecular scissors that are easily programmed to cut and edit, or correct, disease-associated DNA in a patients cell. The location at which the Cas9 molecular scissors cut the DNA to be edited is specified by guide RNA, which is comprised of a crRNA component and a tracrRNA component, either individually or combined together as a single guide RNA (sgRNA). For example, a guide RNA can direct the molecular scissors to cut the DNA at the exact site of the mutation present in the genome of patients with a particular genetic disease. Once the molecular scissors make a cut in the DNA, additional cellular mechanisms and exogenously added DNA will use the cells own machinery and other elements to specifically repair the cut DNA.

There are more than 10,000 known single-gene (or monogenic) diseases, occurring in about 1 out of every 100 births1. Scientists and clinicians are now conducting pioneering research using CRISPR/Cas9 to address both recessive and dominant genetic defects, opening up the potential of gene editing to provide novel transformative gene-based medicines for patients with a large number of both rare and common diseases.

Dr. Emmanuelle Charpentier, one of CRISPR Therapeutics scientific founders, co-invented the CRISPR/Cas9 technology.

The clustered repeats of CRISPR were discovered in 1987 in bacteria2, but their function was unknown. In 2000, these clustered repeat elements were found to be relatively common in bacteria3 hinting to an important role of these elements. The clustered repeats were given the name CRISPR in 2002 and multiple CRISPR-associated (Cas) genes were discovered adjacent to the repeat elements in that same year4.

The function of the CRISPR-Cas system in bacteria as an immune defense mechanism was hypothesized by Mojica in 20055 and experimentally validated at the food ingredient company, Danisco, in 20076.

In 2011, Dr. Charpentiers lab discovered an essential component of the CRISPR-Cas system, tracrRNA, in bacteria7. The following year she and colleagues described how the Cas9 endonuclease works together with crRNA and tracrRNA to form functional molecular scissors to cut at a specific DNA sequence in the genome8. In this same publication the authors also described how to modify, or re-program, the system to direct the molecular scissors to cut at essentially any DNA sequence; how to modify the RNA components into a single guide RNA, simplifying the system into only 2 components; and how to modify the Cas9 molecular scissors to make nicks in the DNA by only cutting one of the two DNA strands. These foundational discoveries enabled transformative gene editing in a wide range of cells, tissues and species, including for the potential benefit of patients suffering from serious genetic diseases.

CRISPR/Cas9 is an easy, effective technology for gene editing that has enabled a wide range of new studies and transformed many areas of research. Thousands of academic laboratories across the world are carrying out research using the technology. Rapid adoption of CRISPR/Cas9 by the broader academic community and the collective efforts of their research are in turn driving tremendous progress in the field.

We have licensed the foundational CRISPR/Cas9 patent estate for human therapeutic use from our scientific founder, Dr. Emmanuelle Charpentier. This IP is directed broadly to CRISPR/Cas9 genome editing and includes many different applications of the technology. We have filed additional IP and will continue to do so in support of our mission to bring transformative gene-based medicines to patients with serious diseases.

In 2011, Dr. Charpentiers lab discovered an essential component of the CRISPR-Cas system, tracrRNA, in bacteria7. The following year she and colleagues described how the Cas9 endonuclease works together with crRNA and tracrRNA to form functional molecular scissors to cut at a specific DNA sequence in the genome8. In this same publication the authors also described how to modify, or re-program, the system to direct the molecular scissors to cut at essentially any DNA sequence; how to modify the RNA components into a single guide RNA, simplifying the system into only 2 components; and how to modify the Cas9 molecular scissors to make nicks in the DNA by only cutting one of the two DNA strands. These foundational discoveries enabled transformative gene editing in a wide range of cells, tissues and species, including for the potential benefit of patients suffering from serious genetic diseases.

CRISPR/Cas9 is an easy, effective technology for gene editing that has enabled a wide range of new studies and transformed many areas of research. Thousands of academic laboratories across the world are carrying out research using the technology. Rapid adoption of CRISPR/Cas9 by the broader academic community and the collective efforts of their research are in turn driving tremendous progress in the field.

We have licensed the foundational CRISPR/Cas9 patent estate for human therapeutic use from our scientific founder, Dr. Emmanuelle Charpentier. This IP is directed broadly to CRISPR/Cas9 genome editing and includes many different applications of the technology. We have filed additional IP and will continue to do so in support of our mission to bring transformative gene-based medicines to patients with serious diseases.

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Our Programs – CRISPR

Here’s Why CRISPR Stocks Have Gained as Much as 169% in 2018 …

What happened

Shares of the three companies pioneering medical applications of CRISPR gene-editing tools have soared higher through the first half of 2018. That’s because, after years of only being able to discuss the possibilities of the technology, investors will soon be able to watch it (hopefully) progress through regulated clinical trials.

According to data from S&P Global Market Intelligence, CRISPR Therapeuticstops the trio with year-to-date gains of 169% and a market cap of nearly $3 billion. Intellia Therapeuticsis next with a 63% rise and a market cap of $1.3 billion. Editas Medicine, which has managed a 25% leap since the beginning of the year, is valued at $1.8 billion. It entered January as the most valuable of the three.

Image source: Getty Images.

All three companies are about to investigate their unique CRISPR tools in the clinic for the first time, and their respective stock performances thus far this year correlate with how close each is to initiating clinical trials.

CRISPR Therapeutics is the furthest along, looking to begin clinical trials for its lead drug candidate, CTX001, as a treatment for blood diseases such as sickle cell by the end of this year. While it was placed on a clinical hold by the U.S. Food and Drug Administration at the end of May, the company and its partner Vertex will proceed with a phase 1/2 trial in Europe as planned. Not wanting to rest on its lead, the company is looking to file its second investigational new drug (IND) application by the end of 2018.

Meanwhile, Editas Medicine told investors it would file an IND for its lead drug candidate in mid-2018, so investors should expect that news any day now. The company will first take aim at LCA10, a rare eye disease.

Intellia Therapeutics is furthest behind, as it doesn’t expect to file an IND until the end of 2019. That could work out in the company’s favor in the long run, however, as it’s working on a novel delivery system (one of the biggest question marks for all three companies) to increase the efficacy and safety of its therapeutics, the first of which will be evaluated to treat a rare metabolic disease called transthyretin amyloidosis.

Company

End Q1 2018 Cash Balance

IND Filing Guidance

CRISPR Therapeutics (NASDAQ:CRSP)

$342 million

Initiating first clinical trial by end of 2018, second IND by end of 2018

Editas Medicine (NASDAQ:EDIT)

$359 million

Mid-2018

Intellia Therapeutics (NASDAQ:NTLA)

$328 million

End of 2019

Data source: Company disclosures.

All three stocks have largely brushed off concerns raised in June that CRISPR tools could potentially set off existing and potentially cancerous mutations within cells. While none of the lead drug candidates would be affected by the approaches being used, all three pipelines will have to navigate that obstacle eventually.

Investors are betting that gene editing will become a game changer in medicine — and they might be right. However, it’s important to remember that CRISPR tools are still in their infancy in the clinic. There are still questions about optimal delivery of the therapeutic payload into human cells in a patient, the best cutting enzyme, and the triggering of DNA repair mechanisms being relied on to finish the genetic surgery procedure. Each has implications for the efficacy and safety of the technology.

Considering these questions (and more) will find their first answers in clinical trials that have yet to begin, and the fact these companies are valued at up to $3 billion, investors should understand the high level of risk involved with CRISPR stocks at this point in development. There could be a long way to go before reality matches the hype.

Maxx Chatsko has no position in any of the stocks mentioned. The Motley Fool owns shares of CRISPR Therapeutics. The Motley Fool recommends Editas Medicine. The Motley Fool has a disclosure policy.

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Here’s Why CRISPR Stocks Have Gained as Much as 169% in 2018 …

CRISPR News – GenScript

CRISPR Plasmids

DNA plasmids for single guide RNA and/or Cas9 expression

Validated knock-out cell line service using CRISPR technology.

Genome-wide or pathway-specific CRISPR knock-out or activation libraries for screening experiments.

Validated knock-out and knock-in mutagenesis in bacteria and yeast.

CRISPR News

July 6, 2017

For the first time, researchers have been able to detect and characterize the mechanism of action by which the CRISPR complex binds and cleaves DNA using electron microscopy. Scientists at Harvard and Cornell have recently created near-atomic level resolution images of the CRISPR/Cas3 complex, a common CRISPR/Cas subtype, which provide structural data that can improve gene editing accuracy and efficiency.

