mRNA UTR Engineering for Cell-Type Specific Protein Translation
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Solution Overview
Problem
The limited understanding of how protein synthesis is controlled in human cells restricts the potential of mRNA therapeutics, and selective delivery of mRNA therapeutics remains a challenge due to the lack of cell-type specificity.
Innovation Solution
The use of oligonucleotide synthesis, high-throughput sequencing, and machine learning to define the rules that regulate protein production by designing RNA untranslated region (UTR) sequences with regulatory elements, which are then cloned upstream or downstream of an mRNA payload, and a trained model is used to predict protein synthesis levels based on these sequences.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If mRNA therapeutics are designed for general protein production, then they can be applied to any indication treatable by gene expression, but they lack cell-type specificity and selective delivery capability
Solution Approach 1:
The patent applies local quality by introducing cell-type specific regulatory elements (such as cell-type specific upstream open reading frames or uORFs, or cell-type specific 3' UTR elements) into specific regions of the mRNA molecule. These localized modifications enable the mRNA to be selectively translated in target cell types while maintaining general applicability across different indications. The regulatory elements are placed at specific locations (5' UTR, 3' UTR) to confer cell-type specificity without compromising the overall therapeutic function.
2Object-affected harmful factors
If regulatory elements are added to mRNA sequences to control protein synthesis, then cell-type specificity can be achieved, but the complexity of mRNA design and synthesis increases
Solution Approach 1:
The patent applies segmentation by dividing the mRNA molecule into functional modules: a coding sequence region and separate regulatory element regions (5' UTR with cell-type specific uORFs, 3' UTR with regulatory elements). This modular design allows independent optimization of each segment and simplifies the design process by enabling combinatorial assembly of proven regulatory modules. The segmentation also facilitates standardized synthesis approaches where regulatory elements can be independently designed and inserted.
Solution Approach 2:
The patent applies preliminary action by pre-identifying and characterizing cell-type specific regulatory elements through computational prediction and experimental validation before therapeutic application. Libraries of characterized regulatory elements with known cell-type specificities are developed in advance, allowing rapid selection and assembly for specific therapeutic indications. This preliminary characterization reduces the complexity of de novo design for each new application.
3Productivity
If the spacing between regulatory elements and start/stop codons is varied to optimize protein synthesis, then translation efficiency can be tuned, but the number of sequence variants to test increases
Solution Approach 1:
The patent applies parameter changes by systematically varying the spacing parameters (distance between regulatory elements and start/stop codons) within defined ranges based on computational predictions and established biological principles. Instead of exhaustively testing all possible sequences, the invention focuses on varying key parameters (spacing distances, element compositions) within biologically relevant ranges to achieve optimal translation efficiency. This parameter-based approach reduces the search space while maintaining the ability to tune protein synthesis levels.
Data Source
AI summary
Systems and methods for determining an effect regulatory untranslated RNA elements are provided. A plurality of RNA untranslated region (UTR) sequences are designed, subject to a requirement that each UTR RNA sequence includes one or more RNA regulatory elements in a plurality of RNA regulatory elements. The plurality of UTR RNA sequences samples a plurality of different spacings between each RNA regulatory element and a start or stop codon of a mRNA payload. The RNA UTR sequences are synthesized and cloned upstream or downstream of a mRNA payload to generate reporter constructs. The translation of each reporter construct is measured in a reporter cell type. These translation measurements, together with the sequences of the RNA UTR sequences, is used to train a model so that the model provides a quantitative translation estimate for a given test RNA UTR sequence whose sequence is inputted into the trained model.