PTAB

IPR2025-00237

Curio Bioscience Inc v. Prognosys Biosciences Inc

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Key Events
Petition
petition

1. Case Identification

2. Patent Overview

  • Title: Spatially Encoded Biological Assays
  • Brief Description: The ’879 patent describes methods for determining the presence or abundance of a nucleic acid at a specific location within a tissue section. The method involves contacting the tissue with an array of features, where each feature has capture agents comprising a sequence to bind the nucleic acid and a "coding tag" that corresponds to the feature's location on the array.

3. Grounds for Unpatentability

Ground 1: Obviousness over Cantor and Knowledge of a POSA - Claims 1, 2, 5, 6, 11, 12, 17, 21, 23, 27, 28, and 30 are obvious over Cantor in view of the knowledge of a Person of Ordinary Skill in the Art (POSA).

  • Prior Art Relied Upon: Cantor (WO 2009/091934).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner argued that Cantor disclosed all key structural elements of the claimed method. Cantor taught using bead arrays where each bead ("feature") is functionalized with capture agents. These capture agents contained a "probe sequence" to bind a target nucleic acid and a unique "identification sequence" (the claimed "coding tag") that identifies the specific bead. Because each bead occupies a known or determinable location in the array, its unique identification sequence necessarily corresponds to that location. Cantor also taught a complete workflow for capturing a target nucleic acid, amplifying it along with the identification sequence, and then sequencing the resulting product to identify both the target and the tag.
    • Motivation to Combine (with POSA knowledge): Petitioner contended that a POSA would have been motivated to apply Cantor's bead array system to a tissue section. The prevailing goal in the art was to obtain spatial information about biological molecules, which could not be achieved with homogenized tissue samples. Applying Cantor's spatially indexed array to an intact tissue section was an obvious step to map the location of nucleic acids within that tissue.
    • Expectation of Success: A POSA would have reasonably expected success, as the techniques for applying tissue sections to arrays, lysing cells to release nucleic acids, and performing hybridization were well-established.

Ground 2: Obviousness over Cantor in view of Armani and Knowledge of a POSA - Claims 1, 2, 5, 6, 11, 12, 17, 21, 23, 27, 28, and 30 are obvious over Cantor in view of Armani and the knowledge of a POSA.

  • Prior Art Relied Upon: Cantor (WO 2009/091934) and Armani (a 2009 journal article titled "2D-PCR: a method of mapping DNA in tissue sections").
  • Core Argument for this Ground:
    • Prior Art Mapping: This ground incorporated the arguments from Ground 1 and used Armani to provide additional motivation and specific technical guidance. Armani taught a method for creating a 2D map of DNA from a tissue section by transferring the tissue onto a multi-well array, lysing the cells in place, and amplifying the released DNA. Petitioner asserted that Armani explicitly showed the successful application of an array-based system to a tissue section to gain spatial data.
    • Motivation to Combine: A POSA would combine Cantor’s sequencing-based detection method with Armani’s spatial analysis workflow. Armani demonstrated the value of spatial mapping but used fluorescence, which had known sensitivity limitations. Petitioner argued that a POSA would have recognized Cantor’s sequencing-based approach as a more sensitive and powerful readout method, making it an obvious improvement to substitute into Armani’s workflow. This combination would allow for the detection of low-abundance mRNAs and simplify the process by enabling multiplexed sequencing.
    • Expectation of Success: Armani's successful use of fresh-frozen tissue sections on a multi-well array would have confirmed a POSA's reasonable expectation of success in combining the teachings with Cantor's bead arrays.

Ground 3: Anticipation by Frisen - Claims 1, 2, 5, 6, 11, 12, 17, 21, 23, 27, 28, and 30 are anticipated by Frisen.

  • Prior Art Relied Upon: Frisen (WO 2012/140224).
  • Core Argument for this Ground:
    • Priority Date Challenge: Petitioner argued the ’879 patent is not entitled to its earliest claimed priority date of April 2010. The petition contended that the priority documents failed to provide adequate written description for the claimed invention, which involves contacting a pre-existing array with a tissue sample. Instead, the early specifications allegedly only described delivering probes onto a previously affixed tissue sample. Petitioner asserted that the first application with proper support was filed in February 2019, making Frisen (published 2012) anticipatory prior art.
    • Prior Art Mapping: Petitioner argued Frisen disclosed every limitation of the challenged claims. Frisen described a method for localized nucleic acid detection in a tissue sample by: (a) providing an array (e.g., an Illumina bead array) with capture probes, where each probe comprises a "capture domain" (to bind the nucleic acid) and a "positional domain" (the coding tag corresponding to its location); (b) contacting the array with a tissue sample to allow hybridization; and (c) generating and sequencing DNA molecules to analyze the nucleic acids and their locations, thereby creating a map of gene expression.

4. Arguments Regarding Discretionary Denial

  • §314(a) (Fintiv): Petitioner argued against discretionary denial under Fintiv, stating that the parallel district court litigation was in an early stage, a stay was likely to be granted, and the trial date of May 2026 would occur around the same time as the Board’s Final Written Decision, minimizing concerns of inefficiency or conflicting outcomes.
  • §325(d): Petitioner contended that denial under §325(d) was inappropriate. For the obviousness grounds, the primary reference (Cantor) was never considered by the PTO. For the anticipation ground, the PTO materially erred by not analyzing the lack of written description support in the priority documents, which prevented the examiner from recognizing that Frisen was anticipatory art.

5. Relief Requested

  • Petitioner requested the institution of an inter partes review and the cancellation of claims 1, 2, 5, 6, 11, 12, 17, 21, 23, 27, 28, and 30 of the ’879 patent as unpatentable.