To solve problems of specificity, we need to understand every step of CRISPR complex formation, states Maofu Liao, a co-author of the study and assistant professor at Harvard. 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.

This discovery uncovers a number of novel, overlapping mechanisms which prevent off-target site cleavage. In the CRISPR/Cas3 system, the assembled CRISPR complex first searches for a corresponding protospacer adjacent motif (PAM) sequence, which indicates a possible target site. Researchers discovered that as the CRISPR complex detects the PAM, it also bends DNA at a sharp angle, forcing a small portion to unwind. This allows an 11-nucleotide stretch of the CRISPR guide RNA to bind onto the target DNA, creating a seed bubble. The seed bubble acts as a fail-safe mechanism to check whether target DNA matches the guide RNA. If correctly matched, the bubble is enlarged and the remainder of the guide RNA binds onto the DNA forming an R-loop structure. Only once the full R-loop structure is formed does the Cas enzyme bind and cut the DNA in the non-target DNA strand. This study is the first to reveal the full sequence of events from seed bubble formation to R-loop formation.

Looking for an affordable and easy way to model disease in vivo?Interested in performing a genome-wide screen?Use CRISPR RNA/Cas9 Reagents or CRISPR Plasmids for high efficiency, customizable gene editing.

Xiao, Y. et al. Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System.Cell170, 48-60.e11 (2017).

June 28, 2017

Today, nearly 1 out of every 68 children born is diagnosed with autism spectrum disorder (ASD). Globally the disease is estimated to affect over 25 million people. And prevalence is expected to rise with ASD identifications doubling in the last decade.

ASD describes a variety of neurodevelopmental disorders which are often characterized by deficits in social communication and interaction, and restricted and repetitive behavior. While no specific causes for ASD have yet been found, a number of genetic and environmental risk factors have been identified. Most recently, a new study from Columbia Universitys Mailman School of Public Health, has discovered that prenatal fever increases autism risk by up to 40%.

Researchers monitored over 95,000 children born between 1999 and 2009. Of that population, 15,701 children were identified to have mothers reporting fever conditions during pregnancy. These children were found to have increased risk of ASD by 34%. Risk increase was highest, at 40%, when fever was reported during the second trimester. And ASD risk was increased by over 300% for the children of women reporting three or more fevers after the twelfth week of pregnancy.

Our results suggest a role for gestational maternal infection and innate immune responses to infection in the onset of at least some cases of autism spectrum disorder, states lead researcher, Associate Professor Mady Hornig. Additional studies are ongoing to determine the role of specific infectious agents in the development of ASD.

Hornig, M. et al. Prenatal fever and autism risk. Molecular Psychiatry (2017). doi:10.1038/mp.2017.119

June 22, 2017

Each year almost 200,000 people in the U.S. require emergency medical care for a serious allergic reaction. This number is expected to grow as food allergy incidence has increased by 50% in the last decade.

Allergies are caused from the hypersensitivity of the immune system to allergens in the environment. Recognition of these allergens triggers a T-cell-mediated immune response, producing cytokines which induce chronic inflammation and mucous hypersecretion.

In a recent study at the University of Queensland, Professor Ray Steptoe has been able to de-sensitize T-cells using a novel gene therapy treatment. Dr. Steptoes research team has engineered bone marrow stem cells to express transgenic allergen proteins. This effectively tricks the body into identifying the transgenic allergen as a self-antigen originating from within the body, leading to negative selection of any reacting T-cells. After treatment, the immune system is memory wiped alleviating airway inflammation and hyperreactivity.

Dr. Steptoe states that the eventual goal will be to devise a single-dose injectable therapeutic, which could replace the various short-term treatments that focus on alleviating allergy symptoms. Potential patents would be those individuals who are suffering from potentially lethal allergies or severe asthma.

AL-Kouba, J. et al. Allergen-encoding bone marrow transfer inactivates allergic T cell responses, alleviating airway inflammation. JCI Insight2, (2017).

June 15, 2017

Each year nearly 2 million people in the USA are infected by antibiotic-resistant bacteria. With antibiotic resistance on the rise, scientists have begun to turn to alternative antimicrobial treatments.

At the University of Wisconsin-Madison, scientists are developing a new probiotic “CRISPR pill” that is effective even against drug-resistant threats. Researchers from the lab of Jan-Peter Van Pijkeren have engineered bacteriophages expressing customized CRISPR guide RNA sequences. These CRISPR RNAs hijack the innate bacterial CRISPR immunity system present in infectious bacteria, causing them to self-destruct by creating lethal breaks in their own DNA. The bacteriophages are packaged in pill form in a mixture of probiotics, allowing them to survive the digestive tract until reaching the intestines.

By utilizing the innate immune system present in bacteria, the CRISPR pill bypasses the main mechanisms of antibiotic resistance. In addition, CRISPR pills may be superior to traditional antibiotics, because of their narrow targeting spectrum which can target specific bacterial species and strains. In contrast, broad-spectrum antibiotics kill off both “good” and “bad” bacteria. And overuse of traditional antibiotics has lead to the rising epidemic of antibiotic-resistant infections.

CRISPR and the CRISPR Associated system (Cas) is a powerful gene editing technology. Originally identified and characterized in bacteria, endogenous CRISPR systems act as an RNA-based defense mechanism against invading phage DNA.

CRISPR was adapted for genome editing in 2013 and has since been exploited for its ability to generate targeted double-stranded DNA breaks, which has revolutionized molecular biology protocols.1,2

This guide covers the basics of CRISPR experimental design and will prepare you to embark upon your own genome editing experiment.

Endogenous CRISPR systems fall into three categories type I, II and II. You can read more about these types in Makarova et al.3 Commercial CRISPR genome editing tools are adapted and simplified from endogenous type II systems and have the following components:

When gRNA and Cas9 are expressed together in a cell, a gRNA:Cas9 complex is recruited to the target DNA sequence, which is located immediately upstream of a motif called a protospacer adjacent motif (PAM).4 The PAM motif targeted by most commercial Cas9 enzymes is NGG (any nucleotide followed by two guanines).

Binding of the gRNA to target DNA occurs via complementary base-pairing between the genomic target sequence and the 20-nucleotide spacer on the gRNA. The Cas9 in the gRNA:Cas9 complex then cuts the genomic DNA, inducing a double-stranded break after the PAM sequence. Crucially, Cas9 cannot digest DNA unless bound to the gRNA, thus providing specificity to the system.

The editing process is completed by repairing the break using the endogenous Non-Homologous End Joining (NHEJ) pathway. While this DNA repair system is the most efficient repair pathway it is error prone, sometimes permitting small insertions or deletions, which can result in frameshifts and reduced protein production. An alternative option is to exploit the endogenous Homology Directed Repair (HDR) system by providing the HR template, as mentioned above. This is used when introducing targeted mutations.

Once you have designed and cloned the gRNA and HR templates, you cotransfect the Cas9 plasmid and your gRNA and HR donor vectors into the chosen cell line. Lipid transfection, electroporation or microinjection are all suitable transfection methods.

Optimizing recombination levels may take some trial and error. Choose a robust cell line (e.g., HEK) for troubleshooting. Once your experiment is up and running, you can move onto more expensive and less robust cell lines, if necessary.

Bear in mind that immortalized cell lines are not only cheaper than primary cells, but their recombination pathways are often less stringent. Therefore, you should ideally achieve a high level of recombination efficiency before moving to primary lines.

In the end, efficiency of your CRISPR experiment is part plan, part luck. The interaction between the system components and Cas9 is still not well understood. Fortunately, there are a few ways you can increase your odds:

If you have done everything right but are still experiencing low efficiency, then it is time to experiment. You may have better luck using sense and anti-sense templates. Others have reported better efficiency with asymmetrical arms.5 Be prepared to design a few setups the efficiencies of overlapping designs can vary widely and be ready to experiment to find the best design for your experiments. For more information about CRISPR, check out this free CRISPR handbook.

How to Optimize Your Lentiviral ExperimentsMarch 7, 2017

There are several aspects to consider if you want to optimize your lentiviral experiments. Check out these helpful tips before you embark on the incessant optimization experiments. Here are three common factors that may be affecting your viral titers:

The 293 cell line was derived from embryonic kidney cells and is commonly used for lentivirus production. HEK 293 cells are sensitive to passage number and should be replaced regularly; cells must be healthy and actively dividing. HEK 293Ts, which contain the SV40 T antigen, are more resilient and can be used for six months or longer with no significant reduction in virus titer.

Clumpy cell cultures with lots of senescent cells will not produce good titers. It is worth doing a test transfection on your cells before you try using them for virus production. If your transfection efficiency is low, then there is no point continuing with virus production, you will need to setup a new cell stock.

