We need to talk about CRISPR

By Gesa Junge, PhD

You’ve probably heard of CRISPR, the magic new gene editing technique that will either ruin the world or save it, depending on what you read and whom you talk to? Or the Three Parent Baby, which scientists in the UK have created?

CRISPR is a technology based on a bacterial immune defense system which uses Cas9, a nuclease, to cut up foreign genetic material (e.g., viral RNA). Scientists have developed a method by which they can modify the recognition part of the system, the guide RNA, and make it specific to a site in the genome that Cas9 then cuts. This is often described as “gene editing” which allows disease-causing genes to be swapped out for healthy ones.

CRISPR is now so well known that Google finally stopped suggesting I may be looking for “crisps” instead, but the real-world applications are not so well worked out yet, and there are various issues around CRISPR, including off-target effects, and also the fact that deleting genes is much easier than replacing them with something else. But, after researchers at Oregon Health and Science University managed to change the mutated version of the MYBPC3 gene to the unmutated version in a viable human embryo last month, the predictable bioethical debate was reignited, and terms such as “Designer Babies” got thrown around a lot.

A similar thing happened with the “Three Parent Baby,” an unfortunate term coined to describe mitochondrial replacement therapy (MRT). Mitochondria, the cells’ organelles for providing energy, have their own DNA (making up about 0.2% of the total genome) which is separate from the genomic DNA in the nucleus, which is the body’s blueprint. Mitochondrial DNA can mutate just like genomic DNA, potentially leading to mitochondrial disease, which affects 1 in 5000-10000 children. Mitochondrial disease can manifest in various ways, ranging from growth defects to heart or kidney to disease to neuropsychological symptoms. Symptoms can range from very mild to very severe or fatal, and the disease is incurable.

MRT replaces the mutated mitochondrial DNA in a fertilized egg or in an embryo with the healthy version provided by a third donor, which allows the mitochondria to develop normally. The UK was the first country to allow the “cautious adaption” of this technique.

While headlines need to draw attention and engage the reader for obvious reasons, oversimplifications like “gene editing” and dramatic phrases like “three parent babies” can really get in the way of broadening the understanding of science, which is difficult enough as it is. Research is a slow and inefficient process that easily gets lost in a 24-hour news cycle, and often the context is complex and not easily summed up in 140 characters. And even when the audience can be engaged and interested, the relevant papers are probably hiding behind a paywall, making fact checking difficult.

Aside from difficulties communicating the technicalities and results of studies, there is also often a lack of context in presenting scientific studies – think for example of chocolate and red wine which may or may not protect from heart attacks. What is lost in many headlines is that scientific studies usually express their results as a change in risk of developing a disease, not a direct causation, and very few diseases are caused by one chemical or one food additive. On this topic, WNYC’s “On The Media”-team have an issue of their Breaking News Consumer Handbook that is very useful to evaluate health news.

The causation vs. correlation issue is perhaps a little easier to discuss than big ethical questions that involve changing the germline DNA of human beings because ethical questions do not usually have a scientific answer, let alone a right answer. This is a problem, not just for scientists, but for everyone, because innovation often moves out of the realm of established ethics, forcing us to re-evaluate it.

Both CRISPR and MRT are very powerful techniques that can alter a person’s DNA, and potentially the DNA of their children, which makes them both promising and scary. We are not ready to use CRISPR to cure all cancers yet, and “Three Parent Babies” are not designed by anyone, but unfortunately, it can be hard to look past Designer Babies, Killer Mutations and DNA Scissors, and have a constructive discussion about the real issues, which needs to happen! These technologies exist; they will improve and eventually, and inevitably, play a role in medicine. The question is, would we rather have this development happen in reasonably well-regulated environments where authorities are at least somewhat accountable to the public, or are we happy to let countries with more questionable human rights records and even more opaque power structures take the lead?

Scientists have a responsibility to make sure their work is used for the benefit of humanity, and part of that is taking the time to talk about what we do in terms that anyone can understand, and to clarify all potential implications (both positive and negative), so that there can be an informed public discussion, and hopefully a solution everyone can live with.

 

Further Reading:

CRISPR:

National Geographic

Washington Post

 

Mitochondrial Replacement Therapy:

A paper on clinical and ethical implications

New York Times (Op-Ed)

 

Engineering Babies One Crispr at a Time

 

By Sophie Balmer, PhD

Over the past few weeks, the scientific community has been overwhelmed with major advances in human embryonic research. Whether researchers report for the second time the use of Crispr to edit the human germline or extend the conditions of in vitro culture of human embryos (also here), these issues have been all over the news. However, as all topics can not be raised in only one post, therefore, I will focus on genome editing studies.

