Dr Malathi Lakshmikumaran and Dr Deepti Malhotra, experts from Lakshmikumaran & Sridharan, give an insight on how CRISPR-Cas9 system occurs naturally as an adaptive immune response in bacteria (prokaryotes) which use this system to detect and kill any viruses that infect them
The ability to manipulate an organism’s genome at will, and make precise changes without leaving a trace is among the holy grails of life sciences. This would allow scientists to find the cure for many genetic diseases, develop better crop varieties, among other varied uses and possibilities to develop breakthrough scientific discoveries. While several genetic engineering technologies have been developed, none demonstrate the accuracy and precision of a newcomer in this field called CRISPR-Cas9.
CRISPR-Cas9 system
CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats, while Cas9 stands for CRISPR-associated protein-9 nuclease and it is an enzyme. The CRISPR-Cas9 system is a complex of Cas9 protein with small ribonucleic acid (RNA), called crRNA. The crRNA acts as a guide for the enzyme to locate specific complementary target DNA sequences in an organism’s genome, while the enzyme, Cas9 possesses the ability to remove the target DNA sequence entirely, and/or introduce a desired sequence in its place. This system occurs naturally as an adaptive immune response in bacteria (prokaryotes) which use this system to detect and kill any viruses that infect them. Although the mechanism was discovered and elaborated in prokaryotes, scientists have now adapted this system for use in plants and animals (eukaryotes).
The patent battle: From origins to current status
The discovery and development of the CRISPR-Cas9 system can be credited to several different researchers over the last two decades, however, the two main groups who at present are involved in extensive patent litigations to claim the right over this invention are Jennifer Doudna and Emmanuelle Charpentier, represented by the University of Berkeley, California; and George Church and Feng Zhang, represented by the Broad Institute, Massachusetts. The Berkeley group were the first to file for a patent which is yet to be granted, while the Broad Institute filed an application for a patent in December 2012. As the Broad group opted for a fast-track review process, the patent was granted in April 2014 (US8697359 B1). The formal process for grant in the US is as per the first-to-file system which was instated post March 2013; however, as the Berkeley group’s application was filed in 2012 this system was not yet applicable. Therefore, they opted for patent interference proceedings against the Broad Group, which in simple terms means that the two patents were directed towards substantially the same invention. The proceedings begun in January 2016, and a year later in February 2017, the Patent Trial and Appeal Board (PTAB) passed a judgement in favour of the Broad Group.
The basis of the PTAB’s decision was on the Broad Group’s motion for no interference-in-fact. This in layman’s terms means that the two contested patents are separate entities that neither cancel nor refuse either party’s claims. The determination of interference is essentially based on the comparison of the claims of the stated invention (the two-way test), to determine if “the subject matter of a claim, would, if prior art, have anticipated or rendered obvious the subject matter of a claim of the opposing party and vice versa” 37 C.F.R 41.203(a).
The verdict was based considering the Berkeley group’s application constituting prior art. The assessment for lack of anticipation was based on the fact that the Berkeley group’s claims were not system i.e. organism specific, while the Broad group’s claims were specifically directed towards eukaryotic systems. Therefore, the judgement was in favour of no interference with regard to the anticipation of Broad group claims vs Berkeley group claims.
The assessment of obviousness was based on the criterion of “whether the prior art would have suggested to one of ordinary skill in the art that this process should be carried out and would have reasonable likelihood of success, viewed in the light of the prior art.” In re Dow Chemical Co., 837 F.2d 469, 473 (Fed. Cir. 1988). The point of significance in this judgment is the understanding of what is considered “reasonable likelihood of success”. In the PTAB’s view, this refers to an assumption that certainty of success is not a requirement. Medichem, S.A. v. 24 Rolabo, S.L., 437 F.3d 1157, 1165–66 (Fed. Cir. 2006), citing In re O’Farrell, 853 F.2d 894, 903–04 (Fed.Cir.1988). The decision was made with the analysis of several witness comments in the interference proceedings. While the board acknowledged Dr Doudna had expressed the intention to extend the system to eukaryotes, the expectation that system would work in higher systems was debatable. The board quoted that Dr Doudna had herself made several attempts to get the system to work in human cells, however, could not achieve success. While the Berkeley group cited evidence that several groups managed to adapt the system to eukaryotic systems only following their initial scientific publication of 2012, the PTAB was not persuaded by this argument as they maintained that this would not convince a person of ordinary skill in the art, that CRISPR-Cas9 is a system that could work well in eukaryotes as well.