Remember:

There are a number different commercial and non-commercial transfection reagents available. Chemical reagents such as calcium phosphate and polyethylenimine (PEI) work effectively and are very budget-friendly. For transfection with PEI or a commercial lipid-based reagent, your 293 cells should be 90-95% confluent at the time of transfection.

Remember:

A lentivirus expression typically contains a transfer plasmid and a packaging plasmid. Plasmids are recommended to be cultivated from bacterial strains such as Stbl3, which have reduced frequencies of homologous recombination. Plasmids containing a Gateway cassette with the ccdBgene will require a compatible ccdB viable strain. Make sure after plasmid purification that plasmid quality is high and of a reasonable concentration (over 100ng/L).

When considering packaging plasmids, make sure not to confuse the second and third generation variants. Second generation transfer plasmids require the presence of HIV-1 Tat protein. Third generation transfer plasmids have eliminated Tat from the packaging system, but are still backwards compatible with second generation transfer plasmids.

Transfer plasmids are the most important factor in virus production, and can result in transduction efficiency differences of 10-50x. The length of sequence between the long terminal repeats can directly influence viral titer, and particle yield decreases as sequence length increases. Including multiple promoters within the transfer plasmid can also result in promoter interference, where the promoters adversely affect expression of the others, resulting in lower viral titer.

Fluorescence microscopy and flow cytometry are two methods that can be used to measure transduction efficiency. Remember though that protein expression can influence fluorescence, and weakly expressed proteins can lead to underestimated viral titer. Therefore, promoter should be a key consideration if transduction is assessed using these methods.

Remember:

Researchers uncover novel fat metabolism pathwayFebruary 20, 2017

A new study in Nature Communications discovered a neuropeptide hormone, FLP-7, which is capable of stimulating fat metabolism. This fat metabolism pathway is the first to be discovered which can activate fat burning without affecting food intake or movement.

FLP-7 had previously been identified over 80 years ago as a muscle stimulant, but no links to fat metabolism was ever established. Flashing forward to 2017, scientists at the Scripps Institute identified FLP-7 during a genetic screen as a suppressor of fat loss in C. elegans roundworms. By fluorescently tagging the hormone, researchers were able to track FLP-7 secretions from the brain in response to elevated serotonin levels. This FLP-7 could then be tracked through the circulatory system to the gut, where it activates fat burning.

Modifying serotonin levels results in serious side effects, broadly impacting food intake, movement and reproduction. Amazingly, adjusting levels of FLP-7 does not result in any obvious changes, worms continue to function normally, while just burning more fat. Researchers hope their finding spur additional research into the weight loss effects of FLP-7 mammalian homologs.

Palamiuc et al. A tachykinin-like neuroendocrine signalling axis couples central serotonin action and nutrient sensing with peripheral lipid metabolism.Nature Communications, 2017; 8: 14237 DOI:10.1038/ncomms14237

How does sugar effect health and aging?February 6, 2016

A new study in Cell Reports has linked sugar intake to lifespan. This process occurs through a newly discovered pathway in which sugar permanently reprograms gene expression, maintaining an altered state even if your diet has improved.

Using fruit flies as a model organism, researchers compared life span of flies consuming a 5% and 40% sugar diet. Any flies raised on the 40% sugar diet averaged a 7% shorter life span. Researchers discovered that excess sugar promotes insulin-signaling pathways which lead to the inactivation of FOXO. FOXO is a transcription factor which alters the expression levels of chromatin modifiers. Crucially, the reprogramming of these transcription networks could not be reversed upon a switch to the lower sugar diet. The study improves our understanding of how changes in diet and gene expression can affect the speed of aging.

Dobson et al.Nutritional Programming of Lifespan by FOXO Inhibition on Sugar-Rich Diets.Cell Reports, 2017; 18 (2): 299 DOI:10.1016/j.celrep.2016.12.029

How does vitamin C fight cancer?January 30, 2016

Vitamin C’s efficacy in cancer prevention has been hotly debated. But, new research has shown that direct, intravenous delivery of vitamin C can more than double survival rates of pancreatic cancer. By avoiding the digestive tract, scientists have been able to increase vitamin C levels in the blood by 100-500 times. And at these extreme concentrations, vitamin C is able to selectively kill cancer cells.

As Vitamin C breaks down through oxidation hydrogen peroxide is generated. Hydrogen peroxide is capable of forming free radicals which can be damaging to DNA. Interestingly, researchers discovered that tumor cells are much less efficient at removing hydrogen peroxide. Tumor cells were found to be deficient in catalase activity, the primary means of detoxifying hydrogen peroxide. On average, tumor cells were able to only metabolize hydrogen peroxide at half the rate of normal cells. And the addition of vitamin C to these tumor cells resulted in ATP depletion, DNA lesions, and cell growth reduced by more than 50%. Clinical trials pairing both high-dosage, intravenous vitamin C and chemotherapy are now underway and in Phase 2 testing.

Doskey et al.Tumor cells have decreased ability to metabolize H2O2: Implications for pharmacological ascorbate in cancer therapy.Redox Biology, 2016; 10: 274 DOI:10.1016/j.redox.2016.10.010

Postdoc vs Industry? Comparing the ReturnsJanuary 23, 2016

A new study published in Nature Biotechnology has found that biomedical postdoctoral opportunities provide diminishing returns in the labor market. Upon graduating, many aspiring postdocs will hope to land a career in tenure track academia, but only 20% of scientists ever manage to attain such a position. The impact from such a decision can be staggeringly high.

Taking a postdoctoral position can cost up to three years worth of lost salary over the first 15 years of a scientist’s career. In 2013, the median starting salary for postdocs in academia was $44,724, compared to $73,662 for postdocs in industry. The academic experience accrued does not improve salary potential either, as scientists switching to industry average salaries equivalent to new, entry-level employees. Overall, academics will average $12,002 lower than though who leave the field.

But current graduates should stay informed of their options, and measure the chance of landing a tenure-track position against the potential financial ramifications.

Kahn and Ginther, 2017. The impact of postdoctoral training on early careers in biomedicine.Nature Biotechnology 2017; 35 (1): 90 DOI: 10.1038/nbt.3766

New mechanism for cancer metastasis discoveredJanuary 16, 2016

Cell biologists at Mount Sinai have identified a combination of changes to oncogenic and tumor suppressor genes which allow for early dissemination of cancer cells before a primary tumor forms. These cells first migrate before attaining additional mutations which lead to uncontrolled cell proliferation. But, a majority of the disseminated cancer cells will remain quiescent. And due to their non-proliferative nature, these cells form a reservoir resistant to chemotherapy and other conventional cancer treatments.

This early dissemination is a result of the activation of the p38 and HER2 pathways. Pathway activation leads to a cell type transition from epithelial to mesenchymal cells, which promotes cell migration. This process occurs normally in development during the formation of mammary and pancreatic ducts. But, the over-activation of both pathways during oncogenesis instead allows cancer cells to migrate into the bloodstream and metastasize instead.

Harper et al., 2016. Mechanism of early dissemination and metastasis in Her2 mammary cancer.Nature DOI: 10.1038/nature20609

Hosseimi et al., 2016. Early dissemination seeds metastasis in breast cancer.Nature DOI: 10.1038/nature20785

Mechanism behind Zika microcephaly revealedJanuary 9, 2016

Zika infection during fetal development has been associated with microcephaly and other birth defects. New analysis of Zika viral proteins has identified the mechanism by which the virus damages brain cells.

Cell biologists at Boston Children’s Hospital have identified the viral enzyme NS3 as the main culprit in Zika-associated neural degeneration. NS3 functions in the cleavage and processing of other Zika viral proteins. But, NS3 also is capable of interacting with and damaging centrioles, which are required for spindle assembly and cell proliferation. These findings are corroborated by genetic studies which have identified an association between centriole stability and microcephaly.

NS3 may prove to be an important drug target for against Zika-related illnesses moving forward. NS3 inhibitors commonly used to protect against dengue, a related virus, were shown to be successful in preventing NS3 binding to centrioles.

Saey, Tina.Cell biologists learn how Zika kills brain cells, devise schemes to stop it ScienceNews ScienceNews, 13 Dec 2016

How Did Mammary Glands EvolveJanuary 2, 2016

Researchers have recently discovered a new network of genes and enhancers responsible for coordinating the formation of mammary glands. Interestingly, this regulatory network functions by hijacking existing limb development processes.

Hox genes are a subset of homeotic genes which control embryonic development and patterning. Hox genes have been shown to regulate limb, head, thoracic, abdomen, and mammary gland formation.