 

About a year ago, one research group in China reported the first genome editing of human embryos using Crispr technology. Although these embryos were not viable due to one additional copy of each chromosome, this study quickly became highly controversial and raised strong concerns. The public and scientific communities questioned whether editing the human germline for therapeutic benefits was legitimate, leading to numerous ethical discussions. A few of weeks ago, a second study reported genome editing of embryos reinforcing the debate around this issue. Additionally, several research proposal involving genomic modification of healthy human embryos’ DNA have been validated recently in other countries. In this post, I want to address several questions. What are the possible advances or consequences of such work? What is the current legislation on human genome editing worldwide? Are these studies as alarming as what is written in some newspaper articles?

 

The emergence of the Crispr technology a few years ago has revolutionized the way scientists work since this method greatly improves the efficiency of DNA alteration of model organisms. However, this powerful tool has also raised many concerns, notably on the possibility to easily tweak the human genome and generate modified embryos.

In the eyes of the general public, this kind of experiment resonates with science fiction books or movies. Because of the high potential of this technique, it is crucial to inform everyone correctly to avoid clichés. Recently, one of my favorite comedian and television host John Oliver depicted in a very bright and amusing way how small scientific advances are sometimes presented in the media. Although the examples he uses are dramatic, every scientific breakthrough gets its share of overselling to the public. In the case of gene-editing of human embryos, pretending we are about to use eugenics principles to engineer babies and their descendants with beneficial genes is pure fiction. However, to prevent any potential malpractice from happening, clear ethical discussions and regulations need to be established and then explained to the public to prevent misunderstanding of these issues.

Within the scientific community, last year’s results triggered the need for new discussions and regulations on human cloning. Modifying the genome of human embryos involves modifying the germline as well, leading eventually to the transmission of the genetic alteration to future generations. However, the consequences of such transmission are unknown. Potentially, this could resolve a number of congenital genetic diseases for the individual him/herself and be used for gene therapy but would result in generations of genetically modified humans.

 

Because of cultural and ethical differences between countries, the legislation (if there is any) around working with human embryos or cells derived from human embryos (hESC for human embryonic stem cells) is variable. International ethical committees have only been able to establish guidelines as instituting international laws on human cloning is impossible. Ultimately, each country is responsible for enforcing these rules. Most countries and international ethics committees agree on a ban on reproductive and therapeutic human cloning. Moreover, following last year published experiments, a summit held in December 2015 gathered experts from all around the world. The consortium concluded that gene-editing of embryos used to establish pregnancy should not be performed (for now) and to follow up on all-related issues, new sets of guidelines are coming out imminently.

 

Still, it seems difficult to get an idea of the consensus depending on the countries in which scientists perform experiments. There is range of possibilities when working with human samples: some countries completely prohibit any manipulation of human embryos or hESC while others authorize genetic modification of the embryo for research purposes only under specific conditions. In between several nations authorize research exclusively on already derived lines of hESC and others authorize derivation of hESC but no manipulation of the embryos themselves.

Besides these general rules and as of today, three countries have approved proposals for gene-editing of human embryos: China, the UK and Sweden. Research proposals in both European countries have authorized Crispr targeting of specific genes in healthy human embryos to assess the function of these genes during early human development. However, these embryos can not be used for in vitro fertilization (IVF) and have to be destroyed at the end of the study. The purpose of these studies would be to confirm what has been described in hESC and in mammalian model systems and contribute to our knowledge of human development.

 

On the other hand, both published studies from China focused on Crispr targeting towards clinical therapies of an incurable blood disease or HIV. The overall purpose of such projects is to test the use of the Crispr technology for gene therapy. Although rendering embryos immune to several diseases using Crispr is an attractive possibility, it seems more urgent to probe the validity of the technique in humans and assess whether the mechanisms of human embryonic development are similar to what has been hypothesized. Gene therapies have already been successfully attempted in humans using other techniques to modify the genome. Yet, the modifications were targeted towards specific cells in already-born individuals. Again, modifying the genome of embryos implies that the mutation will be inherited in future generations and is in a large part the reason of this debate. Moreover, Crispr targeting still leads to unspecific modification of the genome, although very promising results show that newly engineered cas9 could lead to very specific targeting. The consequences of such off-target modification are unknown and could be disastrous for the following generations.

