Barcoded Particle Physical Mapping for Cell Polarity Analysis
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Solution Overview
Problem
Current methods for analyzing cell polarity are low throughput and challenging to automate, failing to provide effective analysis of spatial relationships between cell surface markers, which is essential for understanding cellular functions.
Innovation Solution
A method involving barcoded particles with unique oligonucleotide sequences that are hybridized with bridging moieties to create reaction products, allowing for sequencing and mapping of particle pairs to analyze marker distribution on cells, enabling high-throughput analysis of cell polarity without the need for microscopy.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If microscopy is used to analyze spatial relationships between markers on single cells, then measurement precision is improved, but productivity deteriorates due to low throughput and difficulty in automation
Solution Approach 1:
The patent creates physical map copies of cell surfaces using barcoded particles that represent spatial positions. Instead of directly imaging cells with microscopy, the method generates replicable physical maps through ligation reactions that capture spatial relationships in a format suitable for high-throughput sequencing analysis, thereby maintaining measurement precision while enabling automated high-throughput processing
Solution Approach 2:
The patent replaces the mechanical/optical system of microscopy with a biochemical system based on ligation reactions and next-generation sequencing. By substituting physical imaging with chemical reactions that encode spatial information in DNA sequences, the method achieves comparable spatial relationship analysis with the advantage of automated high-throughput processing
2Productivity
If flow cytometry or compartmental methods are used to analyze cell surface markers, then productivity is improved through high throughput, but measurement precision deteriorates due to lack of spatial relationship information
Solution Approach 1:
The patent introduces barcoded particles as intermediary elements that bridge the gap between high-throughput flow cytometry and spatial resolution. These particles serve as mediators that carry unique barcodes representing spatial positions, allowing spatial relationship information to be captured and transmitted through sequencing while maintaining high-throughput capabilities
Solution Approach 2:
The patent adds a spatial dimension to traditional flow cytometry data by incorporating barcoded particles that encode positional information. This transforms one-dimensional flow cytometry measurements into multi-dimensional data that includes spatial coordinates, enabling simultaneous high-throughput processing and spatial relationship analysis
3Measurement precision
If proximity ligation assays or array-based methods are used to analyze spatial relationships, then measurement precision is improved, but device complexity increases making them difficult to adapt to cell surface marker analysis
Solution Approach 1:
The patent creates a universal method that can analyze various cell surface markers using the same barcoded particle platform. The approach combines elements of proximity ligation assays with flow cytometry-compatible protocols, making it adaptable to different markers and cell types without requiring complex specialized equipment for each application
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 method allows for the high-throughput analysis of cell polarity by creating physical maps of barcoded particles attached to cells, providing detailed information on marker distribution and spatial relationships, thereby enhancing the understanding of cellular functions and immune cell activities.
Implementation Method 1
a population of bridging moieties that comprises oligonucleotide sequences, wherein the bridging moieties are hybridized directly or indirectly to complementary sites in the surface-tethered oligonucleotides
Data Source
AI summary
Provided herein is a method for making a physical map of a population of barcoded particles. In some embodiments, the method may involve: producing a complex comprising: i. a population of barcoded particles, wherein the barcoded particles are uniquely barcoded by surface-tethered oligonucleotides that have unique particle identifier sequences; and ii. a population of bridging moieties that comprises oligonucleotide sequences; wherein the bridging moieties are hybridized directly or indirectly to complementary sites in the surface-tethered oligonucleotides; performing a ligation, polymerization and/or a gap-fill/ligation reaction on the complex, thereby producing reaction products that comprise pairs of unique particle identifier sequences or complements thereof from adjacent barcoded particles: sequencing the reaction products, analyzing the sequences to making one or more physical maps of the barcoded particles. Systems for practicing the method are also provided.