Engineering editopes through programmable RNA editing toward tumor neoantigen generation

Area of Science:

• Biotechnology
• Immunology
• Molecular Biology

Background:

• Neoepitope-based cancer immunotherapies target tumor-specific mutations for potent T-cell responses.
• Clinical application is hindered by challenges in neoepitope discovery and tumor cell presentation.
• Programmable RNA editing offers an alternative for generating immunogenic neoepitopes within cancer cells.

Purpose of the Study:

• To develop a method for generating immunogenic neoepitopes using programmable RNA editing.
• To demonstrate the efficacy of RNA-edited neoepitopes (editopes) in restoring anti-tumor T-cell recognition and controlling tumor growth.
• To create a computational pipeline for identifying neoepitopes suitable for RNA editing across various cancer types.

Main Methods:

• Development of Short Precise-Encodable ADAR Recruiting (SPEAR) gRNAs to direct endogenous ADAR1 for precise A-to-I RNA editing.
• Proof-of-concept study using a melanoma antigen MART-1 model to assess SPEAR-mediated RNA editing.
• In vivo experiments to evaluate tumor control mediated by editope generation.
• Development of a computational pipeline for neoepitope identification.

Main Results:

• Demonstrated successful generation of immunogenic neoepitopes (editopes) via transcript-level RNA editing using SPEAR gRNAs.
• SPEAR-mediated RNA editing restored antigen-specific T-cell recognition in a MART-1 model.
• Achieved significant tumor control in vivo through editope-based immunotherapy.
• Identified candidate tumor-selective neoepitopes across multiple cancer types amenable to guided RNA editing.

Conclusions:

• Programmable RNA editing is a viable strategy for engineering immunogenic editopes.
• SPEAR gRNAs provide a precise tool for harnessing endogenous ADAR1 for therapeutic RNA editing.
• This approach offers a promising framework for neoepitope-directed cancer immunotherapy.