To better understand how some of these body structures evolved, geneticists at the University of Geneva and the Swiss Federal Institute of Technology in Lusanne screened for Hox gene activating sequences in the genome. One of the enhancer sequences identified, MBRE, was found to be responsible for activating Hoxd9, a gene required for mammary gland development. Interestingly, MBRE is conserved only in placental and marsupial mammals, and missing in egg laying mammals, such as the platypus.

But MBRE regulatory network is found to function in all tissues, indicating that the network was present prior to mammary gland evolution. The researchers propose that Hoxd gene regulation in mammary glands evolved by co-opting existing regulatory networks in other body structures.

CRISPR Gene Editing Tested in Humans for the First TimeDecember 12, 2016

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CRISPR News – GenScript

DIY CRISPR Kit – The ODIN

There is currently ~1 week time till shipment.

Due to the overwhelming number of emails we will not respond to emails asking when your item will be shipped. Understand we are doing our best to get it to you.

Comes with an example experiment that teaches you many molecular biology and gene engineering techniques.

Want to really know what this whole CRISPR thing is about? Why it could revolutionize genetic engineering? This kit includes everything you need to make precision genome edits in bacteria at home including Cas9, tracrRNA, crRNA and Template DNA template for an example experiment.

Includes example experiment to make a genome mutation(K43T) to the rpsL gene changing the 43rd amino acid, a Lysine(K) to a Threonine(T) thereby allowing the bacteria to survive on Strep media which would normal prevent its growth.

Kit contains enough materials for around 5 experiments or more

Protocol For Experiment

You can find the plasmid DNA sequences

Cas9 Plasmid

gRNA Plasmid

Some items in this kit need to be stored in a fridge and a freezer upon you receiving them.

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DIY CRISPR Kit – The ODIN

A Crispr Conundrum: How Cells Fend Off Gene Editing – The …

Human cells resist gene editing by turning on defenses against cancer, ceasing reproduction and sometimes dying, two teams of scientists have found.

The findings, reported in the journal Nature Medicine, at first appeared to cast doubt on the viability of the most widely used form of gene editing, known as Crispr-Cas9 or simply Crispr, sending the stocks of some biotech companies into decline on Monday.

Crispr Therapeutics fell by 13 percent shortly after the scientists announcement. Intellia Therapeutics dipped, too, as did Editas Medicine. All three are developing medical treatments based on Crispr.

But the scientists who published the research say that Crispr remains a promising technology, if a bit more difficult than had been known.

The reactions have been exaggerated, said Jussi Taipale, a biochemist at the University of Cambridge and an author of one of two papers published Monday. The findings underscore the need for more research into the safety of Crispr, he said, but they dont spell its doom.

This is not something that should stop research on Crispr therapies, he said. I think its almost the other way we should put more effort into such things.

Crispr has stirred strong feelings ever since it came to light as a gene-editing technology five years ago. Already, its a mainstay in the scientific tool kit.

The possibilities have led to speculations about altering the human race and bringing extinct species back to life. Crisprs pioneers have already won a slew of prizes, and titanic battles over patent rights to the technology have begun.

To edit genes with Crispr, scientists craft molecules that enter the nucleus of a cell. They zero in on a particular stretch of DNA and slice it out.

The cell then repairs the two loose ends. If scientists add another piece of DNA, the cell may stitch it into the place where the excised gene once sat.

Recently, Dr. Taipale and his colleagues set out to study cancer. They used Crispr to cut out genes from cancer cells to see which were essential to cancers aggressive growth.

For comparison, they also tried to remove genes from ordinary cells in this case, a line of cells that originally came from a human retina. But while it was easy to cut genes from the cancer cells, the scientists did not succeed with the retinal cells.

Such failure isnt unusual in the world of gene editing. But Dr. Taipale and his colleagues decided to spend some time to figure out why exactly they were failing.

They soon discovered that one gene, p53, was largely responsible for preventing Crispr from working.

p53 normally protects against cancer by preventing mutations from accumulating in cellular DNA. Mutations may arise when a cell tries to fix a break in its DNA strand. The process isnt perfect, and the repair may be faulty, resulting in a mutation.

When cells sense that the strand has broken, the p53 gene may swing into action. It can stop a cell from making a new copy of its genes. Then the cell may simply stop multiplying, or it may die. This helps protect the body against cancer.

If a cell gets a mutation in the p53 gene itself, however, the cell loses the ability to police itself for faulty DNA. Its no coincidence that many cancer cells carry disabled p53 genes.

Dr. Taipale and his colleagues engineered retinal cells to stop using p53 genes. Just as they had predicted, Crispr now worked much more effectively in these cells.

A team of scientists at the Novartis Institutes for Biomedical Research in Cambridge, Mass., got similar results with a different kind of cells, detailed in a paper also published Monday.

They set out to develop new versions of Crispr to edit the DNA in stem cells. They planned to turn the stem cells into neurons, enabling them to study brain diseases in Petri dishes.

Someday, they hope, it may become possible to use Crispr to create cell lines that can be implanted in the body to treat diseases.

When the Novartis team turned Crispr on stem cells, however, most of them died. The scientists found signs that Crispr had caused p53 to switch on, so they shut down the p53 gene in the stem cells.

Now many of the stem cells survived having their DNA edited.

The authors of both studies say their results raise some concerns about using Crispr to treat human disease.

For one thing, the anticancer defenses in human cells could make Crispr less efficient than researchers may have hoped.

One way to overcome this hurdle might be to put a temporary brake on p53. But then extra mutations may sneak into our DNA, perhaps leading to cancer.

Another concern: Sometimes cells spontaneously acquire a mutation that disables the p53 gene. If scientists use Crispr on a mix of cells, the ones with disabled p53 cells are more likely to be successfully edited.

But without p53, these edited cells would also be more prone to gaining dangerous mutations.

One way to eliminate this risk might be to screen engineered cells for mutant p53 genes. But Steven A. McCarroll, a geneticist at Harvard University, warned that Crispr might select for other risky mutations.

These are important papers, since they remind everyone that genome editing isnt magic, said Jacob E. Corn, scientific director of the Innovative Genomics Institute in Berkeley, Calif.

Crispr doesnt simply rewrite DNA like a word processing program, Dr. Corn said. Instead, it breaks DNA and coaxes cells to put it back together. And some cells may not tolerate such changes.

While Dr. Corn said that rigorous tests for safety were essential, he doubted that the new studies pointed to a cancer risk from Crispr.

The particular kinds of cells that were studied in the two new papers may be unusually sensitive to gene editing. Dr. Corn said he and his colleagues have not found similar problems in their own research on bone marrow cells.

We have all been looking for the possibility of cancer, he said. I dont think that this is a warning for therapies.

We should definitely be cautious, said George Church, a geneticist at Harvard and a founding scientific adviser at Editas.

He suspected that p53s behavior would not translate into any real risk of cancer, but its a valid concern.

And those concerns may be moot in a few years. The problem with Crispr is that it breaks DNA strands. But Dr. Church and other researchers are now investigating ways of editing DNA without breaking it.

Were going to have a whole new generation of molecules that have nothing to do with Crispr, he said. The stock market isnt a reflection of the future.

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A Crispr Conundrum: How Cells Fend Off Gene Editing – The …

GeneHero CRISPR Products and Services | Genecopoeia

GeneCopoeia’s GeneHero CRISPR-Cas9 products and services provide a complete, powerful solution to your genome editing needs. Products and services include:

CRISPR Plasmids. Transfect cells with our CRISPR plasmids with Cas9 and sgRNA for human, mouse, and rat. Search our database of more than 45,000 human, mouse, and rat genes for genome editing using CRISPR.

CRISPR Lentivirus.Genome integration of CRISPR elements using lentivirus. Cas9 and/or sgRNA packed in purified lentiviral particles at 108 TU/ml, ready to infect all cell types.

CRISPR AAV.Episomal expression of CRISPR components with adeno-associated viralparticles carrying Cas9 and/or sgRNA, excellent for tissue and animal transduction.

Cas9 Stable Cell Lines.Premade Cas9-expressing stable cell lines are great for sgRNA library screening and other high-throughput CRISPR-Cas9 applications.

The clustered, regularly interspaced, short palindromic repeats (CRISPR) system is bacterial immunity mechanism for defense against invading viruses and transposons. This system has been adapted for highly efficient genome editing in many organisms. Compared with earlier genome editing technologies such as zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), CRISPR-Casmediated gene targeting has similar or greater efficiency. Genome editing has been used for numerous applications, as shown in Table 1.

Table 1. Applications for CRISPR-mediated genome editing.

