The Federal Court of Australia has delivered judgement in Australia’s landmark CRISPR patent dispute, finding that none of the claims in ToolGen Inc.’s patent application for platform CRISPR technologies are valid. The proceeding is an appeal from a decision of the Commissioner of Patents in which the first respondent – a strawman named Grant Fisher – successfully opposed the grant of ToolGen’s application.
The patent application
The case concerned ToolGen’s application for CRISPR/Cas systems and the use of those systems to introduce a site-specific, double stranded break at a target nucleic acid sequence in a eukaryotic cell.
The application was filed on 23 October 2013 and claims priority from three provisional applications:
- US Provisional Patent Application 61/717,324 (“P1”) filed 23 October 2012;
- US Provisional Patent Application 61/803/599 (“P2”) filed 20 March 2013; and
- US Provisional Patent Application 61/837,481 (“P3”) filed 20 June 2013.
The application includes two independent claims:
Claim 1. A composition comprising a Type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas system for use in introducing a site-specific, double stranded break at a target nucleic acid sequence in a eukaryotic cell, said CRISPR/Cas system comprising (i) a nucleic acid encoding a Cas9 polypeptide comprising a nuclear localization sequence, and (ii) a nucleic acid encoding a guide RNA that hybridizes to a target nucleic acid, wherein the guide RNA is a chimeric guide RNA comprising a CRISPR RNA (crRNA) portion fused to a trans activating crRNA (tracrRNA) portion.
Claim 10. A method of introducing a site-specific, double-stranded break at a target nucleic acid sequence in a eukaryotic cell, the method comprising introducing into the eukaryotic cell a Type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas system, wherein the CRISPR/Cas system comprises:
(a) a nucleic acid encoding a Cas9 polypeptide comprising a nuclear localization signal, wherein the nucleic acid is codon-optimized for expression in eukaryotic cells, and
(b) a nucleic acid encoding a guide RNA that hybridizes to the target nucleic acid, wherein the guide RNA is a chimeric guide RNA comprising a CRISPR RNA (crRNA) portion fused to a trans activating crRNA (tracrRNA) portion, wherein the target nucleic acid sequence comprises a first strand that binds to the crRNA portion and a second strand having a trinucleotide protospacer adjacent motif (PAM), and wherein the Cas9 polypeptide and the guide RNA form a Cas9/RNA complex in the eukaryotic cell, whereby a site-specific, double stranded break at the target nucleic acid sequence is introduced.
Several grounds of validity turned on the meaning of the words “nucleic acid encoding a guide RNA” in both independent claims. ToolGen sought a broad construction of these words, arguing that they encompass both DNA which is transcribed to RNA in a eukaryotic cell and RNA which is transcribed in vitro prior to it being introduced into a eukaryotic cell.[1] ToolGen argued that the verb “encoding” can mean both providing the sequence for producing the guide RNA (through the process of transcription from DNA to RNA) as well as providing the sequence that enables the guide RNA to perform its function.[2] ToolGen placed considerable reliance on claim 19 which, when read with claim 10, requires that the nucleic acid encoding the guide RNA is in vitro transcribed RNA:
Claim 19. The method of any one of claims 10-16, wherein the nucleic acid encoding the guide RNA is in vitro transcribed RNA.
Justice Nicholas rejected these arguments, finding that claim 10, when read in the context of the specification as a whole, indicates that the claim is limited to a method in which the nucleic acid encodes the guide RNA, and that the guide RNA is transcribed from nucleic acid in the eukaryotic cell.[3] His Honour found that the term “encoding” should be given its ordinary meaning as understood by those skilled in the art:
In my opinion, the word “encoding” is used in claim 10 in its conventional sense (ie. as it would be understood by a molecular biologist) to refer to the production of a Cas9 polypeptide by transcription and translation and the production of a guide RNA by transcription in the cell. The nucleic acid referred to in the claim provides the information which is used in the cell to produce the guide RNA. Claim 10 does not encompass a system in which an existing guide RNA is introduced into the cell.[4]
As a consequence of this construction, claim 19 could not be read sensibly with claim 10 and was found to lack clarity.[5]
The priority date
The hearing of the appeal was conducted on the premise that if the claims were not entitled to priority based on P1, then a deferred date of 20 June 2013 established by the filing of P3 would apply. P2 was solely concerned with a method of using RNA-guided endonucleases in restriction fragment length polymorphism analysis, and was not considered to disclose the invention of any of the claims in the patent application.
