Single Cell Protein Interaction Mapping via Proximity Probes
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Solution Overview
Problem
Current techniques for mapping protein abundance and spatial interactions within individual cells are limited, as they cannot resolve spatial interactions and provide information on protein interactions in single cells.
Innovation Solution
A method involving the use of labelled cells with proximity probes and cell barcode molecules to generate barcoded molecules, allowing for the measurement of protein-protein interactions and spatial relationships within single cells.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If FACS or mass cytometry is used to map protein abundance, then total protein abundance can be measured, but spatial and physical interactions within cells cannot be resolved
Solution Approach 1:
The patent introduces proximity probes as intermediary molecules that bridge the gap between proteins of interest. These probes are designed to bind to proteins and carry barcode sequences that enable detection of both protein abundance and spatial relationships. The proximity probes act as mediators that translate physical proximity into detectable signals, resolving the contradiction between measuring total abundance and capturing spatial interaction information.
Solution Approach 2:
The patent adds a new dimension to protein analysis by incorporating spatial coordinate information alongside traditional abundance measurements. Through the use of proximity probes with barcode sequences and partitioning cells into spatial locations, the method transforms one-dimensional abundance data into multi-dimensional data that includes spatial relationships, enabling simultaneous measurement of both protein quantity and interaction context.
2Loss of information
If co-immunoprecipitation or FRET is used to detect protein interactions, then spatial interactions can be detected, but these procedures only work in bulk settings or have extremely limited resolution
Solution Approach 1:
The patent segments the cell population into individual cells through partitioning, and further segments the detection system by assigning unique barcode sequences to different proteins and spatial locations. This segmentation enables single-cell resolution analysis, allowing detection of protein interactions within individual cells rather than averaging signals across bulk populations, thereby achieving both spatial interaction detection and single-cell precision.
Solution Approach 2:
The patent creates molecular copies through the use of barcode sequences that can be amplified and sequenced. Instead of directly observing protein interactions (which is difficult), the method creates informational copies in the form of barcode sequences that encode spatial and interaction data. These copies can be replicated and analyzed through sequencing, enabling high-resolution single-cell detection without requiring direct optical observation of the interactions themselves.
3Loss of information
If proximity probes with barcode sequences are used, then spatial relationships and protein interactions can be resolved in single cells, but the complexity of the labeling and detection system increases
Solution Approach 1:
The patent designs proximity probes that serve multiple functions simultaneously: they bind to target proteins, provide spatial location information through barcode sequences, and enable detection of protein interactions. This multi-functionality reduces the need for separate reagents and procedures, thereby managing system complexity while achieving comprehensive single-cell protein analysis including abundance, location, and interaction data.
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 the resolution of protein interaction events in single cells, providing detailed information on protein abundance and spatial relationships, overcoming the limitations of existing techniques.
Implementation Method 1
the cell barcode molecule comprises a cell barcode sequence that is complementary to the first and second barcode sequences
Data Source
AI summary
Provided herein are methods identifying protein-protein interactions in a single cell context. In some cases, the methods may be used to measure the abundance of protein-protein interactions in a single cell context. In some cases, the methods may be used to map relationships (e.g., spatial relationships) between proteins in a single cell context. Generally, the methods employ the use of proximity probes coupled with splint oligonucleotides to link information about the relationship of proteins within a single cell context, which may then be read in a downstream process (e.g., a sequencing reaction).