In the type II CRISPR systems, the complex of a CRISPR RNA (crRNA) annealed to a trans-activating crRNA (tracrRNA) guides the Cas9 endonuclease to a specific genomic sequence, thereby generating double-strand breaks (DSBs) in target DNA. This system has been simplified by fusing crRNA and tracrRNA sequences to produce a synthetic, chimeric single-guided RNA (sgRNA). The sgRNA contains within it a 20 nucleotide DNA recognition sequence (Figure 1).

Figure 1. Mechanism of CRISPR-Cas9-sgRNA target recognition and cleavage.

When the Cas9-sgRNA complex encounters this target sequence in the genome followed by a 3 nucleotide NGG PAM (protospacer adjacent sequence) site, the complex binds to the DNA strand complementary to the target site. Next, the Cas9 nuclease creates a site-specific double-strand break (DSB) 3-4 nucleotides 5′ to the PAM. DSBs are repaired by either non-homologous end joining (NHEJ), which is error-prone, and can lead to frameshift mutations, or by homologous recombination (HR) in the presence of a repair template (Figure 2).

Figure 2.CRISPR-Cas9-based gene engineering. Left. DSBs created by sgRNA-guided Cas9-mediated cleavage are repaired by NHEJ. Right. DSBs created by sgRNA-guided Cas9 nuclease are repaired homologous recombination between sequences flanking the DSB site, thereby causing “knock in” of sequences on a donor DNA.

While the CRISPR system provides a highly efficient means for carrying out genome editing applications, it is prone to causing off-target indel mutations. Off-targeting is caused by the ability of the Cas9- sgRNA complex to bind to chromosomal DNA targets with one or more mismatches, or non-Watson-Crick complementary. The propensity of CRISPR for off-target modification is a significant concern for some researchers who want to avoid results that are potentially confounded by off-target modification, as well as for those who might be interested in developing CRISPR for gene therapy applications.

Several strategies have been employed to mitigate CRISPR’s propensity for off-target genome modification. One such strategy is to use double nickases to create DSBs. The Cas9 D10A mutant is able to cleave only one DNA strand, thereby creating a “nick”. When two sgRNAs that bind on opposite strands flanking the target are introduced, two Cas9 D10A nickase molecules together create a staggered-cut DSB, which is then repaired by either NHEJ or HR (Figure 3). The double nickase strategy has been shown to greatly reduce the frequency of off-target modification. However, double nickases are limited in utility by design constraints; the sgRNAs must be on opposite strands, in opposite orientation to one another, and display optimal activity when spaced from 3-20 nucleotides apart. In addition, the cleavage activity of double nickases tends to be lower than that of standard Cas9-sgRNA. Further, nickases can still cause some degree of off-target indel formation.

Figure 3. General scheme of Cas9 double-nickase strategy. From Ran, et al. (2013). Two additional strategies, the use of truncated (17-18 nucleotide) sgRNAs, as well as a Cas9-FokI fusion, also dramatically reduce CRISPR-mediated off-target genome modification. However, these methods suffer from even further reductions in on-target activity and/or more severe design constraints compared with the double nickase approach.

Recently, two groups demonstrated that engineering Cas9 variants carrying 3-4 amino acid changes virtually eliminates CRISPR off-target genome modification. These variants still retain high on-target activity, without the design constraints of previous approaches, providing a promising alternative for high-fidelity CRISPR-mediated genome editing.

Watch recorded webinar / Download slides Title: Genome Editing: How Do I Use CRISPR? Presented Wednesday, February 22, 2017

Genome Editing-the ability to make specific changes at targeted genomic sites-is fundamentally important to researchers in biology and medicine. CRISPR is a very widely-used method for modifying specific genome sites, and can be used for many applications, including gene knock out, transgene knock in, gene tagging, and correction of genetic defects. However, researchers are often unaware of some of the work required to identify their desired modification in their cell lines. In this webinar, we discuss what you need to do for CRISPR genome editing after you have obtained your reagents from GeneCopoeia, the so-called Downstream work.

Watch recorded webinar / Download slides Title: GeneCopoeia CRISPR Genome Editing Technology Presented Wednesday, January 25, 2017

The ability to make specific changes at targeted genomic sites in complex organisms is fundamentally important to researchers in biology and medicine. Researchers have developed and refined chimeric DNA endonucleases, such as CRISPR-Cas9, to stimulate double strand breaks at defined genomic loci, allowing the ability to insert, delete, and replace genetic information at will. These tools can also be used without nucleases to induce or repress gene transcription. In this webinar, we discuss CRISPR and other genome editing technologies and the applications they make possible, and provide information on GeneCopoeia’s powerful suite of genome editing products and services.

Watch recorded webinar / Download slides Title: Applications For CRISPR-Cas9 Stable Cell Lines Presented Wednesday, March 22, 2017

The CRISPR-Cas9 system has become greatly popular for genome editing in recent years, due to its ease-of-design, efficiency, specificity, and relatively low cost. In mammalian cell culture systems, most genome editing is achieved using transient transfection or lentiviral transduction, which works well for routine, low-throughput applications. However, for other applications, it would be beneficial to have a system in which one component, namely the CRISPR-Cas9 nuclease, was stably integrated into the genome. In this webinar, we introduce GeneCopoeias suite of Cas9 stable cell lines, and discuss the great utility that these cell lines provide for genome editing applications.

Watch recorded webinar / Download slides Title: Safe Harbor Transgenesis in Human & Mouse Genome Editing Presented Wednesday, April 19, 2017

Insertion of transgenes in mammalian chromosomes is an important approach for biomedical research and targeted gene therapy. Traditional lentiviral-mediated transgenesis is effective and straightforward, but its random integration can often be unstable and harm cells. “Safe Harbor” sites in human and mouse chromosomes have been employed recently as an alternative to random, viral-mediated integration because they support consistent, stable expression, and are not known to hamper cell fitness or growth. In this webinar, we will discuss the merits of Safe harbor transgenesis approaches, and how GeneCopoeia’s CRISPR tools for Safe Harbor knock-in can greatly benefit your research.

Watch recorded webinar / Download slides Title: GeneCopoeia CRISPR sgRNA Libraries For Functional Genomics Presented Wednesday, April 29, 2015

Biomedical researchers are enjoying a Renaissance in functional genomics, which aims to use a wealth of DNA sequence informationmost notably, the complete sequence of the human genometo determine the natural roles of the genes encoded by the genome. As a result, biochemical networks and pathways will be better understood, with the hope of leading to improved disease treatments. Researchers are turning increasingly to CRISPR (clustered, regularly interspaced, short palindromic repeats) for functional genomics studies. Several groups recently adapted CRISPR for high-throughput knockout applications, by developing large-scale CRISPR sgRNA libraries. GeneCopoeia recently launched a number of smaller, pathway- and gene group-focused CRISPR sgRNA libraries, which offer several key advantages over the whole-genome libraries. In this 40 minute webinar, we discuss the merits and applications for CRISPR sgRNA libraries, how to use CRISPR sgRNA libraries, the advantages of using small, pathway- and gene group-focused libraries, and how GeneCopoeia can help you with your high-throughput CRISPR knockout studies.

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Answer:If you are doing simple gene knockouts in humans or mice, you can order CRISPR sgRNAs on our website. All you need to do is go to the , search for your gene, and then choose the appropriate clones that will work for your system. These CRISPR sgRNAs are designed by default to knock out all possible known and predicted transcript variants of your gene, and are targeted early in the coding regions. You can also order donor clones for these knockouts from the search results page. If you are doing a different application, such as introducing a point mutation, then you will need to and, after determining what you need, we will send you a custom quote.

Answer:For sgRNA clones (including both all-in-one Cas9/sgRNA clones and sgRNA-only clones, the default delivery format is bacterial stock. You have the option of ordering purified DNA for these clones for an additional charge. For HDR donor clones, the default delivery format is purified DNA.

Answer:The turnaround time for sgRNA clones (including both all-in-one Cas9/sgRNA clones and sgRNA-only clones) is 2-3 weeks. The turnaround time for HDR donor clones depends greatly on the nature of the modification that the clone is being used for. For HDR donor clones used for simple knockout, the turnaround time is 2-4 weeks. Other HDR donor clones, such as those used for fusion tagging or mutagenesis, can take 6-8 weeks, but can also take longer.

Answer:Yes. We sequence the inserts of each CRISPR sgRNA clone, and provide you with datasheets that show the full sequence of each clone (including HDR donor clones), a map, restriction enzyme digestions sites, and suggested sequencing primers. To obtain these datasheets, you just need to visit our on our website. You will need an account on our website, your catalog number(s), and your sales order number.

