Federal Circuit Affirms Invalidation of Agilent’s CRISPR-Cas gRNA Patents: Lessons on Enablement and Anticipation
Introduction
The Federal Circuit’s recent decision in Agilent Technologies, Inc. v. Synthego Corp. (Nos. 2023-2186, 2023-2187, decided June 11, 2025) signals an essential moment in the intersection of patent law and advanced biotechnology. This case scrutinized the validity of two Agilent patents covering chemically modified guide RNAs (gRNAs) for use in CRISPR-Cas genome editing—a technology at the forefront of genetic engineering. Synthego, a key player in synthetic biology, initiated inter partes review (IPR) proceedings that resulted in the Patent Trial and Appeal Board (PTAB) invalidating all asserted claims. On appeal, the Federal Circuit affirmed the PTAB’s decision, offering guidance on the requirements for anticipation, enablement, and obviousness in the context of rapidly evolving molecular technologies. The case underscores the challenges of securing and defending patent protection in a field where the pace of innovation and the breadth of prior art demand rigorous attention to technical detail and legal doctrine.
Patents at Issue
The litigation centered on two Agilent patents:
U.S. Patent No. 10,337,001 (“the ’001 patent”)
U.S. Patent No. 10,900,034 (“the ’034 patent”)
Both patents claim priority to a series of provisional applications, the earliest of which was filed on December 3, 2014.
Technology
The CRISPR-Cas system enables precise, targeted cleavage of DNA at specific sites within the genome. The gRNA and Cas protein assemble into a complex, with the gRNA serving as the “address label” that directs the complex to a particular DNA sequence. Once the gRNA binds to its target DNA, the Cas protein acts as molecular scissors, cleaving the DNA at that location. For this system to function efficiently, the gRNA must bind its target sequence, remain stable in the cellular environment, resist nuclease degradation, and maintain its ability to guide the Cas protein accurately. Unfortunately, in early CRISPR-Cas systems, degradation of gRNA was a problem.
The inventions at issue focus on chemically modifying the gRNA—specifically, by introducing changes to the phosphodiester backbone or sugar moieties at the 5′ and/or 3′ ends of the RNA molecule. These chemical modifications are designed to enhance the gRNA’s stability, protect it from degradation, and ensure it retains its functionality in guiding the Cas protein to the correct DNA target. The patents describe a variety of such modifications, including 2′-O-methyl, phosphonoacetate (PACE), and thiophosphonoacetate (thioPACE) groups, among others. By improving the chemical robustness of the gRNA, these inventions aim to make CRISPR-based gene editing more reliable and efficient in practical applications.
Representative Claims
Representative claim 1 of the ’001 patent:
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, or
(b) one or 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, a sugar, or both.
Representative claim 1 of the ’034 patent:
A synthetic CRISPR guide RNA comprising:
(a) a crRNA segment comprising (i) a guide sequence capable of hybridizing to a target sequence in a polynucleotide, (ii) a stem sequence; and
(b) a tracrRNA segment comprising a nucleotide sequence that is partially or completely complementary to the stem sequence,
wherein the synthetic guide RNA has gRNA functionality comprising associating with a Cas protein and targeting the gRNA:Cas protein complex to the target sequence, and comprises one or more modifications in the guide sequence, wherein the one or more modifications comprises a 2′-O-methyl.
The dependent claims narrowed the modifications of the nucleotides to particular types of phosphodiester linkage or sugar modifications and combinations thereof. For example, claim 8 in the ‘001 patent recites “[T]he synthetic guide RNA of claim 1 wherein said guide RNA comprises a modified internucleotide linkage or a modified terminal phosphate group selected from a phosphonocarboxylate, a phosphonoacetate, and a phosphonothioacetate group.” Claim 6 of the ‘034 patent recites, “[T]he synthetic guide RNA of claim 1, wherein said one or more modifications comprises a 2’-O-methyl nucleotide with a 3’-phosphonacetate.”
Prior Art
The key prior art was WO 2015/026885 (the ‘885 application) entitled, “Genome Modification Using Guide Polynucleotide/Cas Endonuclease Systems and Methods of Use”, filed by Pioneer Hi-Bred. The ‘885 application:
· Disclosed compositions and methods for employing a guide polynucleotide/Cas endonuclease system for genome modification of a target sequence in the genome of a cell or organism, for gene editing, and for inserting a polynucleotide of interest into a genome.
· Defined “guide polynucleotide” to mean a “polynucleotide sequence that can form a complex with a Cas endonuclease and enables the Cas endonuclease to recognize and optionally cleave a DNA target site”.