 

Overall, no research proposal dares to consider genetically modified embryos to establish pregnancy but as research moves faster, increasing demand for ethical discussion and regulations are brought forward. As more studies come out, it will be interesting to follow the evolution of this debate. Additionally, informing clearly the population of the possibilities and outcomes of ongoing projects should be a priority so that they can give an informed consent towards such research. In any case, a clear boundary needs to be established between selecting the fittest embryo by pre-implantation genetic diagnosis, which is routinely performed for IVF and playing the sorcerer’s apprentice with human embryo’s

Biotech Breakthrough: The CRISPR/Cas System

 

By John McLaughlin

In the last few years, a huge amount of excitement has grown over the CRISPR/Cas system and its use in targeted genome editing; this acronym derives from Clustered Regularly Interspaced Short Palindromic Repeats and their CRISPR-associated genes (Cas). CRISPR loci, which are found in many species of bacteria and most archae, have been collectively described as an RNA-based “immune system,” because of their ability to recognize and destroy foreign phage and plasmid DNA.

 

Although the acronym was first coined in a 2002 paper, CRISPR has only recently been exploited as a research tool. How does the system work and what is its use in the lab? There are at least three distinct types of CRISPR system. A typical “type II” CRISPR locus consists of several protein-coding Cas genes adjacent to an array of direct repeat and spacer sequences. The direct repeats are usually palindromic and conserved, in contrast to the much more variable spacers; these repeat-spacer sequences are transcribed as one unit and then processed into short CRISPR-RNAs (crRNAs).  A 2007 Science article demonstrated that a bacterial population could acquire resistance to phage infection by incorporating DNA fragments from the invading phage genome into a CRISPR locus, in the form of new spacer sequences. The newly acquired spacers are then transcribed and processed into crRNAs, associate with a trans-activating RNA (tracRNA) and Cas protein, and are eventually guided to a homologous DNA sequence to catalyze a double-stranded break.

 

The CRISPR system can be flexibly “reprogrammed” by designing custom chimeric RNAs (chiRNA), which serve the function of both crRNA and tracRNA in one molecule. By co-expressing a “designer” chiRNA with a Cas protein, a targeted and specific DNA break can be created in the genome; after providing an exogenous DNA template to help repair the break, customized knock-ins or knock-outs can be generated. Judging from the rapid technical advances made in the last few years, the system promises to be an efficient and high-throughput format for genome editing. To date, knock-outs have been created in a variety of organisms including rats, flies, and human cells.

 

CRISPR/Cas technology has attracted scientific attention as well as commercial interests. In November 2014, biologists Jennifer Doudna and Emmanuelle Charpentier were honored as co-recipients of the 2015 Breakthrough Prize in the Life Sciences, for their work in dissecting the mechanism of CRISPR’s sequence-specific DNA cleavage. According to its proponents, the possible applications of the CRISPR system seem almost limitless. CRISPR Therapeutics, a recently formed company dedicated to translating the technology into genetic disease therapies, has raised 25 million dollars from new investors. And just last month, the pharmaceutical company Novartis began collaborations with Intellia Therapeutics and Caribou Biosciences in order to pursue new therapeutics using CRISPR/Cas.

 

A technology as potentially lucrative as this one does not develop without controversy. MIT Technology Review recently reported on the competing startup companies aiming to exploit CRISPR technology, and the ensuing battles over intellectual property rights in different organisms. In fact, last year the Broad Institute and MIT were awarded a patent which covers the use of CRISPR genome-editing technology in eukaryotes. Feng Zhang, who is listed as Inventor on the patent, and his lab at MIT were the first to publish on CRISPR’s functionality in human cells.

 

In a few years, this exciting technology may be a commonplace fixture of the biology lab. Only time will tell if the CRISPR craze produces the amazing breakthroughs that scientists, and the general public, are eagerly awaiting.

Sizzling Papers of the Week – Dec 6

 

The Scizzle Team

 

Genetics don’t lie

A cave in Spain – Sima de los huesos – had he largest collections of hominin bones. Now mitochondrial DNA from a femur bone collected from the cave in the 1990s was sequenced. It was believed that the bones found in Sima de los huesos were of Neanderthals but the DNA sequence suggests otherwise and left the researchers bewildered: the phylogenetic analysis showed that the DNA is closer to Denisovans than to Neanderthals – a population believed to live in southwestern Siberia. So the mystery of where our ancestors came from still remains and only more sequencing of ancient DNA will help solve it.

