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US-20260124260-A1 - ENGINEERED YEAST FOR DELIVERY OF IMMUNE CHECKPOINT INHIBITOR PROTEINS TO GASTROINTESTINAL TUMORS

US20260124260A1US 20260124260 A1US20260124260 A1US 20260124260A1US-20260124260-A1

Abstract

Among the various aspects of the present disclosure is the provision of an engineered yeast for delivery of immune checkpoint inhibitor (ICI) proteins to gastrointestinal tumors. The present teachings include methods for suppressing or reducing tumors through the administration of an engineered Sb that can deliver immune checkpoint inhibitors (ICIs) into the gastrointestinal tract. The present teachings also include a composition of a genetically engineered Sb consisting of Sb capable of expressing and secreting ICIs.

Inventors

  • Miranda Wallace
  • Beth Helmink
  • Olivia Gorushi
  • Gautam Dantas
  • Jerome Prusa
  • Suryang KWAK

Assignees

  • WASHINGTON UNIVERSITY

Dates

Publication Date
20260507
Application Date
20250922

Claims (14)

  1. 1 . A composition to suppress or reduce tumors in a patient, the composition comprising an engineered yeast comprising a nucleotide sequence encoding a high-affinity programmed cell death 1 ectodomain protein (haPD-1) comprising a PD-1 ectodomain fused to a IgG1 CH 3 domain, wherein the engineered yeast is configured to secrete the haPD-1.
  2. 2 . The composition of claim 1 , wherein the nucleotide sequence is selected from SEQ ID NOS:1-23.
  3. 3 . The composition of claim 2 , wherein the nucleotide sequence is SEQ ID NO:17.
  4. 4 . The composition of claim 1 , wherein the engineered yeast comprises a yeast species consisting of Saccharomyces cerevisiae var. boulardii (Sb).
  5. 5 . The composition of claim 1 , wherein the composition is further configured for oral administration and for release of the haPD-1 into the patient's gastrointestinal tract.
  6. 6 . The composition of claim 1 , wherein the haPD-1 is configured to bind the patient's programmed death ligand 1 (PD-L1) with high affinity.
  7. 7 . The composition of claim 1 , wherein the composition acts as an immune checkpoint inhibitor (ICI) for reducing gastrointestinal tumors.
  8. 8 . A method of suppressing or reducing gastrointestinal tumors in a patient, the method comprising administering a therapeutically effective amount of a composition comprising an engineered yeast comprising a nucleotide sequence encoding a high-affinity programmed cell death 1 ectodomain protein (haPD-1) comprising a PD-1 ectodomain fused to a IgG1 CH3 domain, wherein the engineered yeast is configured to secrete the haPD-1.
  9. 9 . The method of claim 8 , wherein the nucleotide sequence is selected from SEQ ID NOS:1-26.
  10. 10 . The method of claim 9 , wherein the nucleotide sequence is SEQ ID NO:17.
  11. 11 . The method of claim 8 , wherein the engineered yeast comprises a yeast species consisting of Saccharomyces cerevisiae var. boulardii (Sb).
  12. 12 . The method of claim 8 , wherein the composition is further configured for oral administration and for release of the haPD-1 into the patient's gastrointestinal tract.
  13. 13 . The method of claim 8 , wherein the haPD-1 is configured to bind the patient's programmed death ligand 1 (PD-L1) with high affinity.
  14. 14 . The method of claim 8 , wherein the composition acts as an immune checkpoint inhibitor (ICI) for reducing gastrointestinal tumors.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of priority to U.S. Provisional Application Ser. No. 63/697,214 filed on Sep. 20, 2024, which is incorporated herein by reference in its entirety. STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT This invention was made with government support under A1155893 and AT009741 awarded by the National Institutes of Health. The government has certain rights in the invention. MATERIAL INCORPORATED-BY-REFERENCE The Sequence Listing, which is a part of the present disclosure, includes a computer readable document entitled “020850-US-NP_SEQ_LISTING.XML” (202,665 bytes) created Sep. 22, 2025 comprising nucleotide and/or amino acid sequences of the present invention. The subject matter of the Sequence Listing is incorporated herein by reference in its entirety. FIELD OF THE INVENTION The present disclosure generally relates to engineered yeast that produce therapeutic proteins to treat GI tumors. BACKGROUND OF THE INVENTION Microbes have an increasingly appreciated role in the development and treatment of a myriad of diseases. Although beneficial microbes in their native form have demonstrated clinical utility, such as probiotic formulations and fecal microbiota transplantation, engineered probiotics have been developed in recent years as living carriers of therapeutics that treat a variety of diseases. As many probiotics are capable of heterologous production of various functional therapies, are genetically tractable, and are safe and viable following oral administration, diseases manifesting in the mammalian gastrointestinal (GI) tract are an attractive target for engineered probiotics. Protein-based therapies, or ‘biologics’, represent a recently growing market as exemplified by monoclonal antibodies used for anticancer immunotherapy, GI infections, and inflammatory bowel disease. Engineered probiotics are a promising solution to achieve delivery of protein-based therapies to disease sites in the GI tract following oral administration, as protein-based therapies typically have poor oral bioavailability in the lower GI tract. The probiotic yeast Saccharomyces cerevisiae var. boulardii (Sb) is a strain of Saccharomyces cerevisiae, a model yeast with a wide array of available genetic tools. Sb has a favorable safety profile in humans and can be used to treat diarrhea associated with antibiotic use or infectious disease. Like bacterial probiotics, Sb is capable of robust heterologous protein expression and can survive the harsh environment of the mammalian GI tract. Sb can readily secrete therapeutic payloads into the extracellular space in appreciable quantities, has a short gut transit time, and does not innately colonize the mammalian GI tract, allowing for precise therapeutic regimens without the need for antibiotics or synthetic kill-switches upon completion of treatment. As a yeast, Sb has decreased risk of horizontal gene transfer with the host microbiome. As such, it is less likely to acquire antibiotic resistance genes or virulence factors that could endanger the host in comparison to bacterial probiotics. Lastly, Sb possesses innate therapeutic activity against GI cancers and other GI diseases. Together, these qualities make Sb exceptionally well-suited as a therapeutic delivery chassis to treat diseases of the GI tract. GI cancers are a leading cause of cancer-related mortality worldwide, with colorectal cancer (CRC) accounting for almost two million new cases and nearly one million deaths annually. Immune checkpoint inhibitors (ICIs) have revolutionized the cancer therapy landscape and are highly efficacious in a subset of CRC cases. They work by blocking immunosuppressive pathways exploited by tumors, targeting the programmed cell death protein 1 (PD-1)/programmed cell death ligand 1 (PD-L1) axis or cytotoxic T-lymphocyte-associated protein 4 (CTLA-4). In recent years, “miniature” antibody variants (termed microbodies and nanobodies) have been developed that maintain the functional components required to bind to their target and perform immune checkpoint blockade with improved tissue diffusion and tumor penetration. Alternative delivery strategies utilizing microbes as delivery vessels for ICI variants could further improve ICI efficacy and may expand the subset of patients that benefit from immunotherapies. Current pre-clinical efforts to develop engineered anticancer probiotics have focused largely on engineering bacterial chassis that are administered systemically or intratumorally. Although previous studies have established the utility of engineered Saccharomyces yeasts for GI-directed therapies to treat diseases such as Clostridioides difficile infection, inflammatory bowel disease, and obesity, the potential for probiotic yeasts as a carrier for gut-directed, anticancer therapies is yet to be reported. Furthermore, although the growth and viability of Sb in the harsh and distinct conditions of the GI tract have be