Curio Bioscience, Inc. v. Prognosys Biosciences Inc. et al.

Prosecution History analysis

Examiner Search analysis

Invalidity Framework analysis

Petition

Petition summary

## 1. Case Identification
- Case Number: [IPR2025-00237](https://ai-lab.exparte.com/case/ptab/IPR2025-00237)
- Patent #: 11,001,879
- Filed: November 27, 2024
- Petitioner(s): [Curio Bioscience, Inc.](https://ai-lab.exparte.com/party/curio-bioscience-inc)
- Patent Owner(s): [Prognosys Biosciences Inc.](https://ai-lab.exparte.com/party/prognosys-biosciences-inc) and [10X Genomics, Inc.](https://ai-lab.exparte.com/party/10x-genomics-inc)
- Challenged Claims: 1, 2, 5, 6, 11-12, 17, 21, 23, 27, 28, and 30

## 2. Patent Overview
- Title: Method for Determining Nucleic Acid Presence or Abundance in Tissue
- Brief Description: The ’879 patent describes methods for determining the spatial location and abundance of nucleic acids within a tissue section. The method involves contacting the tissue with an array of features, where each feature has capture agents comprising a sequence that binds the target nucleic acid and a unique "coding tag" that corresponds to the feature's location on the array.

## 3. Grounds for Unpatentability

#### Ground 1: 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:** WO 2009/091934 A1 (Cantor).
- **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 (a "feature") is associated with a single-stranded nucleic acid capture agent. This agent comprised a "probe sequence" that specifically binds a target nucleic acid and a unique "identification sequence" (the claimed "coding tag") that identifies the specific bead. Because each bead occupies a specific location in an array, its unique identification sequence corresponds to that location. Cantor further disclosed capturing a target nucleic acid, amplifying it, and sequencing the resulting product to determine the sequence of both the target and the identification tag.
  - **Motivation to Combine (for §103 grounds):** Petitioner asserted that a POSA would have been motivated to apply Cantor's bead array system to a tissue section, which Cantor explicitly mentioned as a possible sample type. The motivation stemmed from a well-established desire in the art to obtain spatial information about gene expression, which could not be achieved with homogenized tissue samples. Applying Cantor's spatially encoded array to an intact tissue section was an obvious way to achieve this known goal.
  - **Expectation of Success (for §103 grounds):** A POSA would have reasonably expected success because methods for applying tissue sections to arrays, lysing cells to release nucleic acids, and using fresh-frozen tissue samples (for high-quality RNA) were all routine and well-established techniques.

#### Ground 2: 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, and Armani et al., “2D-PCR: a method of mapping DNA in tissue sections,” *Lab Chip* (2009) (Armani).
- **Core Argument for this Ground:**
  - **Prior Art Mapping:** This ground incorporated the teachings of Cantor from Ground 1 and added Armani. Petitioner argued that Armani explicitly taught a method for analyzing nucleic acids in a tissue section by transferring the section (including fresh-frozen sections) onto a multi-well array, lysing the tissue to release DNA, and creating a 2D map of the target DNA's presence.
  - **Motivation to Combine (for §103 grounds):** A POSA would have been motivated to combine Cantor's sequencing-based detection method with Armani's tissue-on-array technique. Armani used fluorescence detection and acknowledged its limitations, particularly for mapping low-abundance RNA. Petitioner contended that substituting Cantor's superior sequencing-based method was an obvious improvement, as it would enable more sensitive detection and simplify the workflow by allowing multiplexed sequencing instead of individual well imaging.
  - **Expectation of Success (for §103 grounds):** The combination had a high expectation of success because Armani demonstrated the successful application and analysis of tissue on an array, while Cantor demonstrated the successful capture and sequencing of nucleic acids using spatially barcoded beads.

#### Ground 3: Claims 1, 2, 5, 6, 11-12, 17, 21, 23, 27, 28, and 30 are anticipated by Frisen.
- **Prior Art Relied Upon:** WO 2012/140224 A1 (Frisen).
- **Core Argument for this Ground:**
  - **Prior Art Mapping:** This ground was predicated on a challenge to the ’879 patent's priority date. Petitioner argued the patent was not entitled to its 2010 provisional filing date because its priority documents lacked written description for the claimed invention. The priority documents allegedly only disclosed delivering probes *to* a tissue sample already fixed on a slide, not contacting a tissue sample *with* a pre-existing array of probes. Petitioner asserted this break in the priority chain meant the claims' effective filing date was no earlier than February 14, 2019, making Frisen (published 2012) anticipatory prior art. Frisen was alleged to disclose every element of the claims, including providing an array (e.g., an Illumina bead array) with capture probes having both a "capture domain" (to bind nucleic acid) and a "positional domain" (the coding tag), contacting the array with a tissue sample, and sequencing the resulting molecules to determine their identity and spatial location.

## 4. Key Claim Construction Positions
- Petitioner stated it applied the claim term understanding used by the Patent Owner in co-pending litigation, where no terms were asserted to require construction.
- The petition highlighted the term "specifically binds" from claim 1. It argued that while step 1(a)(i) only requires a sequence that "binds" the nucleic acid, step 1(b) refers to the nucleic acid "specifically bound" to the capture agent. Therefore, a POSA would understand the claim as a whole to require specific binding.
- Petitioner noted that its invalidity arguments hold regardless of whether a broad (e.g., poly-T probe binding a poly-A tail) or narrow interpretation of "specifically binds" is adopted, as the prior art allegedly discloses both.

## 5. Arguments Regarding Discretionary Denial
- **§314(a) / Fintiv:** Petitioner argued against discretionary denial, stating that the parallel district court litigation was in its early stages with limited investment. With a trial date set for May 2026, a Final Written Decision (FWD) would likely issue around the same time, making the *Fintiv* factors favor institution. Petitioner also stated its intent to file for a stay in the district court.
- **§325(d):** Petitioner argued denial under §325(d) is inappropriate. For Grounds 1 and 2, the primary reference (Cantor) was never cited in an IDS or considered during prosecution. For Ground 3, Petitioner argued the Examiner materially erred by not analyzing the lack of written description support in the priority documents, which would have revealed the anticipatory relevance of Frisen.

## 6. Relief Requested
- Petitioner requests institution of inter partes review and cancellation of claims 1, 2, 5, 6, 11-12, 17, 21, 23, 27, 28, and 30 of the ’879 patent as unpatentable.

10X Genomics' spatial genomics patent faces 3 challenges: Frisen & Cantor cited for anticipation & obviousness against 12 key nucleic acid mapping claims.