Antisense eRNA Targeting for Selective TNFSF10 Gene Control
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Solution Overview
Problem
Current methods for detecting and annotating enhancer RNAs (eRNAs) in the human genome are limited, with only tens of thousands detected despite millions of enhancers, hindering therapeutic development and understanding of their role in gene regulation.
Innovation Solution
A method involving a dense time series of GRO-seq and ChIP-seq data to generate a time-resolved enhancer activity map, identifying highly confident pairs of virus-inducible enhancers and their target genes, and using antisense compounds to inhibit TNFSF10 gene expression by targeting eRNAs.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If current methods for detecting and annotating eRNAs are used, then only tens of thousands of eRNAs can be detected, but this limits the understanding of their role in gene regulation and therapeutic development
Solution Approach 1:
The patent changes the detection parameters from steady-state measurements to dynamic time-series measurements of eRNA and pre-mRNA transcriptional induction. This parameter change enables systematic detection of condition-specific eRNAs and their functional relationships with target genes, resolving the limitation of detecting only tens of thousands of eRNAs while losing regulatory information.
2Ease of manufacture
If steady-state eRNA and mRNA levels are used for target gene prediction, then existing methods can be applied, but functional associations cannot be reliably identified
Solution Approach 1:
The patent transitions from static steady-state measurements to dynamic time-series measurements of transcriptional induction. By measuring how eRNA and pre-mRNA levels change over time in response to conditions, the method reliably identifies functional enhancer-target gene associations while maintaining systematic detectability.
3Adaptability or versatility
If antisense compounds target eRNAs to inhibit gene expression, then selective control of gene expression is achieved, but this requires accurate identification of functional eRNA-target pairs
Solution Approach 1:
The patent uses a feedback approach where transcriptional induction data of eRNAs and pre-mRNAs are integrated to identify functional associations. This feedback mechanism confirms that eRNAs and their target genes are co-induced under specific conditions, enabling accurate identification of eRNA-target pairs for selective antisense compound targeting.
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 allows for dynamic characterization of eRNA functional relationships and target gene regulation, demonstrating the necessity of eRNAs for full induction of target genes and potential for selective control of gene expression, as shown by reducing TNFSF10 expression and modulating interferon-induced apoptosis.
Implementation Method 1
contacting the mammalian cell with a single-stranded antisense compound comprising a sequence selected from a set of SEQ ID NOs: 1, 2, 3, 4, 5, or 6, wherein the antisense compound targets an enhancer RNA (eRNA) transcribed from a genomic enhancer sequence or region
Data Source
AI summary
The disclosure provides for eRNA-targeted transcriptional reprogramming through targeted reduction of eRNAs for a clinically relevant gene, TNFSF10, resulting in a selective control of interferon-induced apoptosis. A method of inhibiting a TNFSF10 gene expression in a human cell is disclosed. The methods described herein comprise contacting the human cell with a single-stranded antisense compound consisting of the sequence selected from a set of SEQ ID NOs: disclosed herein, wherein the antisense compound targets an enhancer RNA (eRNA) transcribed from a genomic enhancer sequence or region. The eRNA is an TNFSF10 eRNA sequence comprising the nucleic acid sequence selected from the SEQ ID NOs disclosed herein which inhibits expression of the TNFSF10 gene in the human cell.