Antisense Oligomer Splicing Modulation for CNS Protein Deficiency

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Solution Overview

Problem

Central nervous system diseases often result from deficiencies in specific gene products, such as STXBP1, where existing treatments fail to effectively increase the expression of these proteins, leading to inadequate protein production and associated neurological disorders.

Innovation Solution

The use of antisense oligomers (ASOs) that target retained-intron-containing pre-mRNA (RIC pre-mRNA) to promote constitutive splicing, thereby increasing the production of functional mRNA and protein levels in cells, specifically for genes like STXBP1, to treat conditions like early infantile epileptic encephalopathy-4 and other CNS diseases.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If conventional treatments are used to address gene product deficiencies, then treatment is provided, but the expression of target proteins is not effectively increased

Engineering Contradiction:

Improveeffectiveness of treatmentVSAvoidproduction of functional protein

Core Design Contradiction:

ReliabilityVSProductivity

Solution Approach 1:

The patent uses antisense oligomers as intermediary molecules that bind to retained intron-containing pre-mRNA to promote constitutive splicing. This intermediary approach enables the conversion of defective pre-mRNA into functional mRNA, thereby increasing target protein expression without directly modifying the gene itself, resolving the contradiction between providing treatment and effectively increasing protein production

Inventive Principle:

Principle #24Intermediary (Mediator)

Solution Approach 2:

The invention changes the splicing parameter of pre-mRNA processing by introducing antisense oligomers that alter the splicing efficiency from retained-intron state to constitutive splicing state. This parameter change enables effective protein production from previously non-functional transcripts, addressing the inadequacy of conventional treatments

Inventive Principle:

Principle #35Parameter changes

2Quantity of substance

If retained introns are present in pre-mRNA, then transcription occurs, but functional mRNA and protein production is reduced

Engineering Contradiction:

Improveamount of pre-mRNAVSAvoidquality of functional mRNA

Core Design Contradiction:

Quantity of substanceVSManufacturing precision

Solution Approach 1:

The antisense oligomers facilitate the extraction and removal of retained introns from pre-mRNA through promotion of constitutive splicing. This taking out the defective intronic sequences converts abundant but non-functional pre-mRNA into functional mRNA, resolving the contradiction between having sufficient transcript quantity and achieving high-quality functional mRNA production

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The antisense oligomers act as mediators that bridge the gap between retained-intron pre-mRNA and constitutive splicing. By binding to specific regions of the pre-mRNA, they facilitate the splicing process and enable conversion to functional mRNA, thereby improving manufacturing precision without reducing the quantity of transcript available

Inventive Principle:

Principle #24Intermediary (Mediator)

3Adaptability or versatility

If gene mutations or deletions occur, then genetic diversity is created, but protein expression is deficient

Engineering Contradiction:

Improvegenetic variationVSAvoidlevel of target protein

Core Design Contradiction:

Adaptability or versatilityVSQuantity of substance

Solution Approach 1:

The patent converts the harmful effect of retained introns (which result from gene mutations) into a beneficial therapeutic target. By designing antisense oligomers that specifically bind to and promote splicing of mutant pre-mRNA containing retained introns, the invention transforms the genetic defect into a treatable condition, thereby increasing target protein expression despite the presence of genetic variations

Inventive Principle:

Principle #22Blessing in disguise (Convert harm into benefit)

Solution Approach 2:

The antisense oligomers serve as intermediaries that specifically recognize and bind to mutant pre-mRNA sequences containing retained introns. This selective binding enables the promotion of constitutive splicing for mutant transcripts while preserving normal gene function, thereby compensating for protein expression deficiency caused by genetic mutations without eliminating genetic diversity

Inventive Principle:

Principle #24Intermediary (Mediator)

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

This approach enhances the expression of target proteins, leading to improved treatment outcomes for CNS diseases by increasing the production of mature mRNA and functional proteins, effectively addressing deficiencies caused by mutations or deletions in genes like STXBP1.

Implementation Method 1

the ASO is complementary to a targeted portion of a retained-intron-containing pre-mRNA (RIC pre-mRNA)

Methodology Applied

Scientific EffectComplementary base pairing:

Data Source

PatentEP3389725B1Compositions and methods for treatment of central nervous system diseases

Publication Date: 2022.04.06 COLD SPRING HARBOR LABORATORY INC

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AI summary

Provided herein are methods and compositions for increasing the expression of ATP1A2, CACNA1A, SETD5, SHANK3, NF2, DNMT1, TCF4, RAI1, PEX1, ARSA, EIF2B5, EIF2B1, EIF2B2, NPC1, ADAR, MFSD8, STXBP1, PRICKLE2, PRRT2, IDUA, or STX1B, and for treating a subject in need thereof, e.g., a subject with deficient ATP1A2, CACNA1A, SETD5, SHANK3, NF2, DNMT1, TCF4, RAI1, PEX1, ARSA, EIF2B5, EIF2B1, EIF2B2, NPC1, ADAR, MFSD8, STXBP1, PRICKLE2, PRRT2, IDUA, or STX1B protein expression.