Multiplex Cell Analysis Through In Situ Barcode Detection
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current single cell-based approaches for profiling biological targets are costly and have low throughput, limiting their potential value in applications such as genomic, transcriptomic, or proteomic analysis.
Innovation Solution
A method utilizing an in situ analytical platform to multiplex labeled cells or nuclei from multiple samples, allowing for high-throughput analysis with single-cell resolution by combining single-cell and in situ assays, using labeled cells with binding moieties and reporter oligonucleotides, and probes that bind to sample-specific and analyte-specific sequences for detection.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If single-cell sequencing is used for profiling biological targets, then measurement precision is improved, but productivity deteriorates due to low throughput and high cost
Solution Approach 1:
The patent combines single-cell labeling with in situ analysis by depositing labeled cells onto a substrate and performing multiplexed probe hybridization directly on the cells. This merging enables simultaneous single-cell resolution and high-throughput analysis, as multiple cells can be processed in parallel on the same substrate without requiring sequential sequencing of each cell individually.
Solution Approach 2:
The patent introduces a substrate as an intermediary platform that enables in situ analysis of labeled cells. The substrate serves as a mediator between single-cell labeling and high-throughput detection, allowing multiple cells to be fixed, probed, and analyzed simultaneously while maintaining single-cell resolution through spatial mapping of probes to individual cells.
2Measurement precision
If single-cell sequencing is used for profiling biological targets, then measurement precision is improved, but cost increases
Solution Approach 1:
The patent employs disposable, inexpensive reagents and substrates that can be easily discarded after use. The substrate and probes are designed as single-use components, eliminating the need for expensive, complex sequencing instruments and reducing overall operational costs while maintaining single-cell analysis capability.
Solution Approach 2:
The patent replaces complex mechanical sequencing systems with optical microscopy-based detection. Instead of using expensive sequencing instruments to read cellular genetic information, the system uses fluorescent probes and microscopy to detect analytes in labeled cells, significantly reducing equipment costs and operational expenses.
3Productivity
If in situ analysis is used to analyze multiple cells, then productivity is improved through high throughput, but measurement precision may deteriorate due to loss of single-cell resolution
Solution Approach 1:
The patent applies local quality by maintaining distinct physical and chemical properties at different locations on the substrate. Each labeled cell is deposited at a specific location and maintained as a discrete unit with its own labeling and probe hybridization characteristics, ensuring that analysis at any location reflects the properties of that specific cell while enabling parallel analysis of multiple cells across the substrate.
Solution Approach 2:
The patent segments the cell population into individually labeled and spatially separated units on the substrate. Each cell is labeled with sample-specific barcodes and probes are hybridized to specific locations within each cell, enabling simultaneous analysis of multiple cells while maintaining single-cell resolution through spatial segmentation and individual 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
Enables high-throughput analysis of up to 100,000 cells in a 1 cm² substrate area with significant cost benefits compared to single-cell sequencing, providing valuable spatial and abundance information on analytes.
Implementation Method 1
a binding moiety that binds to the cell
Implementation Method 2
a reporter oligonucleotide that hybridizes to the probe
Data Source
AI summary
Provided herein in some aspects are methods, compositions, kits, and systems for performing multiplexed single-cell analysis on an in situ platform, providing alternatives which have a higher cell throughput and/or lower cost per cell compared to current single-cell analysis techniques. In some embodiments, the methods disclosed herein comprise using labeling agents that comprise sample-specific barcodes and/or cell feature specific barcodes (e.g., analyte specific barcodes) to label single-cell populations, immobilizing the labeled cells, and performing in situ detection of the labeling agents and/or other features including cellular analytes of the labeled cells.