Histone Binding Agent Enrichment for Circulating Tumor DNA
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Solution Overview
Problem
Current methods for extracting and analyzing circulating tumor DNA (ctDNA) and nucleosomes from blood, serum, or plasma face challenges due to low concentrations and contamination with non-tumor DNA, making it difficult to detect and isolate tumor-specific markers effectively.
Innovation Solution
The use of a binding agent that specifically binds histone H3.1, H3.2, and H3t for affinity purification and enrichment of cell-free nucleosomes and associated ctDNA, allowing for improved isolation and analysis of tumor-derived nucleosomes and DNA.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional DNA extraction methods are used to isolate ctDNA from blood, then total DNA can be obtained, but the low concentration of tumor-specific DNA and contamination with non-tumor DNA make it difficult to detect tumor markers effectively
Solution Approach 1:
The method segments the total DNA population by size, isolating the smaller ctDNA fragments (50-200 bp) from larger genomic DNA. This size-based segmentation enables selective enrichment of tumor-derived DNA without requiring tumor-specific sequence information, thereby improving detection accuracy despite low ctDNA concentration
Solution Approach 2:
The patent introduces an intermediary enrichment step using nucleosome isolation as a mediator. Since ctDNA is predominantly packaged in nucleosomes and released as such from apoptotic tumor cells, this intermediary approach captures tumor DNA in its native packaged form, enhancing detection sensitivity while filtering out non-nucleosomal DNA
2Loss of information
If tissue biopsy is performed to obtain tumor DNA for analysis, then comprehensive tumor genetic information can be obtained, but repeated biopsies are invasive, expensive, and may not sample all tumor clones
Solution Approach 1:
The method extracts tumor genetic information from the bloodstream rather than from tissue, taking out the diagnostic capability from the invasive biopsy procedure. By isolating and analyzing ctDNA packaged in nucleosomes from blood samples, the method obtains comprehensive tumor genetic information without requiring repeated invasive tissue sampling
Solution Approach 2:
The nucleosome isolation method serves multiple functions: it enriches tumor DNA, preserves epigenetic markers, and enables both genetic and epigenetic analysis from a single blood sample. This multi-functional approach replaces multiple specialized procedures including tissue biopsy, reducing overall invasiveness while maintaining diagnostic comprehensiveness
3Reliability
If standard DNA extraction protocols are used, then DNA can be obtained for analysis, but the presence of non-tumor DNA contaminants reduces the specificity of tumor marker detection
Solution Approach 1:
The method applies local quality enhancement by specifically targeting and enriching the nucleosome-associated DNA fraction, which has different physical and chemical properties than bulk genomic DNA. This localized enrichment of the nucleosome-containing fraction increases the proportion of ctDNA from less than 1% to potentially much higher concentrations, thereby improving detection reliability
Solution Approach 2:
The patent changes the physical parameter of DNA organization by isolating nucleosomes as discrete entities rather than extracting free DNA. This parameter change in the state of DNA (from chromatin-bound to isolated nucleosomes) selectively enriches tumor-derived DNA while removing contaminants, enhancing both specificity and concentration of detectable tumor markers
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 quality and specificity of ctDNA and nucleosome samples, enabling more accurate detection and monitoring of cancer, even in low concentrations, by isolating tumor-specific markers from non-tumor contaminants.
Implementation Method 1
The use of a binding agent that specifically binds histone H3.1, H3.2, and H3t for affinity purification and enrichment of cell-free nucleosomes and associated ctDNA
Data Source
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AI summary
The invention relates to the use of histone binding agents for detecting, isolating and/or purifying cell free nucleosomes of tumor originor circulating tumor DNA from a biological sample. The invention also relates to methods and kits using said histone binding agents.