AI-enabled RNA nanotechnology DElivery SysTem for INformATION transfer into cells.

Project Information

DESTINATION

Grant agreement ID: 899833

DOI

10.3030/899833

Project closed

EC signature date 20 January 2021

Start date 1 April 2021

End date 31 December 2025

Funded under

• EXCELLENT SCIENCE - Future and Emerging Technologies (FET)

Total cost

€ 3 381 888,75

EU contribution

€ 3 381 888,75

Coordinated by

SIXFOLD BIOSCIENCE LTD
United Kingdom

Periodic Reporting for period 2 - DESTINATION (AI-enabled RNA nanotechnology DElivery SysTem for INformATION transfer into cells.)

Reporting period: 2022-04-01 to 2023-09-30

Summary of the context and overall objectives of the project

DESTINATION is an EU FET-Open project. By combining the interdisciplinary fields of AI/machine learning with RNA nanotechnology, biochemistry and advanced imaging methods, DESTINATION aims to create an RNA-based delivery platform (RNano) for effective delivery of information such as mRNA into cells in vivo. mRNA translates the information encoded in a cell’s DNA into the proteins that are essential for diverse cell function and can be deficient in disease. Administering mRNA into a cell could enable diverse novel functions such as production of its own medicine by replacing the faulty mRNA or engineering cells to fight diseases from genetic disorders and cancer to infectious diseases. However, the ability to deliver mRNA to specific cells in a targeted organ remains an unmet challenge that limits its clinical and commercial potential. Addressing this challenge requires a novel, biocompatible and scalable system capable of:

(1) protecting the mRNA from degradation in blood;
(2) evading the immune response;
(3) and providing high selectivity for targeted cells.

DESTINATION will generate an intelligent library of:

(a) programmable RNano scaffolds for attachment of packaged mRNA and
(b) RNA aptamers for laser-specific internalization of RNanos into cells.

Promising candidates will be tested in vitro, with lead candidates progressing to novel animal models. Super resolution imaging will allow for the evaluation of the technology, with an iterative R&D approach aimed at demonstrating 3 breakthrough preclinical proof-of-concepts including phenylketonuria treatments. RNanos utilise a unique and disruptive strategy compared to competitors, designed to ensure the following competitive advantages: enhanced safety, efficacy, and scalable synthesis, manufacturing and production.

This project is important for society, as it is targeting 3 diseases of highly unmet need: Phenylketonuria, Melanoma and B-Cell Lymphoma. Successful validation of RNanos could eventually improve safety and efficacy of treatments and ultimately decrease cost for end users/public health systems.

Overall objectives include:

Development of an AI discovery platform
Validation of an RNano scaffold for therapeutic delivery
Creation of an intelligent library of lead cell-internalizing aptamers
Animal models for proof-of-concept in vivo CAR-T, mRNA and CRISPR therapies
Novel methods based on multicolour single molecule imaging tailored for RNA imaging
DNA/RNA origami synthesis and conjugation to RNanos
Logic gates (for mRNA protection)
Optimised synthesis workflows
Communication of outputs via international conferences, workshops and high-impact publications.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Work performed during Year 1 of DESTINATION (RP1) includes:
Enabling algorithms/ scripts for scaffold optimisation (WP1)
Biological-based controls of origami assemblies (WP2)
Development and preliminary validation CD3 targeting aptamers (WP3)
Endosomal escape candidates generated and tested in vitro. Protein corona modulation validated (WP4).
Preparation, submission and approval of in vivo experimental design to ethical authorities. Training on IVIS system (WP5).
Effective management & collaboration established. Data management plan, dissemination and communication plan, project website and Twitter launched.

Work performed during M13-30 of DESTINATION (RP2) includes:
Development of new software tools (REVNANO) for analysing DNA origami structures (WP1);
Further development on packaging/unpackaging of mRNA (WP2);
Continued development of CD3 targeting aptamers; continued development of promising in vivo targeting origami for gene therapy (WP3);
Small-scale synthesis of lead candidates per indication for testing. Further understanding of PK properties of delivery systems. Modulation of protein binding via commercially available chemical modifications. In vitro imaging of cellular uptake of aptamers to assess uptake and functionality (WP4);
Set up and validation of three murine models for human pathologies: phenylketonuria, cutaneous melanoma and B cell lymphoma (WP5);
Establishment of workflows for effective and high-yield, upscaled synthesis. Process and purification optimisation (WP6).

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Progress beyond state of the art to-date:
Enabling algorithms/ scripts for scaffold optimisation (WP1)
Biological-based controls of origami assemblies (WP2)
Development and preliminary validation CD3 targeting aptamers (WP3)
Endosomal escape candidates generated and tested in vitro. Protein corona modulation validated (WP4).

Expected results until end of the project:
Development of an AI discovery platform
Validation of an RNano scaffold for therapeutic delivery
Creation of an intelligent library of lead cell-internalizing aptamers
Animal models for proof-of-concept in vivo CAR-T, mRNA and CRISPR therapies
Novel methods based on multicolour single molecule imaging tailored for RNA imaging
DNA/RNA origami synthesis and conjugation to RNanos
Logic gates (for mRNA protection)
Optimised synthesis workflows

Potential impacts (including socio-economic & wider societal implications of the project so far):
Investment in skills to build scientific expertise in the growing but underdeveloped field of nucleic-acid engineering in the EU
Support of growth of jobs & revenue in the Advanced Therapy Medicinal Product (ATMP) industry and the associated supply chain.
RNano could catalyse therapy cost reduction and increase in “druggable” indications through more accurate drug delivery, increasing access and quality of life for patients.
DESTINATION could lead to the creation of novel markets such as in vivo intracellular mRNA, CAR-T and CRISPR therapies.
The versatility of RNanos could be used to deliver alternative cargo (e.g. lnRNA, siRNA, miRNA).
Aptamers (internalizing and/or fluorescent) themselves could be used for development of diverse targeted therapies e.g. bi-specifics, tri-specifics in immuno-oncology, diagnostics and theranostics.
DESTINATION builds leading research and innovation capacity across Europe by bringing together 7 partners, from 6 different European countries and with diverse but complementary expertise.
RNanos’ breakthrough indications are aimed at showcasing the therapeutic versatility of the
platform via information knock-in, knock-out and reprogramming to affect large patient groups suffering from melanoma and blood cancer as well as rare disorders (e.g Phenylketonuria).

DESTINATION Iterative R&D Process