Cover image of 3rd Annual Re-writing Genomes conference program. Image credit to Innovative Genomics Initiative (IGI).

Cover image of 3rd Annual Re-writing Genomes conference program. Image credit to Innovative Genomics Initiative (IGI).

For the past few years, at the end of August, UC Berkeley has played host to a prestigious and cutting edge conference on genome engineering. This conference is organized by Dirk Hockemeyer and Jennifer Doudna. The very way in which genome engineering is done dramatically changed due to the Doudna Lab’s research involving a bacterial protein system, CRISPR/Cas 9. This system has dramatically decreased both the time and specialized expertise needed to perform genome engineering in the laboratory. In recognition of this discovery Dr. Doudna has been featured in TIME, and won a Breakthrough Science Award among other honors. The CRISPR/Cas9 system was a shared discovery with Dr. Emmanuelle Charpenteir, who also spoke at the conference. On August 24th, I attended the third annual Re-Writing Genomes conference at UC Berkeley. The conference was an enlightening experience and an excellent way to hear the very latest discoveries and paths of inquiry across the country in the field of genetic engineering.

CRISPR Cas9 diagram

Graphical representation of the CRISPR/ Cas 9 system performing a genetic correction with a donor DNA strand. Image credit, Barbara J. Bailus.

The opening talk was given by Jennifer Doudna and she focused mostly on the continuing basic science research being done on the CRISPR/Cas9 system (to learn more about this system see our previous blog here). This basic science approach is extremely important to better help understand how to best utilize CRISPR/Cas 9 as a potential therapeutic. The actual discovery of the CRISPR/Cas 9 system came from a basic science inquiry, in which Doudna’s lab was examining bacterial immune responses to viral infection. CRISPR/Cas 9 is a bacterial immune system that is able to target bacteria infecting viral DNA. The CRISPR/Cas 9 system has since been co-opted by scientists to target and modify any organisms DNA, creating a powerful tool for genetic manipulation. With this powerful tool comes ethical concerns, of which the genome engineering filed is increasingly aware of, a few months ago scientists in China used the CRISPR/Cas 9 system to genetically modify human embryos (see our SAGE blog on this ethical discussion). None of the embryos were brought to maturity, but the ethics of engineering human embryos is a serious concern. In light of these experiments, a future summit discussing the ethical implications with the leading scientists, and other professionals will be taking place this fall. This is the first step in future discussions about how this new technology should progress. It was refreshing to hear such a prominent scientist acknowledge the ethical implications of this work, and to encourage those present to participate in such discussions.

A major concern emerging from the study in China done on human embryos was the “off-target” effects from CRISPR/Cas 9. Scientists in the genome engineering field have known about the perils of having multiple “off-target” events, where there is cutting of the DNA at a non-targeted site, often resulting in a mutation. This problem is relatively harmless in cell culture, where one can screen cells and select against those with off-target events. In the case where minimization off target effects is needed, such as a therapy where cells are genetically corrected and then re-inserted into the donor, full sequencing on the cells could be performed before giving the genetically modified cells back to the donor. However, if one is intending to actually perform the genome engineering inside the patient, then these potential safeguards can’t be applied. To make in-vivo genetic correction possible, off-target sites must be minimized and predictable, in order to best understand potential side effects of the treatment. Several of the talks focused on this issue, with better screening tests for off-target sites, how to choose more specific target sites or how to change the Cas 9 itself to make it more discriminating when binding a target site. The work presented sounds extremely promising. Although, I doubt there will ever be a Cas 9 that only binds to one site in the DNA, I do feel that the prediction of potential off-target sites in dramatically improving, making it possible to understand what potential side-effects of a CRISPR/Cas 9 treatment might have.

Dr. Emmanuelle Charpenteir started her talk reminding us scientists that what seems impossible now, will be ordinary in the future, when she quoted Dr. Jacques Monod who stated “humans will never be able to manipulate DNA.” At a conference where the attendees manipulate DNA everyday this elicited a good laugh. Her talk focused mostly on how exactly the CRISPR/Cas 9 is able to recognize viral DNA. The CRISPR/Cas 9 system also includes a “library” of viral DNA that when transcribed into RNA joins with the Cas 9 protein, creating an active CRISPR system, this then binds to the viral DNA that has infected the cells and cuts it into pieces. The exact way in which this “library” of viral DNA is assembled is a topic of much investigation in multiple labs. One of the aspects I enjoyed most about this talk was that it reminded me of how important basic science research is, and how it forms the foundation for translational science and therapeutics.

CRISPR Graph

Graph representing the exponential increase in CRISPR/Cas 9 associated publications in the last 13 years. Image credit, PubMed.

Several of the talks highlighted the applied use of the CRISPR/Cas 9 system toward understanding human diseases or even the potential to cure them. One method presented used the CRISPR/Cas 9 system to screen cancer cells for genes that could be novel targets for cancer treatment.  The screen was a success with several new potential targets uncovered.  Someday it might even be possible to utilize the screening method on an individual patient basis, to understand what a single patients cancer is vulnerable to, moving personalized medicine toward reality. Even closer toward moving from bench to bedside was the presentation given by Sangamo, a company focused on bringing genome engineering to medicine. Sangamo chose to highlight on of their many in development products, this one utilizing Zinc Finger Nucleases (another type of genome engineering protein) targeted toward restoring Factor IX, the blood clotting factor that is missing, in hemophilia patients. Their methods sounded extremely promising, showing marked improvement in clotting time in pre-clinical animal trials. I suspect in 10-15 years we may see this come to market. This was a fitting to the conference as it allowed for the audience to see the evolution of a basic science discovery through to a clinical application. The technology of CRISPR/Cas 9 seems to be ever expanding, like a new galaxy being born, in 15 years it will potentially be a standard of care for genetic screens and genetic diseases. CRISPR/Cas 9 enters a new phase as the ethics surrounding its use are now being discussed, this signifies that the technology has advanced enough to inspire serious discussions on its use beyond the research lab. The next few years should be extremely exciting as this technology goes from discovery to tool to therapeutic.