P1 is a relatively short document; it does not include any claims and resembles a journal article to which an additional paragraph headed “Summary of the Invention” had been added. The CRISPR/Cas9 system described in P1 was derived from Streptococcus pyogenes and used a single chimeric guide RNA comprising a crRNA portion fused to a tracrRNA produced in vitro. P1 did not disclose a system in which DNA (or viral RNA) is introduced into the cell in order to transcribe the guide RNA in vivo. P1 also did not describe what other bacterial species have Type II CRISPR/Cas systems or how to determine the endogenous crRNA and tracrRNA sequences for such a species.
The question, then, was whether the disclosure of P1 was sufficient to establish a priority date for any of the claims in ToolGen’s application.
The priority date test in Australia is the same as the test for sufficiency of disclosure. That is, each claim is entitled to claim priority from an earlier application, provided the earlier application discloses the claimed invention in a manner that is clear enough, and complete enough, for the invention to be performed by a person skilled in the relevant art.[6]
In relation to the words “nucleic acid encoding a guide RNA”, his Honour accepted that it would not be a difficult exercise for a molecular biologist in possession of the information in P1 coupled with the common general knowledge to use a plasmid encoding a guide RNA to produce the guide RNA in vivo using standard techniques that were well known at the priority date. His Honour also accepted that it would be obvious to the skilled addressee that he or she could use plasmid DNA encoding a guide RNA as a means of generating the guide RNA in the cell.[7]
However, P1 did not disclose the use of DNA (or viral RNA) encoding a guide RNA, as defined in the claims but, rather, a guide RNA produced in vitro which is then introduced into the cell. His Honour found that P1 did not disclose the same invention as that claimed in ToolGen’s application, and as such, that none of the claims were entitled to claim priority from P1:
Claims 1 and 10 (and, with the exception of claim 19, the dependent claims) are directed to an invention in which the guide RNA of the claims is introduced into the cell in the form of nucleic acid (DNA or viral RNA) which then encodes the guide RNA in the eukaryotic cell. P1 does not disclose any such system either explicitly or implicitly. It follows that those claims are not entitled to priority based on P1.[8]
The next question was whether P1 discloses a system for cleaving DNA using a Cas9 polypeptide derived from a bacterial species other than S. pyogenes in a manner which is clear enough and complete enough for the claimed invention to be performed by a person skilled in the art. It was common ground among the parties that P1 disclosed a CRISPR/Cas9 system derived from S. pyogenes. Nicholas J accepted that P1 disclosed, in a general sense, the existence of Cas9 proteins derived from other bacterial species and the possibility that they may be used to mediate DNA cleavage in eukaryotic cells.[9] However, the possibility of using Cas9 proteins derived from other bacterial species was described as just that – a mere possibility. P1 did not include any further discussion of this possibility, nor did it present any evidence or commentary from which it may be inferred that all, or even some, Type II Cas9 proteins derived from other bacterial species could reasonably be expected to work with particular PAMs to mediate DNA cleavage in eukaryotic cells.
Moreover, there was nothing disclosed in P1 which would indicate that S. pyogenes was likely to be representative of other bacterial species with a Type II CRISPR/Cas system or that the results of the experimentation with S. pyogenes derived components provided any reasonable scientific basis for inferring that Cas9 polypeptides derived from other bacterial species could also be expected to cleave DNA in eukaryotic cells.[10] In that context, the evidence showed there was considerable uncertainty as to whether or not a CRISPR/Cas9 system derived from any particular bacterial species other than S. pyogenes would work in eukaryotic cells, and that significant experimental work would need to be done to validate the use of the system in eukaryotic cells.[11]
His Honour found that the work that the person (or team) skilled in the art would need to undertake at the priority date to perform the invention of claims 1 and 10 using a bacterial species other than S. pyogenes would involve a significant research project:
In my opinion the skilled team would be required to carry out prolonged research and experimentation and would most likely encounter significant difficulties along the way. Much of the work would be non-routine and would be carried out in circumstances where P1 provided no meaningful guidance or direction and no assurance of success.