· Disclosed that a guide polynucleotide could be a single molecule or a double molecule, and a “guide polynucleotide” that solely comprises ribonucleic acids was also referred to as a “guide RNA”.
· Described in Example 4, modifying the nucleotide base, phosphodiester bond linkage, or molecular topography of the guiding nucleic acid component(s) of the guide polynucleotide/Cas endonuclease system for increasing cleavage activity and specificity.
· Disclosed that bond modification could be introduced to reduce unwanted degradation to increase the effective lifespan or stability of the nucleic acid component(s) of the guide polynucleotide/Cas endonuclease system in vivo.
According to Agilent, the ‘855 application also disclosed broad, prophetic examples of potential gRNA modifications but failed to demonstrate any working examples. Moreover, Agilent argued that the ‘855 application did not disclose the claimed modification but “over a quadrillion possible combinations,” without any guidance on which combinations would work.
In addition to the ‘885 application, the Board relied on two additional prior art references:
· Richard N. Threlfall et al., Synthesis and Biological Activity of Phosphonacetate – and Thiophosphonoacetate-modified 2’-O-methyl Oligoribonucleotides, 10 Org. Biomol. Chem., 746-54 (2011) (“Threlfall”).
o Taught chimeric 2’-O-methyl oligoribonucleotides (2’-OMe ORNs) containing internucleotide linkages modified with PACE or thio-PACE.
o Disclosed that oligoribonucleotides with 2’-OMe ORNs were known to be nuclease resistant and increase the stability of a duplex formed with complementary RNA.
o Disclosed that in a prior study, oligodexoynucleotides modified with PACE or thioPACE were nuclease resistant.
· Glen F. Deleavey et al., Designing Chemically Modified Oligonucleotides for Targeted Gene Silencing, 19 Chem & Bio. Review, 937-54 (2012) (“Deleavey”).
o Taught that there were several “obstacles” with using chemically modified oligonucleotides, including RNA molecules for gene regulation purposes such as (1) their poor extracellular and intracellular stability, (2) low efficiency of intracellular delivery to target cells or tissues; and (3) the potential for “off-target” gene silencing, immunostimulation, and other side effects.
o To overcome these “obstacles,” a vast array of chemical modifications had been developed, including specific chemical modifications to internucleotide linkages and to nucleotide sugars.
Proceedings before the PTAB
Synthego filed two IPR petitions for all claims of the ‘001 and ‘034 patents. The PTAB found all claims of both patents unpatentable. Specifically, the Board:
Held that the ‘885 application anticipated most claims of the two patents, finding that it disclosed functional, chemically modified gRNAs as required by the claims and that its disclosure was enabling.
Found that dependent claims reciting specific modifications (e.g., PACE, thioPACE), were obvious in view of the ‘885 application combined with Threlfall and Deleavey, which disclosed the relevant chemical modifications and their benefits for RNA stability.
Rejected Agilent’s arguments that the ‘885 application did not expressly disclose the required gRNA functionality or that its disclosure was not enabling, and also found a reasonable expectation of success for the claimed modifications.
Issues on Appeal
Agilent raised three issues before the Federal Circuit:
Whether substantial evidence supported the Board’s finding that the ‘885 application expressly disclosed the claimed gRNA functionality.
Whether the ‘885 application was enabling as an anticipatory reference.
Whether substantial evidence supported the Board’s finding that a skilled artisan would reasonably expect PACE and thioPACE modifications to gRNA in a CRISPR-Cas system to be successful.
Agilent also raised procedural arguments under the Administrative Procedure Act, claiming a lack of notice regarding the Board’s reasoning.
Federal Circuit’s Findings/Holding
The Federal Circuit affirmed the PTAB’s decisions in full, holding:
Anticipation: Substantial evidence supported the Board’s finding that the ‘885 application expressly disclosed gRNAs with the claimed functionality (association with Cas protein and DNA targeting). The Court rejected Agilent’s arguments that the ‘885 application merely proposed a research plan or failed to distinguish functional from non-functional guides.
Enablement:
The Federal Circuit summarized certain of the relevant case law regarding enablement of the prior art:
Prior art is presumed to be enabling. Impax Labs, Inc. v. Aventis Pharms., 545 F.3d 1312, 1216 (Fed. Cir. 2008).
