CRISPR – The Future of Synthetic Biology

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I am excited to be interning at Lux Capital this summer because I am passionate about commercializing emerging technologies. Lux’s focus on partnering with passionate entrepreneurs solving difficult hard science problems is an ideal platform for me to explore the technologies that will define the future. Today’s post is on a piece of technology known as CRISPR that has revolutionized the genetic engineering industry, and holds keys to a future often described in science fiction.

CRISPR

CRISPR, short for clustered regularly interspaced short palindromic repeats, is an important component of the CRISPR/Cas9 system for genomic editing. It represents a huge improvement over previous tools: Zinc finger nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs). The CRISPR/Cas9 system is much faster, more customizable, and cheaper than both Zinc fingers and TALENs, and has dramatically improved researchers’ ability to manipulate genomes.

Origin & Development

The origin and adoption of CRISPR/Cas9 for genomic editing is fascinating and quite serendipitous, since the original mechanism comes from nature. CRISPRs are repeated sequences of DNA that were first identified in the E. coli bacteria in the late 80s, but their true purpose and mechanism were not understood for approximately two and a half decades. These sequences are now understood to provide the bacteria with adaptive immunity. When attacked by viruses, bacteria can copy the virus’ genetic code and store it in between CRISPR sequences. Whenever the bacteria runs into the same virus again, this code is transcribed into RNA that corresponds with the viral DNA. A CRISPR associated protein (Cas protein) then cleaves the virus’ DNA, rendering it harmless. In this way, CRISPRs act as a library to store information on previous attacks, with future instructions on how to utilize Cas9 to identify and fight its assailants.

In 2012, Dr. Emmanuelle Charpentier and Dr. Jennifer Doudna published a groundbreaking paper that showed how you could use the CRISPR/Cas9 system with an RNA sequence to selectively cut DNA in a test tube. A few months later, Dr. George Church and Dr. Feng Zhang published two papers simultaneously that showed that this system could be used to edit genomic material within the human genome. Although some might argue that the later research applying the system to the human genome could not have happened without Charpentier and Doudna’s original work, the US Patent office rewarded US Patent No. 8,697,359 to Feng Zhang of the Broad Institute and MIT in April 15, 2015, sparking an intense patent battle.

Despite the patent ownership issues, use of CRISPR has rapidly increased amongst researchers. Over the last 10 years, papers mentioning CRISPR have skyrocketed from 6 in 2005 to 645 in 2014.

Application

CRISPR represents a major step change in genetic engineering for a number of reasons. First, CRISPR increases genomic editing speed, allowing researchers to perform the same experiments that used to take months, in days and weeks. Further, it is a magnitude of order improvement on cost from existing systems. Customized Zinc finger and TALENs systems can cost anywhere around ~$5000 or ~$500 respectively, while a CRISPR/Cas9 system can cost as little as $30. The increase in speed and reduction in cost provided by CRISPR will allow researchers to perform more experiments and reach conclusions and insights sooner. CRISPR’s use in genetic research has become ubiquitous in the three years since Charpentier and Doudna’s first paper.

Beyond being an improved tool for researchers, CRISPR’s promise lies in its potential for genomic disorders to be edited in vivo. Several papers have now been published claiming use of the CRISPR system to suppress or even inactivate and viruses such as the human papillomavirus and hepatitis B virus. More exciting is the potential for the system to be used to neuter disease carrying insects or even to directly fix genetic defects in living, breathing, humans.

However, this amazing potential does not come without its complications. The ease and low cost of CRISPR will make genetic engineering more feasible for research and inevitably drive towards modifying things even more controversial than genetically modified food. This risk is magnified when CRISPR is paired with what’s known as a “gene drive,” which biases inheritance such that populations are significantly more likely to inherit modified genes. While this combination of techniques is very powerful and could allow for a rapid defense against parasites or harmful organisms, any hidden consequences would be drastically exacerbated. This tremendous potential has already led to rapid experimentation including a recent controversial experiment editing the genome of monkey embryos.

To illustrate the danger, I’d like to tell a hypothetical story that could happen 5 years from now: CRISPR technology has developed to the point that we are able to modify one of the parasites that causes malaria, Plasmodium falciparum. P. falciparum is THE worst malaria causing parasite, responsible for the most malarial deaths every year. By coupling a clever CRISPR edit with a gene drive, scientists can change P. falciparum‘s code to render it harmless. The gene drive allows this edit to spread throughout the population of parasites in a matter of weeks. While this looks like a huge net positive for humanity, genetics is a complex beast. This genomic edit actually results in a previously unknown secondary effect that allows P. falciparum to cause a malaria-like disease in cattle wiping out food supply. If this story sounds like scary science fiction, it should. However, what makes this story scarier is that multiple papers have already been published about using CRISPR to edit P.falciparum, indicating that this hypothetical story may be a reality much sooner than 5 years from now.

The Future

Several startups have sprouted in the last year and a half with varying degrees of involvement from the original authors of the aforementioned groundbreaking papers. Despite the ongoing patent battle, Caribou BiosciencesEditas Medicine, CRISPR Therapeutics, and Intellia Therapeutics have all been founded in the past few years. Though their websites describe their mission in a vague way, these startups are focused on developing therapies based on editing the human genome using CRISPR. Though gene therapy has made progress in the past few decades, previous solutions have been limited to development of specific therapies targeted at individual genetic problems. CRISPR offers a platform that allows for rapid customization of therapies.

Here are a few business cases that CRISPR could achieve:

  1. Build a research platform – Build a product/service that reduces researcher pain points. Cost may be difficult to reduce, but time to run experiments, control of inputs, and standardized reproducibility could all be improved.
  2. Build a delivery system – Until now, gene therapy has been limited by our ability to deliver healthy genes to where they are needed in the body. CRISPR offers a mechanism for editing genes in situ, but some sort of delivery system is still necessary to get the desired CRISPR system in the right cell at the right location.
  3. Build a killer app – Develop a targeted gene therapy that was previously unachievable. This path was possible prior to the development of CRISPR, but CRISPR has dramatically reduced the difficulty of doing so. Large inherited genetic disorder markets such as hemophilia or cystic fibrosis could be targeted.

Despite the tremendous potential for CRISPR applications outside of research, there needs to be a dialogue to develop rules and protocols that protect against rash use of CRISPR that could irreversibly alter ecosystems. Nonetheless, the discovery of CRISPR is an immediate step change improvement for researchers, with long-term implications that are promising, potentially risky, but currently undetermined.

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