Tissue Preferential Codon Modified Expression Cassettes
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Solution Overview
Problem
Current gene therapy vectors face challenges in achieving high-level expression of gene products in specific tissues, such as muscle and respiratory epithelium, due to limitations in codon usage optimization and tissue-specific expression.
Innovation Solution
Development of expression cassettes and vectors with codon-optimized genes, specifically designed for enhanced expression in non-secretory and secretory tissues, using recombinant adeno-associated virus (AAV) vectors with modified open reading frames and AAV8 capsids, optimized for muscle and respiratory epithelium, and incorporating tissue-preferential promoters.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional codon optimization is used for gene expression, then expression levels improve in general host cells, but tissue-specific expression levels remain insufficient
Solution Approach 1:
The patent applies local quality by creating distinct codon optimization patterns tailored to specific tissue types. Different codon frequency tables are generated for different tissues (e.g., muscle tissue vs. secretory tissues), allowing each tissue to have its own optimized codon usage pattern. This enables the same gene to be expressed at high levels in multiple different tissue types by simply changing which codon table is used during vector construction.
2Reliability
If standard AAV vectors are used for gene delivery, then viral vector delivery is achieved, but expression levels in target tissues are limited
Solution Approach 1:
The patent applies parameter changes by modifying the codon composition parameters of the transgene based on tissue-specific codon frequency data. By adjusting the codon usage parameters to match the target tissue's preferences, the expression level parameter is significantly enhanced. The patent generates multiple codon frequency tables with different parameter sets for different tissues, allowing optimization of expression levels for any desired target tissue.
3Productivity
If generic codon optimization is applied, then expression is improved across multiple tissues, but high-level expression in specific tissues cannot be achieved
Solution Approach 1:
The patent applies segmentation by dividing the general codon optimization problem into tissue-specific segments. Instead of using a single generic codon optimization approach, the patent creates separate codon frequency tables for different tissue types (e.g., muscle, liver, respiratory epithelium). This segmentation allows precise optimization for each tissue, achieving both high overall expression and tissue-specific precision simultaneously.
Data Source
AI summary
Described herein are synonymously altered gene sequences which express protein in differing levels within secretory as compared to non-secretory target tissue. An expression cassette comprising an open reading frame (ORF) for a protein under the control of regulatory sequences which direct expression of the product in cell, which ORF has been modified to preferentially increase expression levels in a selected tissue, wherein the modified ORF is characterized by a triplet frequency of any one of Tables 3-12, 16 or 17.