Taking Gene Editing by Storm
Article Mar 04, 2016
Angelo DePalma, Ph.D.
Photo of A549 (ATCC® CCL-185™) by Christopher Chin, Massachusetts General Hospital. This cell
line is the first product of ATCC's CRISPR/Cas9 efforts.
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The CRISPR/Cas9 system – often abbreviated to “CRISPR" – has been the most significant development in genome editing in years. The
two components of CRISPR/Cas9 are a “homing” mechanism consisting of guide RNA sequences and Cas9, an endonuclease. The guide RNA directs
CRISPR/Cas9 to a precise location on the target organism’s genome, where Cas9 produces a double-stranded break.
mechanism for double-stranded breaks is error-prone, leading to mutations that disable or knock down the gene. It is possible to replace the
mutant gene at this stage by adding DNA sequences that pair up with the cut ends.
Almost anyone with college-level biology
expertise can run CRISPR/Cas9 experiments. All that is necessary to create CRISPR reagents for a new target is to synthesize the 20-bp guide
sequences in CRISPR. The well-established TALEN gene-editing tool requires synthesizing an appropriate protein as well.
In its 2015
year-end issue the journal Science named CRISPR “breakthrough of the year.” Noting the popularity of earlier gene-editing techniques – and
CRISPR’s runner-up status in the 2014 and 2013 year-end editions – correspondent John Travis wrote that CRISPR “broke away from the pack,
revealing its true power in a series of spectacular achievements.”
Nagging Off-Target Questions
experiments are subject to off-target effects. For CRISPR that includes targeting the incorrect sequence to create the double-stranded break,
or the effects of repair mechanisms crashing.
How serious are off-target effects? “It’s highly debated,” says Kryngle Daly, Ph.D.
CEO at KBioBox (Worcester, Massachusetts, USA). “It’s serious enough that people are concerned about it, particularly for clinical
applications.” In a CRISPR the guide RNA is composed of a three base pair sequence known as the PAM, and 20 trailing base pairs. Researchers
believe the number, location, and degree of mismatches between the guide RNAs at the target may affect off-target activity. Mismatches in or
near the PAM greatly reduce the potential for off-target events, while mismatches in the end of the guide RNA opposite from the PAM allow an
In January, 2016 a group at Massachusetts General Hospital led by Keith Joung, M.D., Ph.D., discovered improvements
to the CRISPR/Cas9 protocol that reduce unwanted, non-specific DNA breaks to undetectable levels. This invention should significantly
accelerate therapeutic applications of CRISPR, while enabling finer control over gene manipulations in animals, plants, cells, and
At the time Joung said of his invention that, “Its impact will also be incredibly important for research
applications because off-target effects can potentially confound the results of any experiment. As a result, we envision that our high-
fidelity variant will supplant the use of standard Cas9 for many research and therapeutic applications.”
Basic research has always had
a relatively high tolerance for variability. As Cas9 constructs enter clinical trials, particularly for in vivo therapies, off-target
risk should be reduced to as close to zero as possible. “You have to be able to predict off-target effects and their seriousness,” Daly says.
“That implies understanding the biology a few additional layers deep, including the effects of changes to non-coding regions. Will those
changes disrupt critical protein pathways, or induce only trivial changes?”
KBioBox offers two web-based services for predicting off-
target effects of CRISPR/Cas9 experiments. The algorithms are completely new and do not rely on public-domain algorithms like the MIT and E-
Crisp tools. KBioBox predicts 97% of off-target effects; the open source software is only about 50% accurate.
KBioBox’s “Off Target Analysis” service takes a given guide RNA design and in under a minute reports the “top
ten” potential off targets, including location and annotation information. Complimenting this service is KBioBox’s biodesign service
which determines an ideal guide RNA design for a given application. Given a species, gene, and intended effect, the biodesign service
will calculate the “top ten” guide RNA designs, included with each design is an off target analysis report such that users can further select
for their purposes. Both of these services are extensible to any species or chemistry (e.g. TALEN, or custom enzymes).
effects are not always undesirable. Scientists exploit the chaotic double-strand repair mechanisms, which result in insertions and deletions
at the break site, as a simple method for knocking genes out.
Variations on a Cancer Cell Like Theme
ATCC (Manassas, VA, USA), the leading cells standard organization in the U.S., licensed CRISPR/Cas9 gene editing technology from the Broad
Institute of MIT and Harvard. ATCC plans to use the gene editing technology to develop new products and services to support basic and
translational research. The first such product, EML4-ALK Fusion-A549 Isogenic Cell Line (ATCC® CCL-185IG™) is now available for researchers
working on non-small cell lung cancer (NSCLC).
Scientist Metewo Enuameh, Ph.D at ATCC calls the in-licensing “exciting” for the
organization and its customers. “Based upon results in the gene editing field, it is generally agreed that CRISPR is much easier to use
compared to other gene editing methods like ZFNs (zinc finger nuclease) and TALEN.”