I am persuaded that as at the priority date, P1 did not enable a skilled team including a molecular biologist specialising in genome editing in eukaryotic cells and a microbiologist with expertise in CRISPR/Cas systems in prokaryotes, to make the compositions of claim 1, or perform the methods of claim 10, using a bacterial species other than S. pyogenes, without undue burden.[12]
With regard to the guide RNA itself, P1 disclosed a single chimeric guide RNA comprising a crRNA portion fused to a tracrRNA portion without providing any information as to how it was designed or how its length might be altered.[13] Nicholas J considered that it would be an undue burden for the skilled person to redesign the single guide RNA disclosed in P1 or to design and construct a single guide RNA using a bacterial species other than S. pyogenes.[14]
His Honour found that P1 failed to disclose the claimed invention in a manner that was clear enough, and complete enough, for the invention to be performed by a person skilled in the relevant art. None of the claims were entitled to claim priority from P1.
Enablement
Section 40(2)(a) of the Patents Act 1990 (Cth) states that a complete specification must disclose the invention in a manner which is clear enough and complete enough for the invention to be performed by a person skilled in the relevant art. The requirement for enablement is similar to that applicable in other jurisdictions, particularly Europe and the UK.
The respondents accepted that the patent application, unlike P1, discloses an invention that comprises “a nucleic acid encoding a guide RNA”. They did not contend that the invention of the claims is, in this particular respect, not sufficiently enabled.
However, none of the examples disclosed in the patent application used CRISPR/Cas9 components from any species other than S. pyogenes. The respondents submitted that the patent application did not enable an invention comprising a system derived from a bacterial species other than S. pyogenes without undue burden. His Honour accepted that submission essentially for the reasons given in relation to P1.[15]
Similarly, in relation to the guide RNA, there was considered to be no material difference between the disclosures of P1 and the patent application regarding the design of the sgRNA including its tracrRNA component. Accordingly, his Honour found that the patent application did not provide an enabling disclosure of a sgRNA having a length different from that disclosed in the patent application.[16]
Support
Section 40(3) of the Patents Act 1990 (Cth) states that the claims must be supported by the matter disclosed in the specification. This provision requires that the technical contribution to the art disclosed by the specification justify the breadth of the claim.[17]
In considering the overlapping requirements of enablement and support, his Honour noted that there may be instances where a claim might meet the requirements of section 40(2)(a) by providing an enabling disclosure, but not meet the requirement of section 40(3). However, he found it difficult to see how a claim to an invention for which there was no enabling disclosure could meet the support requirement because, in such circumstances, the scope of the monopoly defined by the claim could not be justified by the technical contribution to the art.[18] Having found that the invention was not sufficiently enabled under section 40(2)(a), his Honour found that all of the claims lacked support under section 40(3).
Novelty and inventive step
Three journal articles published after the filing date of P1 but before the filing date of P3 were relevant to the issues of novelty and inventive step:
- Cong et al, “Multiplex Genome Engineering Using CRISPR/Cas Systems” (2013) Science 339, 819-823 and Supplementary Materials;
- Mali et al, “RNA-Guided Human Genome Engineering via Cas9” (2013) Science 339, 823-826 and Supplementary Materials; and
- Wang et al, “One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering” (2013) Cell 153, 910-918 and Supplementary Information.
Having decided that ToolGen’s application was not entitled to the priority date established by P1, his Honour found that claims 1 to 20 lacked novelty and an inventive step, and that claim 21 lacked an inventive step in light of the prior art.
ToolGen has the option of applying to amend its claims. However, the respondents have already foreshadowed that they will oppose any such application that may be made by ToolGen.
[1] ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 (ToolGen FCA) at [114].
[2] ToolGen FCA at [122].
[3] ToolGen FCA at [130].
[4] ToolGen FCA at [143].
[5] ToolGen FCA at [145].
[6] Patents Act 1990 (Cth) s 43(2) and (2A); Patents Regulations 1991 (Cth) regs 2.12(4) and 3.13A.
[7] ToolGen FCA at [207].
[8] ToolGen FCA at [212].
[9] ToolGen FCA at [221].
[10] ToolGen FCA at [320].
[11] ToolGen FCA at [325], [327]-[328].
[12] ToolGen FCA at [362]-[363].
[13] ToolGen FCA at [366]-[377].
[14] ToolGen FCA at [369]-[370].
[15] ToolGen FCA at [387].
[16] ToolGen FCA at [388].
[17] Merck Sharp & Dohme Corporation v Wyeth LLC (No 3) [2020] FCA 1477, [547].
[18] ToolGen FCA at [410].