The new IP battleground in CRISPR-Cas
While much attention has been focused on the major IP battle affecting foundational patents covering CRISPR-Cas9 systems as gene modifiers, another battle has erupted concerning modified guide ribonucleic acids (RNAs) for use with Cas enzymes. The most visible recent sign of this was the invalidation of all claims of two US Patents of Agilent, US10,900,034 and US10,337,001, by a Patent Trial and Appeal Board (PTAB) of the US Patent and Trademark Office (USPTO) in inter partes review proceedings instigated by Synthego.
These proceedings resulted in written decisions issued on May 17, 2023 as IPR2022-00402 and IPR2022-00403. Of particular importance in these proceedings was the fact that the independent claims specify a synthetic guide RNA (or crRNA) which has “gRNA functionality comprising associating with a Cas protein and targeting the gRNA:Cas protein complex to a target polynucleotide”.
For example, claim 1 of the ‘001 US patent reads: “A synthetic CRISPR guide RNA having at least one 5’-end and at least one 3’-end, the synthetic guide RNA comprising (a) one or more modified nucleotides within five nucleotides from said 5’-end, orone or (b) more modified nucleotides within five nucleotides from said 3’ end, or (c) both (a) and (b); wherein said guide RNA comprises one or more RNA molecules, and has gRNA functionality comprising associating with a Cas protein and targeting the gRNA:Cas protein complex to a target polynucleotide, wherein the modified nucleotide has a modification to a phosphodiester linkage, sugar or both.”
The claims of the ‘034 US patent focus on inclusion of one or more 2’-O-methyl modifications. Not surprisingly, Agilent has indicated intent to pursue appeal. This is even less surprising if one views more recent events on the European Patent Office (EPO) file for the corresponding European patent application, EP3227447A.
Prior art controversy
Issue of the above-noted IPR decisions was followed by the filing of anonymous third-party observations (TPOs) against the corresponding European application, but to no avail. The Rule 71(3) Communication (Notice of Allowance) issued soon after, with brief reasoning of the relevant Examining Division (ED) on why it saw the TPOs as providing no sound reasoning to back track from the proposed grant.
Further TPOs followed in October 2023 but have not had a better effect. Rather, they merely resulted in addition to the EPO file of a document entitled “Information about non-relevance of third-party observations”. It is especially notable that this document sets out at length why the ED disagrees with the third party observer and in its comments is expressing a divergent opinion from the PTAB on the key prior art document for both patentability of the claims in the above-noted US patents and the EPO claims of note, namely Published International Application WO2015/026885 in the name of Pioneer Hi-Bred International (designated document “D10”).
Ahead of the studies leading to the relevant patent application filings, it had long been the case that modified ribonucleotides such as 2-O-methyl ribonucleotides and ribonucleotides with phosphorothioate linkage had been included in RNAs such as interference RNAs to aid stability in cells.
Can patentability reside in transferring the same type of modifications to a functional gRNA? In answering this question, pertinent to inventive step, D10 introduces the additional question: does it matter that this document has a table providing sequences for a gRNA within the main independent claims but without any test data?
It is when considering this question that it is seen that the ED is not aligned with the PTAB. The ED has noted that Examples 4 and 5 of D10 provide relevant sequence information open to consideration for novelty and inventive step in light of priority analysis but that the same examples provide no data relating to testing of function of any modified gRNA as part of a CRISPR-Cas9 complex.
In response to raising those examples as prejudicial prior art for validity, the ED initially stated in response: “The skilled person reading D10 would conclude that D10 only discloses a suggestion to try such chemical modifications.. It is only a disclosure of candidate modified guide RNAs that still have to be tested because whether they work or not was unknown at the date of filing of D10. … It is obvious to try chemical modifications suggested in D10, but there was only a hope to succeed, no reasonable expectation of success.”
This view has since been reinforced by the ED with the addition: “This is, in the ED’s opinion, closer to an invitation to start a research programme than a ‘try and see’ situation.” The ED’s comments have not silenced the third-party observer but enticed still further observations to be added to the EPO file with view to securing withdrawal of the Notice of Allowance. Will the ED re-open examination or see post-grant opposition as the more appropriate route for the observer to pursue invalidity attack?
Clarity in 2024
In the meantime, EP3280803B (Agilent and Leland Stanford Junior University) which has in vitro method claims relating to use of a modified single guide RNA with a Cas protein for inducing gene regulation in a primary cell, is already under opposition with attack on the priority claims. The priority entitlement is important for relationship of the foundational PCT Application under Article 54(3) to the priority claims of EP322447A and the ability of a journal publication of the inventors to be cited as prior art: Hendel et al. Nature Biotech (2015): “Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells”.
The above-mentioned D10 has also given rise to a European Patent (EP3036327B) to Pioneer Hi-Bred which is under opposition (appeal oral proceedings scheduled for July 25, 2024) but interestingly with claims focusing on substitution in a guide RNA of a targeting component which is composed of DNA or a DNA/RNA hybrid. Such CRISPR hybrid RNA-DNA guides have been termed “Chardonnays” (chRDNAs) by Caribou Biosciences and are the subject of further patent claims in the name of Caribou Biosciences, including the claims of EP3250691B deriving from an application assigned from Pioneer Hi-Bred, and a related pending divisional.
Use of chRDNAs is promoted and under trial as a means of reducing off-target effects in taking CRISPR-Cas gene modification from lab to clinic for a number of therapeutic applications. Further guide RNA stability can be important for many CRISPR-Cas complex applications. So, while patent interference decisions in the US and EPO opposition appeal decisions in 2024 may bring some light to the IP complications over the use of Cas9 and other Cas enzymes, it is worth keeping in mind that a CRISPR-Cas complex must have a nucleic acid component for targeting and any modification of this cannot be ignored on the basis of the RNA interference (RNAi) art.
Claire Irvine is a partner and patent attorney at HGF. She can be contacted at cirvine@hgf.com
