Liver-Specific NARE Sequences for Compact High-Potency Gene Expression
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Solution Overview
Problem
Existing methods for engineering nucleic acid regulatory elements (NAREs) are time-consuming and expensive, requiring in vitro optimization, and there is a need for NAREs with enhanced potency, reduced size, and tissue specificity for efficient gene therapy applications.
Innovation Solution
Development of a library of NAREs using advanced artificial intelligence models to predict promoter potency, incorporating enhancer elements and optimizing spacing, combined with in silico mutagenesis, resulting in enhanced NAREs with increased potency and specificity for liver expression.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional low-throughput rational design or high-throughput MPRA methodologies are used to engineer NAREs, then NAREs with desired tissue specificity and potency can be obtained, but the process becomes expensive and time-consuming requiring in vitro optimization
Solution Approach 1:
The patent uses deep learning models trained on existing NARE sequence data to predict and generate new NARE sequences with desired properties. Instead of relying solely on time-consuming in vitro optimization, the system creates computational copies and predictions of effective NARE sequences, significantly reducing the experimental iteration cycle while maintaining reliability through AI-driven sequence design
Solution Approach 2:
The patent systematically varies NARE sequence parameters (nucleotide composition, spacing, motif arrangements) using AI models to predict their impact on potency and tissue specificity. This computational parameter optimization allows rapid identification of high-performing NARE variants without proportionally increasing experimental time, as the AI model guides which parameter combinations to test
2Length of moving object
If NARE size is reduced to allow efficient packaging of larger transgene cargo into viral vectors, then packaging efficiency improves, but there is a risk of sacrificing NARE strength or specificity
Solution Approach 1:
The patent identifies and utilizes core functional segments within NARE sequences that are essential for potency and tissue specificity. By segmenting the NARE into critical motifs and non-critical regions, the design can retain only the essential segments, creating compact NAREs that maintain full functionality while reducing overall size for efficient viral vector packaging
Solution Approach 2:
The patent extracts and removes non-essential portions of NARE sequences while preserving the core functional elements required for liver-specific expression and potency. This extraction process creates minimized NARE designs that fit within viral vector packaging constraints without sacrificing the reliability of transgene expression
3Reliability
If larger viral vector doses are administered to achieve desired gene expression levels, then expression efficacy improves, but immune responses and safety risks increase
Solution Approach 1:
The patent optimizes NARE sequence parameters to maximize transcriptional potency, achieving higher gene expression levels per unit of viral vector. This enhanced potency allows administration of smaller viral doses to reach the same therapeutic effect, thereby reducing immune responses and safety risks while maintaining expression efficacy
Data Source
AI summary
The application relates to nucleic acid regulatory elements (NAREs) that are able to enhance expression of genes in the liver. The application further relates to methods employing NAREs and uses of the NAREs. Expression cassettes and vectors containing NAREs are also disclosed. These are particularly useful for applications using gene therapy.