Answer:In the presence of drug, the only way for cells to survive is to integrate the plasmid into the chromosome, so it is possible to get drug-resistant clones that were only transfected with the donor plasmid. However, such integration is random. CRISPR increases donor targeting frequency by several orders of magnitude.

Answer:Our genome editing products can be used for virtually all species. Our standard plasmids for CRISPR are designed for work in mammalian cells. In addition, these plasmids can be used as templates for T7 promoter-driven in vitro transcription, for introduction into mice, zebrafish, Drosophila, and many other model organisms. Further, we can generate custom constructs that can be used in a wide variety of organisms.

Answer:Yes. The donor must be present when the DSB is formed in order to be used as a repair template. Otherwise, the cell must use non-homologous end joining (NHEJ) in order to repair the DSB, because unrepaired DSBs are lethal.

Answer:Our CRISPR plasmids typically do not integrate into the host genome in transfection experiments. However, after clonal selection for edited cells, we recommend screening clones for those which have lost the nuclease plasmids. This can be done by testing clones to see if they have become sensitive to the antibiotic of the resistance gene on the plasmid, or if they no longer express the plasmid’s fluorescent marker (where applicable). Our lentiviral clones are expected to integrate randomly into chromosomes.

1. If you are making an insertion or deletion, the easiest way to screen your cells is by PCR using primers flanking the modified site, provided that the insertion or deletion is large enough to detect by standard agarose gel electrophoresis.

2. For very small insertions or deletions, you can screen your clones using GeneCopoeia’s IndelCheck T7 endonuclease I assay, which is a method that detects mutations by cleaving double stranded DNA containing a mismatch. You can also screen using Sanger sequencing of PCR products.

3. If you are introducing a point mutation, then you can use either real-time PCR or Sanger sequencing to detect the modification.

4. If the modification you are introducing creates or destroys a restriction enzyme site, then enzyme cleavage of PCR products can be used to distinguish between modified and unmodified alleles.

5. Finally, either Sanger sequencing of PCR products or Next Generation sequencing of whole genomes can be used to screen for modifications. Regardless of which screening method you choose, it is also important that you are able to determine whether only a portion or all of the alleles have been modified.

In order to reduce the amount of time and effort required to identify edited clones, GeneCopoeia recommends our donor plasmid design and construction service. We will construct a donor plasmid that contains a defined modification, flanked by a selectable marker such as puromycin resistance, and homologous arms from your target region. The donor may or may not also include a fluorescent reporter such as GFP. The markers can be flanked by loxP sites, to permit Cre-mediated removal, if desired. Use of a GeneCopoeia-designed donor plasmid allows you to select for edited clones and reduces the number of clones required for screening. You can also purchase our donor cloning vectors for do-it-yourself donor clone construction.

Answer:Yes. Even though frameshifts are not possible with miRNAs and other noncoding RNAs, an indel occurring in a critical region, such as the mature sequence of a miRNA, should be enough to abolish its function.

Answer:The vector backbones of our CRISPR sgRNAs are designed to not replicate in the host. These plasmids, which are transiently transfected, will typically be lost after several rounds of cell division and will not further affect the host cell. After transfection, cells are plated at low density to promote the formation of single colonies. These colonies should be screened to ensure that they have lost the plasmid(s). This can be done by testing clones to see if they have become sensitive to the antibiotic of the resistance gene on the plasmid, or if they no longer express the plasmid’s fluorescent marker (where applicable). However, even if the TALEN or CRISPR plasmid integrates, it can no longer cut the site after it is edited, because NHEJ destroys the TALEN or sgRNA recognition site. To be completely assured that the transfection is transient, we recommend delivering RNA instead of plasmid DNA. If you are using HDR, we recommend engineering synonymous mutations into the donor to destroy the TALEN or sgRNA recognition site.

Answer:Yes. CRISPR has been shown to be able to disrupt multiple copies at once. The efficiency varies depending on different factors, such as cell type, transfection efficiency and TALEN/CRISPR activity.

Answer:Yes. We have the reagents for the Cas9 D10A nickase, and have successfully tested our double nickase designs. However, in order to create mutagenic DSBs, the nickase requires the correct targeting of two appropriately-spaced sgRNAs on opposite strands, flanking the break site. Because proper sgRNA targeting requires the presence of the N-G-G PAM site immediately following the recognition site, it might not always be possible to use the nickase for DSB formation. There are also high-fidelity variants of Cas9 nuclease that edit genes with greater specificity than wild type Cas9, but sometimes with reduced efficacy and with increased design constraints. However, since these high fidelity variants use only one sgRNA, they are easier to work with than Cas9 niclases.

Answer:Yes. To create a DSB, the nickase requires the correct targeting of two appropriately-spaced sgRNAs on opposite strands, flanking the break site. This is sufficient to stimulate HDR between the target site and the donor. While this method has the advantage of potentially fewer off-target NHEJ-mediated mutations, since single strand nicks are repaired with higher fidelity than DSBs, it is not without limitations. Proper sgRNA targeting requires the presence of the N-G-G PAM site immediately following the recognition site. Therefore, it might not always be possible to use the nickase for HDR.

Answer:We only sell plasmids containing our custom-designed CRISPR sgRNAs. If you need a negative control, we also sell a CRISPR plasmid containing a scrambled sgRNA.

Answer:Yes.

Answer:Yes. There is a double mutant of the Cas9 nuclease that completely abolishes nuclease activity. This mutant can be fused to a transcriptional modulator such as VP64 and targeted to specific genes. You can also use the catalytically dead Cas9 with properly-designed sgRNAs to repress, or interfere with, gene expression.

Answer:Yes. We have both non-viral and lentiviral formats. We also have , in which we can provide you with lentiviral particles expressing both Cas9 and sgRNAs.

Answer:Unfortunately, no. Lentiviruses enter cells as RNA, but HDR donors must enter the cells as DNA at the same time as Cas9 and the sgRNAs.

Answer:Lentiviral particles, transfection-ready DNA, and bacterial stock.

Answer:Yes. The lentiviral plasmids are “dual-use”, so that they can either be packaged into lentiviral particles or transfected into cells by standard transfection methods.

Answer:Our sgRNA representation does not need to be validated by Next Generation Sequencing. Each library is small compared with the genome-wide libraries, and each sgRNA clone is constructed individually, cultured in E. coli individually, then pooled as E. coli in approximately equal amounts. From those pools we prepare DNA and then, if necessary, lentiviral particles.

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GeneHero CRISPR Products and Services | Genecopoeia

CRISPR Background CRISPR Update

Targeted gene editing began with the discovery of zinc finger proteins in the 1980s and continued to improve through the 1990s and early 2000s with the discovery of Transcription activator-like effector nucleases, or TALENS (1, 2). Both of these techniques rely on complex protein structures being engineered to target specific DNA sequences and containing a fused nuclease that nicks a single strand of the DNA duplex. In order to induce the double stranded break (DSB) needed for non-homologous end joining (NHEJ) or homology directed repair (HDR) two zinc finger or TALEN proteins are needed, each targeting one strand of the DNA duplex. While these techniques are reliable, the challenges in designing the protein structures needed to target specific DNA sequences limited their widespread adoption. In 2012 the CRISPR/Cas system was found to target and cut specific DNA sequences using only a nuclease and RNAs to target specific DNA sequences (3). The ease with which this system allows for targeting any gene has set off a new era in targeted gene editing.

Clustered Regular Interspaced Palindromic Repeats, or CRISPRs, were originally identified in the late 1980s in bacteria as short segments of repeating DNA separated by unique spacer sequences however their significance was originally, not known (4). It was not until the early 2000s that the term CRISPR was coined and specific genes, named CRISPR-Associated genes, or Cas genes, were identified (5). Throughout the next decade it was found that the unique spacer sequences were homologous to phage DNA and that certain Cas proteins (i.e. Cas9) used transcribed CRISPR RNA to target and cleave phage DNA, thus acting as an adaptive immune system for bacteria (3, 610). The CRISPR system is composed of two RNA components, crRNA and tracrRNA. Both are transcribed and are required for Cas9 cleavage activity (7). The crRNA is the RNA moiety that targets a specific gene sequence; it contains the transcribed unique spacer RNA as well as a palindromic repeat. The tracrRNA contains a palindromic repeat (the complementary sequence to the crRNA) and a region that can bind to Cas9. Upon duplexing of the crRNA and tracrRNA, this RNA complex can join with Cas9 to target DNA complementary to the unique spacer region of the crRNA (3). Once the crRNA forms a duplex with DNA and the PAM sequence is engaged, Cas9 will cut both strands of the DNA resulting in a double stranded break (DSB), thereby inducing the host DNA repair mechanisms.