A mitochondrial genome sequence of a hominin from Sima de los huesos. Meyer at al., Nature. 2013.

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Future of genome therapy is looking CRISPR

Two studies published in Cell Stem Cell using the CRISPR-Cas9 system to cure diseases in mice and human stem cells.  They CRISPR/Cas9 system was originally discovered as the “immune system” of archaea and bacteria.  In the first study  the system was used in mice to correct the Crygc gene that causes cataracts; in the second study the CRSPR-Cas9 system was used to correct the CFTR locus in cultured intestinal stem cells of CF patients. These findings serve as a proof-of-concept that diseases caused by a single mutation can be “fixed” with genome editing using the CRISPR-Cas9 system.

Correction of genetic disease in mouse via use of CRISPR-Cas9. Wu et al. Cell Stem Cell. 2013.

Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of Cystic Fibrosis patients. Schwank et al., Cell Stem Cell. 2013.

Want to stay on top of  the CRISPR/Cas9 genome editing and curing diseases? Create a feed for CRISPR, Cas9 and diseases.

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You smell so good!

After being traumatized by what really happens inside you when a mosquito bites we thought there’s no hope that we’ll ever be mosquito-bite free. But a new study published in Cell opens the door to new, safe and pleasantly smelling way to lure mosquitoes away. The female mosquito detects CO2 using a class of olfactory receptor neurons, but the neurons and receptors that detects skin odor are a mystery. The researchers found  one neuron important for attraction to skin odor and then screened half a million compounds to find those who lured mosquitoes to traps effectively as CO2 does. Joking aside, finding safe and affordable ways to control mosquitoes is a key way to preventing them from transferring deadly diseases.

Targeting a dual detector of skin and CO2 to modify mosquito host seeking. Tauxe et al. Cell. 2013.

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It Runs in the family

Scientists showed that behavioral experiences can shape mice epigenetically in a way that is transmittable to offspring.  Male mice conditioned to fear an odor showed hypomethylation for the respective odor receptor in their sperm; offspring of these mice showed both increased expression of this receptor, and increased sensitivity to the odor that their fathers had been conditioned on.  Does this suggest that memories can be inherited?

Parental olfactory experience influences behavior and neural structure in subsequent generations, Dias, B.G. and Ressler, K.J., Nature Neuroscience. Published online December 1st 2013

Fascinated by the possibility of inheriting memories? Create a feed for epigenetics and memory and don’t miss our post about this article and all the buzz –  family fear?

A pathway for the worst sides of addiction?

Opioid drugs, such as heroin, appear to have a specific pathway mediating some of the worst aspects of addiction; the κ opioid receptor is involved the dysphoria of withdrawal and the need to constantly increase dosage.  Inhibiting the κ receptor blocked dosage escalation in rats and reduced their motivation to administer the drug.  This receptor pathway may be crucial to the urge to avoid withdrawal, which itself is a powerful component of addiction.

Long-Term Antagonism of κ Opioid Receptors Prevents Escalation of and Increased Motivation for Heroin Intake, Schlosburg, J.E, et al., The Journal of Neuroscience. December 4 2013

From bacteria to behavior

Is there anything gut bacteria can’t do?  A new study this week shows that the little critters may have a role in ameliorating autism.  It’s been known for some time that autistic individuals are more likely to suffer various gastrointestinal problems.  Researchers found that a mouse model for autism suffers from gut inflammation similar to that seen in colitis.  The bacteria B. fragilis, which has been show to help repair these symptoms in illnesses such as Chrons disease. help repair the autistic mice’s intestines as well.  More amazingly, treatment with the bacteria also improved behavioral symptoms of autism.

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopment Disorders, Hsiao, E.Y., et al., Cell. 2013.

Stay on top of the growing list of things we can thank or blame gut microbiota for? Create a feed for gut microbiota.

It wasn’t my fault…line

Japan’s Tohoku-Oki earthquake in 2011 was not only devastating, but in many ways surprising even to scientists.  Investigators are striking back in a full throttle attempt to glen information about the fault zone implicated in the 2011 quake.  A collection of papers published this week in Science characterize the fault zone’s structure and composition, examined the physics underlying slippage during the quake, and tracked the physical conditions and stresses that the fault zone is exposed to, allowing an unprecedented understanding of the underlying causes of this natural disaster.

Chester et al, Ujiie et al, and Fulton et al   Science. December 6 2013.