While the judgement of the PTAB has been appealed by the Berkeley group, as it stands, the verdict causes ambiguity to the licensing process. While the Berkeley group’s claims are broad and cover the application of CRISPR technology across different platforms, the question as to whether licenses will be required from both or one of the contending groups is a source of confusion among companies. To add to the uncertainty regarding this technology, the EPO has recently favoured the grant of the Berkeley Patent. Furthermore, the Broad group’s patent has been recently revoked due to procedural issues with regards the inventors listed on the said patent filed at the EPO.
The Berkeley group has recently filed an appeal with the US Court of Appeals for the Federal Circuit in Washington, DC; to appeal the PTAB’s impugned decision on the lack of interference in favour of the Broad group that had given them the rights to a separate patent. The Broad group provided their arguments at the Appellate court on October 25, 2017, and the court ruled in favour of the Broad group.
Hence, the opposing decisions at the USPTO and the EPO and the various licenses that may be required by the third-party practitioners leave everything up in the air with regards the future of the CRISPR technology. Further, with the advent of the competing gene-editing technology within the CRISPR-Cas9 realm, like Cpf1 nuclease, C2c1, C2c2 and C2c3 nucleases to name a few, the competition is diversifying and the patent as well as licensing landscape only becoming more involved albeit confusing. None of the same patent battles mar the new CRISPR-nuclease systems, thus leading to more clarity in the associated patent landscape for the alternative CRISPR-nuclease systems.
Further, populating the confusion and yet providing options in the realm of gene-editing with similar systems is the recent compilation of studies published in Science issue dated January 25, 2018, where it is reported that 10 more immune systems have recently been discovered in bacteria that use inherent tools to protect themselves against phages and plasmids, opening up the possibility of addition of new tools to the molecular biology toolbox and opening the gene-editing patent landscape further.
A fight which is likely to be fought to the end, CRISPR-Cas9 future will pave the path to new advances in medical and agricultural sciences; the question of who owns the invention needs a ‘crisp’ resolution.
Licensing the disputed technology
Exclusivity in the market-place is a good place to stand, and the same holds true for exclusive licensing of the patented products, especially if the license-holder wishes to enter clinical trials. But, this may be difficult feat to achieve for a disputed and distributed technology such as Crispr gene-editing system, wherein a number of patent holders hold key patents and the pioneers have a confusing stand under the various jurisdictions. With that in mind, last year, Denver, Colorado–based MPEG LA, LLC formed a patent pool for CRISPR-Cas9 technologies, inviting relevant parties to submit their patented tools to a single consortium that would simplify the licensing process—one license would grant licensees access to the pool’s slew of patents. This should ease the pressure on the licensee and allow the access through non-exclusive licensing agreements to various players be it small or big and yet, allow profit to be gained by the patent owners through royalty payments. Since, the patent landscape for the Crispr-Cas9 system is ever-so crowded, licensing every relevant patent can be costly and time-consuming, restricting the number of licenses a small company can obtain. Thus, for a complex situation as that of the Crispr-Cas9 system and similar debated and shared technologies to emerge in the coming future. A pool, however, would allow the patent holders to achieve a broader scope of licensing of their IP rights, while promoting equivalent access to a greater and variant number of players. However, this leaves the issue of exclusivity, wherein a market monopoly incentivises companies to take on the costs and liability of developing CRISPR-based treatment for disease. There is a reason for the non-existence of similar patent pools for other therapies and medical advances. One approach may be to opt for target-specific, disease-specific exclusive licenses in therapy that would allow exclusive marketing albeit with the non-exclusive license of the foundational patents.
Would Crispr be one solution to all gene editing problems in disease?
While, CRISPR provides the probability to revolutionise therapy for genetic and environmental diseases via gene therapy, the genetic diversity in the nucleotide sequence level may stand in the way of one size fits all and prevent mass production of treatments. Variations in DNA sequences are common among humans as well as in patients, especially in diseases like cancer. Whereas, the therapy may be personalised to enhance efficacy and reduce off-target effects, it would still entail detailed genomic studies. Thus, the on-going and approved clinical trials are highly anticipated to determine the therapeutic potential of the Crispr system.
The issue of regulation or lack thereof?
Interestingly, in the realm of plants and agro-biotechnology, recent decisions from the United States Department of Agriculture (USDA) have stated that the CRISPR-Cas9-edited plants can be cultivated and sold in the markets free from regulation. The change in the USDA’s attitude towards genetically modified plants, which maintains a very stringent and unrelenting attitude towards genetically modified organisms (GMO) produced by Agrobacterium-mediated transformation and generation of transgenic plants that in USDA’s opinion comprise of foreign DNA from “plant pests,” the CRISPR-Cas9-edited plants have been deemed to lie outside such a scope because the technology manipulates or knocks out the plant’s own genetic material i.e. works on endogenous genes. Thus, CRISPR-Cas9-edited plants are slated to be given a free pass on entry into the market. However, the IP licensing on the same remains shrouded in doubt.