After cleavage, DNA can by repaired one of two ways. The simplest, most efficient repair mechanism is referred to as Non-Homologous End-Joining (NHEJ) repair and is the result of enzymes adding and/or removing DNA bases at random to repair the break. This process can result in mutations, by either introducing a premature stop codon or by causing a frameshift mutation. Either one of these mutations ultimately results in a non-functional gene product. NHEJ is routinely used when researchers want to knockout a specific gene. Less efficient than NHEJ is Homology Directed Repair (HDR). HDR is used to insert/knockout genes or to make a specific change at a DSB. In addition to needing the CRISPR/Cas9 machinery, HDR requires a sequence of DNA whose ends are homologous to the ends of the DSB. After inducing a DSB, the cell inserts the new sequence through homologous recombination. To induce specific mutations in cells lines, addition of a donor DNA is needed.

In 2012 Jennifer Doundas group at University of California-Berkley characterized the activity of Cas9 and found that the two RNA component of Cas9 could be modified into a single strand of RNA. This new RNA fragment was coined the guide RNA (gRNA), also known as a single guide RNA. The gRNA is composed of a truncated tracrRNA sequence coined the scaffold sequence fused to a ~20 nucleotide user defined spacer or targeting sequence (3). This system can theoretically be used to target any sequence in a genome provided it meets two conditions. First, the sequence must be unique when compared to the rest of the genome and second, the target sequence has to be immediately followed by the Protospacer Adjacent Motif (PAM). The PAM is a 3-5 nucleotide sequence that is required for Cas cleavage activity. Cas9 has a three nucleotide PAM NGG while other Cas proteins have been identified with different PAM sequences (11). Additionally, protein engineering has been used to create Cas9 variants with different PAM sequences thus expanding the number of genomic targets possible.

Identification of CRISPR mutations depends on which repair mechanism is employed. When large genes are inserted by HDR, PCR amplification of the transgene can easily identify which lines are positive for the desired event. When HDR is used to repair small sections of DNA that do not result in large insertions, sequencing or heteroduplex cleavage are used to identify the changes. A DSB repaired via NHEJ can be detected using a heteroduplexing and endonuclease assay such as T7EI or Surveyor. Upon heteroduplexing of the mutated sequence with a wild-typesequence, T7EI or Surveyor can cleave at the mismatched DNA bases. Successfully modified sequences are then identified by comparing the fragment sizes produced by the assay with the theoretical fragment size of the CRISPR targeted sequence. The ease at which CRISPR/Cas systems can be programed to target virtually any gene in any genome potentially allows for widespread adoption in a number of industries and applications. . Right now, CRISPR is being used to understand how different genes impact human disease through the use of several model animal systems. It is also being used to engineer the next generation of production crops and animals. In the more immediate future CRISPR gene editing may be used to potentially fight widespread zoonotic diseases such as malaria. The applications are endless. While no one can be certain how far reaching the impact CRISPR technology will be, it has undoubtedly revolutionized molecular biology.

Continued here:
CRISPR Background CRISPR Update

Antibodies Part 1: CRISPR – Radiolab

Hidden inside some of the worlds smallest organisms is one of the most powerful tools scientists have ever stumbled across. It’s a defense system that has existed in bacteria for millions of years and it may some day let us change the course of human evolution.

Out drinking with a few biologists, Jad finds out about something called CRISPR. No, its not a robot or the latest dating app, its a method for genetic manipulation that is rewriting the way we change DNA. Scientists say theyll someday be able to use CRISPR to fight cancer and maybe even bring animals back from the dead. Or, pretty much do whatever you want. Jad and Robert delve into how CRISPR does what it does, and consider whether we should be worried about a future full of flying pigs, or thesimple fact that scientists have now used CRISPR to tweak the genes of human embryos.

As of February 24th, 2017 we’ve updated this story.

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Antibodies Part 1: CRISPR – Radiolab

Crispr gene editing ready for testing in humans – ft.com

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Ever since scientists began decoding the human genome in 1990, doctors have dreamt of a new era of medicine where illness could be treated or even cured by fxing flaws in a persons DNA. Rather than using medicine to fight disease, they would be able to hack biology to combat sickness at its source.

The dream started to become a reality in 2013, when researchers demonstrated how a gene editing technique, known as Crispr-Cas9, could be used to edit living human cells, raising the possibility that a persons DNA could be altered much as text is changed by a word-processor.

Now, two biotech companies say they plan to start testing the technology in humans as early as this year.

Crispr Therapeutics has already applied for permission from European regulators to test its most advanced product, code-named CTX001, in patients suffering from beta-thalassaemia, an inherited blood disease where the body does not produce enough healthy red blood cells. Patients with the most severe form of the illness would die without frequent transfusions.

The Switzerland-based company says it also plans to seek a greenlight from the US Food and Drug Administration this year so it can trial CTX001 in people with sickle cell disease, another inherited blood disorder.

Editas Medicine, Crisprs US-based rival, says it plans to apply for permission from the FDA in the middle of the year so it can test one of its one of its own Crispr gene-editing products in patients with a rare form of congenital blindness that causes severe vision loss at birth. If the FDA agrees, it should be able to commence trials within 30 days of the application.

If those trials are successful, Crispr, Editas and a third company, Intellia Therapeutics, say they plan to study the technique in humans with a range of diseases including cancer, cystic fibrosis, haemophilia and Duchenne muscular dystrophy.

In China, where regulators have taken a more lenient approach to human trials, several studies are already under way, although they have yet to produce any conclusive data.

Crispr-Cas9 is best thought of as two technologies that make gene editing possible: Cas9 acts as a pair of molecular scissors that can snip strands of DNA, removing faulty genetic material and creating space for functioning genes to be inserted. Crispr is a kind of genetic GPS that guides those scissors to the precise location.

Katrine Bosley, chief executive of Editas, says the field of gene editing is moving at lightning speed, but that the technique will at first be limited to illnesses where there are not other good options.

That is because, as with any new technology, scientists and regulators are not fully aware of the safety risks involved. We want it to be as safe as it can, but of course there is this newness, says Ms Bosley.

Francisco Mojica at the University of Alicante, Spain becomes the first researcher to discover Crispr sequences

Alexander Bolotin at the French National Institute for Agricultural Research observes Cas9 genes in the bacteria Streptococcus thermophilus

Scientists at Danone study how Crispr techniques can help Streptococcus thermophilus, widely used in commercial yoghurt making, ward off viral attacks

Biochemists Jennifer Doudna and Emmanuelle Charpentiere show that Crispr can be used to edit DNA in test tubes

Feng Zhang of the Broad Institute reports using Crispr to edit DNA in human cells, opening the door for the tool to be used in medicine

Crispr is used to edit the genomes of everything from flies to mice

British scientists use Talen gene editing to treat a childs leukaemia

Still, Ms Bosley points out that of the more than 6,000 genetic disorders, which are the most obvious candidates for gene editing, roughly 95 per cent are untreatable. This provides plenty of areas for companies like hers to explore.

Although Crispr-Cas9 has not yet been trialled in humans in Europe or the US, the technology has already benefited medical research greatly by speeding up laboratory work. It used to take scientists several years to create a genetically modified mouse for their experiments, but with Crispr-Cas9 these transgenic mice can be produced in a few weeks.

Cellectis, a French biotech group, has used an older gene-editing technique known as Talen, to create a pioneering blood cancer treatment known as chimeric antigen receptor therapy or Car-T, which is currently being tested in humans.

Car-T products are already on the market, but rely on an expensive and laborious process that involves extracting a persons white blood cells, transporting them by aeroplane to a lab where they are re-engineered to attack cancer, before returning them and inserting them into the patient.

Cellectis hopes its approach of using gene editing to alter the cells will cut out this lengthy re-engineering process.

Some proponents of Crispr-Cas9 dismiss the Talen technique as old, slow and expensive, but Andr Choulika, Cellectis chief executive, disagrees.

We asked readers, researchers and FT journalists to submit ideas with the potential to change the world. A panel of judges selected the 50 ideas worth looking at in more detail. This fourth tranche of 30 ideas (listed below) is about the latest advances in healthcare. The fifth and final chapter, looking at Earth and the universe, will be published on March 29, 2018.

Were not talking about iPhones here, he says. Maybe [Crispr] is a new technology, its easy to design and its cheap, but who cares? This is not what the patient needs. The patient needs a super-active, super-precise product.

