Oligonucleotide Probes for Single Cell Spatial Encoding
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Solution Overview
Problem
Current techniques for concomitant spatial and molecular measurements of biological cells are impractical for handling millions of distinct cells, as they require separate storage and processing, which is inefficient and not feasible for large-scale applications.
Innovation Solution
The method involves delivering molecular probes with unique oligonucleotide sequences into biological cells using vessels like retroviruses, disulfide-linked cell-penetrating peptides, or bead micro-particles, which encode the cell's position within a biological sample, allowing for positional delivery and encoding, and subsequent single cell RNA sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If image-based analysis with microscopy is used for spatial and molecular measurements, then measurement precision is improved, but device complexity and processing difficulty increase for millions of cells
Solution Approach 1:
The patent combines spatial information and molecular information into a single integrated measurement system. By using in situ sequencing that captures both the location and molecular composition of cells simultaneously within the tissue architecture, the method merges what were previously separate measurement processes into one unified approach, eliminating the need for separate storage and processing of spatial and molecular data
Solution Approach 2:
The sequencing system performs multiple functions simultaneously: it captures spatial coordinates, identifies cell types through molecular profiling, and preserves tissue architecture context. This multi-functional approach allows a single experiment to replace what would otherwise require multiple separate experiments and processing workflows
2Measurement precision
If separate storage and processing of individual cells is implemented, then measurement accuracy is maintained, but productivity and ease of operation deteriorate when handling millions of cells
Solution Approach 1:
The method processes millions of cells simultaneously in their tissue context rather than handling them individually. By performing sequencing directly in situ on tissue sections containing vast numbers of cells, the system achieves high throughput while maintaining the ability to resolve individual cell identities and states through unique molecular barcodes and spatial coordinates
3Measurement precision
If cells are dissociated for molecular profiling, then molecular measurement sensitivity is improved, but loss of spatial information occurs
Solution Approach 1:
The system performs spatial encoding before molecular analysis by capturing the location of each cell while it remains in situ. Unique spatial coordinates are assigned to each cell based on its position in the tissue section before any dissociation or molecular extraction occurs, thereby preserving spatial information throughout subsequent processing steps
Solution Approach 2:
The patent uses unique molecular barcodes and spatial coordinate systems as intermediaries that link molecular identity to spatial position. These intermediary elements are attached to or associated with each cell in situ, allowing the system to track and retrieve spatial information even after cells are dissociated for molecular profiling
Data Source
AI summary
Techniques for positional delivery and position encoding by oligonucleotides of biological cells for single cell RNA sequencing are provided. In one aspect, a method of positional delivery and encoding of cells in a biological sample includes: encoding the cells in the biological sample for single cell sequencing by delivering molecular probes inside the cells that encode a position of the cells in the biological sample. A system for positional delivery and encoding of cells in a biological sample is also provided.