Associated British Foods v. Cornell Research Foundation Inc

1. Case Identification

• Case #: IPR2019-00579
• Patent #: 7,829,318
• Filed: January 23, 2019
• Petitioner(s): Associated British Foods PLC, AB Vista, Inc., PGP International, Inc., Abitec Corporation, AB Enzymes, Inc., and AB Enzymes GmbH
• Patent Owner(s): Cornell Research Foundation, Inc.
• Challenged Claims: 1-5

2. Patent Overview

• Title: Overexpression of Phytase Genes in Yeast Systems
• Brief Description: The ’318 patent discloses methods for producing the enzyme phytase, which is used as an animal feed additive. The claimed method involves expressing an E. coli appA polynucleotide in a Pichia yeast host to produce a phytase that exhibits increased thermostability compared to the same phytase expressed in E. coli.

3. Grounds for Unpatentability

Ground 1: Claims 1-5 are obvious over Kretz, Cheng, and Olsen

• Prior Art Relied Upon: Kretz (Patent 5,876,997), Cheng (Patent 5,985,605), and Olsen (a 1991 journal article).
• Core Argument for this Ground:
  • Prior Art Mapping: Petitioner argued that Kretz disclosed an E. coli phytase (an obvious variant of the claimed appA phytase) and taught expressing it in yeast hosts. Cheng taught specific methods for producing bacterial phytases in the yeast Pichia to achieve high yields and efficiency. The combination of Kretz and Cheng rendered the core process of claim 1 obvious. Olsen taught that expressing a bacterial enzyme in yeast, as opposed to a bacterial host like E. coli, results in glycosylation that confers substantially higher thermostability. This teaching supplied the "increased thermostability" limitation of claim 1. Dependent claims reciting secretion via a signal peptide (claim 2), high concentration yields (claim 3), use of a transcriptional enhancer (claim 4), and a stable vector (claim 5) were all argued to be disclosed or suggested by Kretz and Cheng as standard, well-known techniques in recombinant protein production.
  • Motivation to Combine: A POSITA would combine Kretz’s highly stable E. coli phytase with Cheng’s efficient Pichia production system to increase the volume and efficiency of enzyme production while reducing costs. Olsen provided a further, independent motivation by teaching that such a combination would be expected to improve the enzyme’s thermostability, a desirable characteristic for commercial animal feed additives.
  • Expectation of Success: A POSITA would have a high expectation of success because Kretz already taught expressing its phytase in yeast, and Cheng provided established methods for expressing various bacterial phytases in the well-characterized Pichia host system.

Ground 2: Claims 1-5 are obvious over Greiner, Dassa, Cheng, and Olsen

• Prior Art Relied Upon: Greiner (a 1993 journal article), Dassa (a 1990 journal article), Cheng (Patent 5,985,605), and Olsen (a 1991 journal article).
• Core Argument for this Ground:
  • Prior Art Mapping: This ground replaced Kretz with a more direct combination teaching the specific claimed phytase. Dassa disclosed the complete nucleotide sequence for the E. coli gene it named "appA," and Greiner subsequently characterized the expressed protein as a phytase with high stability and specificity, making it an attractive option for animal feed. The combination of Dassa and Greiner thus explicitly taught the claimed appA polynucleotide and its function. Cheng and Olsen were relied upon for the same reasons as in Ground 1: Cheng provided the methods for expression in Pichia, and Olsen provided the teaching that this expression would inherently increase thermostability.
  • Motivation to Combine: A POSITA would be motivated to express the specific, highly stable E. coli AppA phytase disclosed by Greiner and Dassa in an efficient and economically viable host system. Cheng provided the motivation to use Pichia for its high yields and cost-effectiveness. Olsen’s teachings on increased thermostability provided further motivation to select a yeast host over a bacterial host.
  • Expectation of Success: Petitioner argued a POSITA would have a high expectation of success based on Cheng’s teaching of expressing various bacterial phytases in industrially-recognized yeast hosts like Pichia.

Ground 3: Claims 1-5 are obvious over Greiner, Dassa, Romanos, Van Gorcom, and Olsen

• Prior Art Relied Upon: Greiner (1993 article), Dassa (1990 article), Romanos (1995 article), Van Gorcom (Patent 5,436,156), and Olsen (1991 article).
• Core Argument for this Ground:
  • Prior Art Mapping: This ground used the same Greiner/Dassa/Olsen combination from Ground 2 but substituted Romanos and Van Gorcom for Cheng to teach the expression system. Romanos identified Pichia as a "mainstream expression host" known to produce "extremely high yields" of proteins. Van Gorcom taught detailed, industrially-viable methods for expressing other phytases (Aspergillus) in various microbial hosts, including yeasts, on an economical, industrial scale. Together, these references showed it was obvious to produce the known AppA phytase in the high-yield Pichia host using established industrial methods.
  • Motivation to Combine: The primary motivation was to produce the desirable AppA phytase (from Greiner/Dassa) in a host known for superior yields (Pichia, per Romanos) using the established industrial-scale methods taught by Van Gorcom. A POSITA would have been motivated to substitute the E. coli AppA phytase for the Aspergillus phytase in Van Gorcom’s method due to the known advantageous properties of the E. coli version. Olsen again supplied the motivation for achieving enhanced thermostability.
  • Expectation of Success: A POSITA would reasonably expect success because Romanos taught that Pichia was a suitable host for bacterial enzymes, and Van Gorcom taught a "high degree of homology" among phytase genes from different microbial species, suggesting that substituting one phytase gene for another in an established expression system was a predictable and obvious modification.

4. Key Claim Construction Positions

• "appA polynucleotide": Petitioner argued that while the invalidity grounds apply under any plausible construction, the term should be construed narrowly as "The gene originally defined as E. coli periplasmic phosphohydrolase gene, which contains 129[9] nucleotides and is identified by GenBank accession number M58708." Petitioner asserted that proving unpatentability under this narrower construction necessarily proves unpatentability under the Patent Owner’s broader construction.

5. Arguments Regarding Discretionary Denial

• Petitioner argued that the grounds presented were not cumulative of issues previously considered by the USPTO, and thus discretionary denial under 35 U.S.C. § 325(d) would be inappropriate. Petitioner contended that while some of the asserted references were before the examiner in related applications, they were never applied in the combinations asserted in the petition. Specifically, the examiner failed to consider Greiner’s disclosure of the phytase activity of the AppA enzyme or Olsen's explicit teaching that expressing bacterial enzymes in yeast increases thermostability—a key limitation added during prosecution to overcome prior art.

6. Relief Requested

• Petitioner requested the institution of an inter partes review and the cancellation of claims 1-5 of the ’318 patent as unpatentable under 35 U.S.C. §103.