Amid the excitement, the nascent field of gene editing has been hampered by several setbacks. Editas had hoped to start human trials earlier, but was forced to move the date back after it encountered manufacturing delays. Crispr has lost several key executives in recent months, while Cellectis had to suspend its first trial briefly last year after a patient died.

Meanwhile, a bitter patent dispute over which academic institution discovered Crispr-Cas9, and therefore which biotech company has the rights to the patents, has cast a pall over gene editing.

The field is in its infancy and progress in any new area of science is never smooth. If gene editing lives up to its promise, it could one day save or dramatically change the lives of tens of millions of patients with hitherto untreatable diseases.

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Crispr gene editing ready for testing in humans – ft.com

CRISPR – YouTube

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

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SOURCES AND FURTHER READING:

The best book we read about the topic: GMO Sapiens

https://goo.gl/NxFmk8

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Help us caption & translate this video!

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CRISPR – YouTube

Researchers advance CRISPR-based tool for diagnosing disease …

The team that first unveiled the rapid, inexpensive, highly sensitive CRISPR-based diagnostic tool called SHERLOCK has greatly enhanced the tools power, and has developed a miniature paper test that allows results to be seen with the naked eye without the need for expensive equipment.

The SHERLOCK team developed a simple paper strip to display test results for a single genetic signature, borrowing from the visual cues common in pregnancy tests. After dipping the paper strip into a processed sample, a line appears, indicating whether the target molecule was detected or not.

This new feature helps pave the way for field use, such as during an outbreak. The team has also increased the sensitivity of SHERLOCK and added the capacity to accurately quantify the amount of target in a sample and test for multiple targets at once. All together, these advancements accelerate SHERLOCKs ability to quickly and precisely detect genetic signatures including pathogens and tumor DNA in samples.

Described today in Science, the innovations build on the teams earlier version of SHERLOCK (shorthand for Specific High Sensitivity Reporter unLOCKing) and add to a growing field of research that harnesses CRISPR systems for uses beyond gene editing. The work, led by researchers from the Broad Institute of MIT and Harvard and from MIT, has the potential for a transformative effect on research and global public health.

SHERLOCK provides an inexpensive, easy-to-use, and sensitive diagnostic method for detecting nucleic acid material and that can mean a virus, tumor DNA, and many other targets, said senior author Feng Zhang, a core institute member of the Broad Institute, an investigator at the McGovern Institute, and the James and Patricia Poitras 63 Professor in Neuroscience and associate professor in the departments of Brain and Cognitive Sciences and Biological Engineering at MIT. The SHERLOCK improvements now give us even more diagnostic information and put us closer to a tool that can be deployed in real-world applications.

The researchers previously showcased SHERLOCKs utility for a range of applications. In the new study, the team uses SHERLOCK to detect cell-free tumor DNA in blood samples from lung cancer patients and to detect synthetic Zika and Dengue virus simultaneously, in addition to other demonstrations.

Clear results on a paper strip

The new paper readout for SHERLOCK lets you see whether your target was present in the sample, without instrumentation, said co-first author Jonathan Gootenberg, a Harvard graduate student in Zhangs lab as well as the lab of Broad core institute member Aviv Regev. This moves us much closer to a field-ready diagnostic.

The team envisions a wide range of uses for SHERLOCK, thanks to its versatility in nucleic acid target detection. The technology demonstrates potential for many health care applications, including diagnosing infections in patients and detecting mutations that confer drug resistance or cause cancer, but it can also be used for industrial and agricultural applications where monitoring steps along the supply chain can reduce waste and improve safety, added Zhang.

At the core of SHERLOCKs success is a CRISPR-associated protein called Cas13, which can be programmed to bind to a specific piece of RNA. Cas13s target can be any genetic sequence, including viral genomes, genes that confer antibiotic resistance in bacteria, or mutations that cause cancer. In certain circumstances, once Cas13 locates and cuts its specified target, the enzyme goes into overdrive, indiscriminately cutting other RNA nearby. To create SHERLOCK, the team harnessed this off-target activity and turned it to their advantage, engineering the system to be compatible with both DNA and RNA.

SHERLOCKs diagnostic potential relies on additional strands of synthetic RNA that are used to create a signal after being cleaved. Cas13 will chop up this RNA after it hits its original target, releasing the signaling molecule, which results in a readout that indicates the presence or absence of the target.

Multiple targets and increased sensitivity

The SHERLOCK platform can now be adapted to test for multiple targets. SHERLOCK initially could only detect one nucleic acid sequence at a time, but now one analysis can give fluorescent signals for up to four different targets at once meaning less sample is required to run through diagnostic panels. For example, the new version of SHERLOCK can determine in a single reaction whether a sample contains Zika or dengue virus particles, which both cause similar symptoms in patients. The platform uses Cas13 and Cas12a (previously known as Cpf1) enzymes from different species of bacteria to generate the additional signals.

SHERLOCKs second iteration also uses an additional CRISPR-associated enzyme to amplify its detection signal, making the tool more sensitive than its predecessor. With the original SHERLOCK, we were detecting a single molecule in a microliter, but now we can achieve 100-fold greater sensitivity, explained co-first author Omar Abudayyeh, an MIT graduate student in Zhangs lab at Broad. Thats especially important for applications like detecting cell-free tumor DNA in blood samples, where the concentration of your target might be extremely low. This next generation of features help make SHERLOCK a more precise system.

The authors have made their reagents available to the academic community through Addgene and their software tools can be accessed via the Zhang lab website and GitHub.

This study was supported in part by the National Institutes of Health and the Defense Threat Reduction Agency.

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Researchers advance CRISPR-based tool for diagnosing disease …

Researchers use CRISPR to detect HPV and Zika

The first study comes from the lab of CRISPR pioneer Jennifer Doudna. Her team discovered that a CRISPR system different from the CRISPR-Cas9 one we’re used to hearing about can not only snip away specific bits of double-stranded DNA, but can then also cut single-stranded DNA that’s near it. After they uncovered this ability of CRISPR-Cas12a, they used it to detect two common types of HPV. Once their CRISPR-Cas12a system detected HPV DNA in infected cells, it cleaved a another piece of DNA that then released a fluorescent signal, providing a visual sign of the presence of HPV. The researchers dubbed the system DETECTR and The Verge reports that it takes around an hour to work and costs less than a dollar.

The lab of another CRISPR pioneer, Feng Zhang, has now improved on a previous system it developed last year. SHERLOCK, as it’s called, can detect specific bits of DNA and RNA to determine whether viruses like Zika or dengue are present in a blood sample, identify mutations in tumor DNA and spot the presence of harmful bacteria. In their latest study, the research team describes SHERLOCK version 2.0, which is not only over three times as sensitive as the first version, but can also detect both Zika and dengue in the same sample. Their system uses several CRISPR enzymes, including Cas13 and Csm6, and can be loaded onto a paper strip, making it incredibly easy to use. You can see examples of the strips in the GIF below. Jonathan Gootenberg, one of the authors of the study, told The Verge, “The fact that we can put all these different enzymes into a single tube and have them not only play nice with each other, but also tell us information we couldn’t get otherwise — that is really spectacular and it speaks to a lot of the power of biochemistry.”

Lastly, Harvard University’s David Liu published a study showing that CRISPR can be used to track certain ongoings in a cell. Seeing what a cell has been exposed to in the past has been a rather hard thing to do, but CRISPR systems provide a way for researchers to do just that. Liu’s team used CRISPR in two different ways to record when a cell was exposed to certain chemicals. In the first, CRISPR was used to snip bits of DNA called plasmids if it came in contact with a particular chemical, such as an antibiotic or a nutrient. By comparing the ratio of the plasmid types that were destroyed by CRISPR to other, similar plasmids that were left alone, the researchers were able to determine just how often the cells were exposed to those chemicals. Another version of the system changed individual letters, or bases, of DNA rather than snipping plasmids and the team was able to determine when cells were exposed to antibiotics, nutrients, viruses and light by examining those changes in the DNA bases.

While all three of these systems need further development before they can be used outside of the lab, they show that CRISPR has quite a lot of uses, beyond just treating disease. The technology is incredibly versatile and we’re sure to see even more applications going forward.

Image: Zhang Lab, Broad Institute of MIT and Harvard

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Researchers use CRISPR to detect HPV and Zika

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

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

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

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

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

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

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

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

IBD’S TAKE:Biotech companies account for a large share of recent IPO stocks, yet investing in them before they have profits or sales can be risky. Learn to identify the best IPOs and how to trade themfor potential big gains.

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

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

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

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

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

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

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

She likens CRISPR technology to a word processor.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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