Curio Bioscience v. Prognosys Biosciences Inc

1. Case Identification

• Case #: IPR2024-01289
• Patent #: 10,480,022
• Filed: September 10, 2024
• Petitioner(s): Curio Bioscience, Inc.
• Patent Owner(s): Prognosys Biosciences Inc. and 10x Genomics, Inc.
• Challenged Claims: 1-7, 11-15, 17, 19, and 27-29

2. Patent Overview

• Title: Spatially Encoded Biological Assays
• Brief Description: The ’022 patent describes a method for determining the spatial location of a biological molecule (e.g., a nucleic acid) within a tissue sample. The method involves using a plurality of beads, where each bead has binding agents configured to interact with the biological molecule and a unique nucleic acid "coding identifier" that corresponds to a specific location.

3. Grounds for Unpatentability

Ground 1: Obviousness over Cantor - Claims 1-7, 11-15, 17, 19, and 27-29 are obvious over Cantor in view of the knowledge of a POSA.

• Prior Art Relied Upon: Cantor (WO 2009/091934).
• Core Argument for this Ground:
  • Prior Art Mapping: Petitioner argued that Cantor disclosed all structural elements of the claimed method. Cantor taught using bead arrays where each bead comprises a single-stranded nucleic acid construct with two key parts: a "probe sequence" that functions as the claimed "binding agent" to hybridize with a target nucleic acid, and a unique "identification sequence" (ID) that functions as the claimed "coding identifier." Because each bead in Cantor's array has a unique ID and occupies a known or determinable coordinate, its ID necessarily corresponds to its location. Cantor expressly disclosed that its method could be applied to tissue samples.
  • Motivation to Combine (with POSA knowledge): A person of ordinary skill in the art (POSA) would have been motivated to apply Cantor's bead array system to analyze tissue samples to determine the spatial distribution of nucleic acids, a well-known goal in the art. Petitioner asserted this motivation was documented in multiple other references known to a POSA, which taught using nucleic acid arrays to map gene expression in tissue.
  • Expectation of Success: A POSA would have had a reasonable expectation of success in using Cantor's system for spatial analysis of tissue. The process involved known techniques: hybridizing nucleic acids from a tissue sample to probes on a bead array, and then sequencing the resulting products to read both the target sequence and the bead's unique ID sequence, thereby correlating the biological molecule to a specific location.

Ground 2: Obviousness over Cantor in view of Armani - Claims 1-7, 11-15, 17, 19, and 27-29 are obvious over Cantor in view of Armani.

• Prior Art Relied Upon: Cantor (WO 2009/091934) and Armani (a 2009 journal article in Lab on a Chip).
• Core Argument for this Ground:
  • Prior Art Mapping: This ground incorporated the analysis of Cantor from Ground 1. Armani was added to provide further motivation and specific techniques for contacting a bead array with a tissue sample. Armani disclosed a method for mapping DNA in tissue by transferring a tissue section onto a multi-well array, lysing the cells to release genomic DNA, and then amplifying and detecting the DNA. Cantor also disclosed that its beads could be arranged in substrates with multiple wells.
  • Motivation to Combine: A POSA would combine Cantor and Armani to improve spatial analysis of tissue. Armani identified mapping mRNA as a desirable goal but noted its fluorescence-based detection methods were not sensitive enough for low-abundance transcripts. A POSA would have been motivated to replace Armani's detection method with Cantor's sequencing-based readout, which is more sensitive and well-suited for mRNA. The combination would involve placing Cantor's barcoded beads into the wells of an array, applying a tissue sample as taught by Armani, and then proceeding with Cantor's sequencing protocol. This would simplify Armani's workflow by eliminating several detection steps.
  • Expectation of Success: Success was reasonably expected because the combination involved applying known techniques in a predictable manner. Armani provided a proven method for preparing a tissue sample on a multi-well array, and Cantor provided a proven method for barcoding and sequencing nucleic acids from such an array.

Ground 3: Anticipation by Frisen - Claims 1-7, 11-15, 17, 19, and 27-29 are anticipated by Frisen.

• Prior Art Relied Upon: Frisen (WO 2012/140224).
• Core Argument for this Ground:
  • Prior Art Mapping: Petitioner first argued that the ’022 patent is not entitled to its claimed priority date of 2010. The priority documents allegedly failed to provide written description support for the claimed invention, instead describing a different method where reagents are delivered onto a pre-affixed tissue sample, rather than contacting a tissue sample with a pre-made bead array. Therefore, the patent's effective filing date is its actual filing date of February 14, 2019, making the 2012 Frisen publication prior art under AIA §102.
  • Petitioner contended that Frisen disclosed every element of the challenged claims. Frisen described a method for localized detection of nucleic acids in a tissue sample using arrays, including Illumina bead arrays. Frisen's capture probes are single nucleic acid molecules comprising: (1) a "positional domain" that corresponds to the probe's position on the array (the "coding identifier"), and (2) a "capture domain" that hybridizes with target nucleic acids (the "binding agent"). The method explicitly involved contacting the array with a tissue sample and then sequencing the resulting molecules to analyze the sequence and its corresponding positional domain, thereby determining the spatial location of the target nucleic acid.

4. Arguments Regarding Discretionary Denial

• §314(a) (Fintiv): Petitioner argued discretionary denial under Fintiv is unwarranted. The parallel district court litigation is in its early stages, with a trial scheduled for May 2026. An FWD in this IPR would be expected in March 2026, well in advance of trial, thus conserving judicial and party resources.
• §325(d): Petitioner argued denial under §325(d) is inappropriate because the petition raises arguments and art not previously considered by the USPTO. Cantor was not before the examiner during prosecution. Furthermore, the examiner did not critically evaluate the §112 written description support for the priority claim, an issue central to the anticipation argument based on Frisen.

5. Relief Requested

• Petitioner requests institution of an inter partes review and cancellation of claims 1-7, 11-15, 17, 19, and 27-29 of the ’022 patent as unpatentable.