A549 is a standard cancer cell line for researching
NSCLC, particularly for drug screening. “We added a genomic rearrangement that occurs in a subset of NSCLC patients.” In tests the new cell
line responds to anti-cancer drugs similarly to cells taken directly from this NSCLC patients.
“The cells provide a functional in
vitro readout,” Enuameh adds. “The beauty is that we now have a mutated cell line, which can be compared to the parental line for drug
The time-saving nature of the CRISPR gene editing platform enables faster creation of controlled model test systems with
precisely the desired mutations.
In certain cancers, subsets of patients exist who are susceptible or resistant to various anti-cancer
therapies. As these genetic variants are uncovered, ATCC will use CRISPR to generate new cell lines endowed with resistance or susceptibility
to anti-cancer therapies, which will enable drug developers to test the effects of various compounds against cells that carry these
This development holds huge implications for personalized medicine. Based on knowledge gained through screening
studies and patient biopsies, physicians of the future will be able to prescribe precisely the drug that will most likely to help the
patient, and avoid ineffective treatments that will provide no relief and may introduce toxicity.
Instead of diagnosing and
treating all NSCLC patients the same with standard treatments, variants on the gene-editing idea will allow rapid screening of drugs and
treatments based on the patient’s genetic makeup. “Drug therapy will become more science-based,” Enuameh says.
Anja Smith, Ph.D., R&D Director at Dharmacon (A GE company; Denver, Colorado, USA) explains that “we have
historically had reagents for knocking down or over-expressing genes. CRISPR-CAS9 allows complete knockouts.” More sophisticated custom
genome engineering, including knock-ins, requires a template for repairing the break caused by CRISPR. This allows replacement or insertion
of disease-related mutations, for example insufficient production of insulin or blood clotting factors. Knockdowns become routine in the
chaotic atmosphere of a double-stranded break.
Dharmacon has to date focused more on knockout, which is more efficient in mammalian
cells. Upcoming product offerings will include knock-in tools as well.
Knock-ins are more complicated as they also use CAS9 and
the CRISPR’s RNA components to create the double-strand break. But in the presence of a donor template, part of which is homologous to the
region where the double strand break occurred, the desired donor sequence inserts at the double-strand break.
“Knock-ins are not
very efficient in mammalian cells,” Smith explains. “Reagents and protocols that improve the efficiency of the break/insertion process will
also improve knock-in efficiency.”
CRISPR/Cas9 Knock-ins have perhaps received most of the press, but many researchers are interested
in knock-out for functional genomics studies. Numerous studies, for example, have demonstrated by knockouts which genes are essential in
Knock-ins are more elegant because they produce fundamental, permanent genomic changes. Clinical applications involving
the correction of genetic diseases or inserting genes for therapeutic proteins are probably years away. However several companies are using
knock-ins as part of immunotherapy protocols.
The problem with direct knock-ins into organs is the difficulty of systemic delivery of
gene therapies. For the time being ex-vivo therapies make more sense. In this model, immune system cells are removed from patients and
genetically modified to have cancer surface antigens. Once they are re-infused they “teach” the patient’s immune system to attack the
Another potential application is xenotransplantation, which has thus far been unsuccessful due to organ
rejection. Using CRISPR, one could potentially knock out genes in animal organs that induce host-vs.-graft reactions. However, extremecare
must be taken with these approaches because they are capable of transferring endogenous animal viruses into humans.
in Clinical Trials
Gene editing based on TALEN (transcription activator-like effector nuclease) and zinc finger nuclease have
produced encouraging results in immunotherapies for cancer and HIV. Given the extremely high anticipated cost of these therapies if they are
approved, it is likely that immunotherapy companies newly entering the field would turn to the simpler and less expensive
“The reason,” says Anja Smith, is that when you target gene ‘X’ with ZFNs and TALEN you must engineer the protein
part of the complex, which is extremely costly and time-consuming. Researchers often must test several versions of the protein before finding
one that works. And if you want to target gene ‘Y’ you must start over.”
CRISPR/Cas9 is the only gene editing technique that allows
“gene drive,” a process by which two copies of a desirable gene may be inserted. For example, in late 2015 at group at the University of
California led by Prof. Anthony James used CRISPR/Cas9 to engineer mosquitos that are incapable of carrying the malaria parasite. According
to reports 99.5% of the offspring of the engineered mosquitos exhibited the desirable trait. With no additional help these mosquitos would
likely breed with non-engineered mosquitos in the wild, thus reducing the malaria resistance by 50% every generation. After a few generations
the trait would disappear. The California investigators employed gene drive, which creates “selfish” versions of the anti-malaria genes,
which pass on two copies the anti-malaria gene to all offspring.
Angelo DePalma is a freelance writer living in Newton, New Jersey,
Synthetic biology (SB) is an umbrella term that covers a wide range of scientific applications. In this article we'll explore work aiming to synthesize genes faster than ever before, expand the genetic alphabet and turn DNA into a storage medium. To this end, we interviewed two leading figures in the field, Emily Leproust PhD, CEO of Twist Bioscience and Floyd Romesberg PhD, a Professor of Chemistry at the Scripps Institute.READ MORE