Further to my recent article about the 2020 Nobel Prize announcements, the winners of the 2020 Chemistry Nobel Prize were announced as Emmanuelle Charpentier and Jennifer Doudna on 7 October 2020 "for the development of a method for genome editing". This, of course, refers to the revolutionary “genetic scissors” technology, CRISPR/Cas9. For this article, I’ve teamed up with my colleague Jamie Atkins, whose specialisms include prosecution of CRISPR-related patent applications at the EPO, to get into the details of the winning technology.
In this article, we explore:
Diversity in the Chemistry Nobel Prize;
The winning technology;
What is CRISPR and how does it work?;
How can CRISPR be used?;
CRISPR Patents; and
The future – could CRISPR be used to combat COVID -19?
Diversity in the Chemistry Nobel Prize
Before looking at the patent side of things, it is worth noting that this is the first Nobel Prize awarded to two women. Charpentier commented shortly after the prize announcement that:
“My wish is that this will provide a positive message to the young girls who would like to follow the path of science, and to show them that women in science can also have an impact through the research that they are performing… This is not just for women, but we see a clear lack of interest in following a scientific path, which is very worrying”.
While there is still a significant gender gap in the Laureates of the Chemistry Nobel Prize, it is encouraging that there are now an additional two female winners to add to the previous five: Marie Curie (1911), Irène Joliot-Curie (1935), Dorothy Crowfoot Hodgkin (1964), Ada Yonath (2009) and Frances H. Arnold (2018). We hope this figure continues to increase each year, along with wider recognition of other under-represented groups, for example in terms of BAME and LGBTQ+ representation.
The winning technology
At face value, CRISPR/Cas9 (“CRISPR”) seems to be more biological than chemical, but this only serves to highlight the breadth of chemistry as a field. As described in Nobel’s will, the Nobel Prize in Chemistry is to be awarded to “the person who shall have made the most important chemical discovery or improvement”, and this requirement is surely met by CRISPR.
What is CRISPR and how does it work?
The CRISPR/Cas9 editing tool developed by the Nobel Prize winners is based on the discovery of a naturally occurring system used by bacteria to defend against viral infection. When a virus is detected, the bacteria produce short RNA sequences that guide a DNA cutting enzyme (Cas9) to viral DNA matching the RNA sequence. Cas9 cuts the viral DNA, thereby disabling the virus. Doudna and Charpentier made several important discoveries leading to a better understanding of this bacterial system, developed a simplified version of the system and crucially showed that it could be programmed to target almost any DNA sequence of interest, as reported in the seminal Jinek et al. 2012 paper:
''Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA‑programmable genome editing”.
The basic components of the CRISPR/Cas9 system are the DNA cutting enzyme (Cas9) and the guide RNA based on the target DNA sequence, which directs the nuclease to the desired cutting location. Once the DNA in a cell is cut, the cell tries to fix the break using its own repair mechanisms. Due to the error-prone nature of such mechanisms, this “fix” can actually disable a gene. Alternatively, by supplying a template sequence together with the CRISPR machinery, the cell’s DNA repair mechanisms can be exploited to replace a section of DNA with the template sequence of choice.
Building on this foundational work of the Nobel Laureates, many complementary genome editing tools based on the CRISPR principle have been developed. For example, in a technique known as “base editing”, a deactivated Cas9 is fused to a cytidine deaminase enzyme, which allows targeted conversion of the cytidine base (“C”) to thymine (“T”) without cleaving the DNA (Komor et al, 2016). Another example is “prime editing”, in which deactivated Cas9 is fused to reverse transcriptase. This is coupled with a guide RNA that specifies the target site and encodes a desired replacement sequence, allowing new genetic information to be written into a specified DNA target site (Anzalone et al, 2019).
How can CRISPR be used?
There are innumerable exciting possibilities that stem from the ability to edit the genome of any living cell in a targeted manner using these basic principles. For example, CRISPR is already revolutionising genetic research by providing a quicker and easier way for researchers to knock out specific genes in order to investigate the function of those genes and their role in cellular pathways. There also important applications in agriculture, where it is being used to speed up the generation of improved crop varieties and could play an important role in food security.