A finding of anticipation does not require the actual creation or reduction to practice of the prior art subject matter – it only requires an enabling disclosure. Schering Corp. v. Geneva Pharms., 339 F.3d 1373, 1380 (Fed. Cir. 2003). An anticipatory reference only needs to enable subject matter that falls within the scope of the claims at issue, nothing more. Id. at 1381.
Enablement of the prior art requires that the reference teach a skilled artisan at the time of filing, to make or carry out what it discloses in relation to the claimed invention without undue experimentation. In re Morsa, 803 F.3d 1374, 1377 (Fed. Cir. 2015). For a prior-art reference to be enabling, it need not enable the challenged claim in its entirety, but only needs to enable a single embodiment of the claim. Id.
The Court found no error in the Board’s conclusion that the ‘885 application was enabling.
The Court distinguished this case from Impax and Amgen v. Sanofi, 598 U.S. 594 (2023), noting that the prior art provided sufficient guidance and exemplified the claimed modifications, and that a skilled artisan would not require undue experimentation to make and use the claimed inventions.
The prior art patent in Impax disclosed hundreds or thousands of compounds, several diseases, and broad and general dosage guidelines without sufficient direction or guidance to prescribe a treatment regimen.
Amgen was different in two ways. First, the issue in Amgen was whether the asserted claims were sufficiently enabling to be valid under 35 U.S.C. §112, not whether a prior-art reference was enabling and could support anticipation. This was an important distinction as §112 requires the specification to enable one skilled in the art to use the invention, whereas §102 does not require an anticipatory disclosure. Second, the patent in Amgen required painstaking experimentation to identify what worked. In contrast, the Board found that a person of ordinary skill in the art understood how the different elements of a CRISPR/Cas system were used and functioned together, including the role of gRNA; the types of chemical modifications that had been successfully used in other systems to reduce RNA degradation while preserving functionality, and that standard techniques for making gRNAs with modifications were disclosed and exemplified in the ‘855 application.
Obviousness: Agilent argued: (1) the ‘855 application did not expressly disclose the functionality of the claimed PACE- or thioPACE-modified guides; and (2) the Board failed to explain its reasonable expectation-of-success finding. The Court found neither argument persuasive and held that the Board’s findings regarding the obviousness of the dependent claims were supported by substantial evidence. The Court stated that obviousness did not require that all of the limitations in the dependent claims be expressly disclosed in the ‘855 application. The Court agreed that combining the ‘885 application with Threlfall or Deleavey would have motivated a skilled artisan to use PACE or thioPACE modifications with a reasonable expectation of success and that the Board provided a thorough analysis on both points.
Key Takeaways
Anticipatory Prior Art: Enablement Threshold: The Federal Circuit reiterated that for a prior art reference to be anticipatory, it need only enable a single embodiment within the scope of the claim, not the full breadth required under §112 for a patentee. This distinction is critical in biotechnology, where claims often cover broad classes of molecules or modifications.
Functional Limitations: Context Matters: The decision highlights that contextual disclosures and exemplified embodiments in prior art can satisfy functional claim limitations, even if every functional detail is not spelled out. Practitioners should be mindful that courts will look to the substance and context of disclosures, not merely their explicit language.
Obviousness in the Age of Advanced Techniques: By 2014, the art of chemically modifying RNA to improve stability was sufficiently mature that a skilled artisan would have had a reasonable expectation of success in applying known modifications, such as PACE and thioPACE, to CRISPR gRNAs. The case demonstrates that the bar for non-obviousness rises accordingly as technical knowledge in a field matures.
Enablement: Prior Art vs. Patentee Requirements: The Federal Circuit drew a clear line between enablement under §102 (anticipation) and §112 (patentee’s disclosure). While patentees must enable the full scope of their claims, an anticipatory reference only needs to enable what it discloses. This distinction was central to the outcome and is a key consideration for patent prosecution and litigation.
Final Thoughts
The Agilent v. Synthego decision is a cautionary tale for innovators in the life sciences: in fields characterized by rapid technical advancement and a deepening body of prior art, the hurdles for patentability are formidable. Applicants must demonstrate novelty and non-obviousness and ensure that their claims are sufficiently differentiated from what is already known, especially when relying on functional language or established chemical modifications. For practitioners, the case reinforces the necessity of comprehensive enablement analyses and a proactive approach to distinguishing claimed inventions from the prior art. As CRISPR and related genome editing technologies continue to evolve, this decision will serve as a touchstone for both patent prosecution and post-grant challenges, reminding stakeholders that robust patent protection demands both scientific and legal precision.
This post was written by Lisa Mueller.