Another key application is in the filed of diagnostics (more on that below), but perhaps one of the most exciting and lucrative CRISPR applications is in the field of medicine. Doudna is a co-founder of Intellia and Charpentier is a co-founder of CRISPR Therapeutics, both of which are developing CRISPR-based therapies, some of which are already in early stage clinical trials, e.g. for the treatment of sickle cell anaemia. Many current trials involve editing the genome of cells extracted from the body (e.g. hematopoietic stem cells) before reinserting the modified cells back into the patient. An alternative approach also being explored is delivering the CRISPR machinery directly into the body, for example to disable faulty disease-causing genes. This year saw the first delivery of CRISPR machinery to a patient in an attempt to treat an inherited form of blindness called Leber congenital amaurosis 10 (LCA10).
Any new technology with such a great potential for commercial application is an ideal candidate for patent protection. The European Patent Office (EPO) has published 32 European patent applications naming Doudna as an inventor and 7 European patent applications naming Charpentier as an inventor. Patent applications are published 18 months after their effective filing date, so there may be many more unpublished patent applications that have already been filed naming these Laureates as inventors.
CRISPR patents have also been at the centre of attention in both Europe and the US over recent years. In Europe, we’ve seen the high-profile “CRISPR priority” appeal, in which one of the Broad Institute’s fundamental CRISPR patents (EP2771468, claiming an earliest priority date of 12 December 2012) was revoked for lack of novelty over some of the seminal CRISPR papers. These papers became prior art because the patent was found not to be entitled to its claimed priority dates (see our articles here, here and here from earlier this year for the details). Doudna and Charpentier’s patents have also come under attack in Europe; their 2013 patent EP2800811 was opposed by seven parties, and maintained in amended form in May 2020.
In the US, high profile interference proceedings between University of California and others and the Broad Institute and others (“Broad”) before the US Patent Trial and Appeal Board culminated in a decision in favour of Broad, which was upheld in 2018 by the Court of Appeals for the Federal Circuit. Further such proceedings are currently in progress.
Stay tuned for a more in-depth discussion of the ongoing challenges relating to CRISPR patents.
The future – could CRISPR be used to combat COVID -19?
Shortly after the Nobel Prize was announced, Charpentier was asked whether CRISPR could be used to make a vaccine for COVID-19. She indicated this was unlikely in a direct way, but that it could be useful indirectly by allowing researchers to understand the virus in ways that help them develop a vaccine (e.g. understanding what is important for the virus to replicate). The full Q&A with Charpentier is available here.
It has in fact already been deployed in a fast and accurate diagnostic test for Covid-19. This test, referred to as SARS-CoV-2 DNA Endonuclease-Targeted CRISPR Trans Reporter (DETECTR), harnesses the targeting function of the guide RNAs of the CRISPR system to bind to coronavirus sequences, and the cutting function of Cas12 (a nuclease related to Cas9) to cleave a reporter molecule, to confirm detection of the virus. Fittingly, Doudna’s own lab recently announced its own CRISPR-based diagnostic test that can detect SARS-CoV-2 in just 5 minutes. This high processing speed is achieved by avoiding the need to amplify the viral genome (as required by earlier assay formats). Instead, the new test uses combinations of CRISPR RNA which target different parts of the virus RNA and activate multiple Cas nucleases (Cas13a) per piece of viral RNA, boosting the fluorescent signal generated when a reporter molecule is cut. Moreover, the researchers showed that the fluorescence could be measured with a mobile phone camera, “demonstrating the simplicity and portability” of the assay.
As mentioned above, clinical trials involving CRISPR-based approaches are already underway, and we look forward to seeing more success stories in the coming years. While these are no doubt exciting times, it is clear that extreme caution must be exercised to fully understand and mitigate the risk of CRISPR acting off-target. There are also ethical debates to be had about how far to take gene editing. Should scientists be permitted to introduce heritable changes into the genome even if this can be done safely and efficiently?
One thing is for sure, the work conducted by Doudna and Charpentier has revolutionised the field of genetic engineering, and for that work these inspirational inventors should be celebrated.
For more information or advice, please contact Jessica Smart, Jamie Atkins or your usual Kilburn & Strode advisor.