Spatial Protein Analysis Using Localization Tags and Sequencing
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Solution Overview
Problem
Existing methods for identifying molecules from a sample while retaining information regarding its spatial origin are limited, particularly in analyzing a large number of unknown proteins within a tissue sample, and lack the ability to provide cellular features such as cell types or phenotypes.
Innovation Solution
A method involving the use of localization tags, such as unique molecular identifiers (UMIs), to label polypeptides in a spatial sample, followed by analyzing these tags to generate localization sequences, performing an assay to determine the extended recording tag sequences, and correlating them with spatial locations, thereby associating protein sequences with their spatial information.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If antibodies or target-specific reagents are used to identify and visualize protein location, then spatial information is retained, but the ability to analyze a large number of unknown proteins is limited
Solution Approach 1:
The method segments the analysis process into two independent components: (1) spatial tagging using localization tags that capture positional information, and (2) protein identification using sequencing assays. This segmentation allows each component to be optimized independently, enabling the system to handle both spatial retention and high-throughput protein analysis simultaneously.
Solution Approach 2:
The localization tag serves as a universal marker that can be attached to any protein in the sample, making the system adaptable to analyze any protein without requiring protein-specific antibodies or reagents. This universal tagging approach enables high-throughput analysis of unknown proteins while preserving spatial information.
2Productivity
If imaging based approaches are used for large numbers of cells, then throughput is improved, but the ability to provide cellular features information such as cell types or phenotypes is lost
Solution Approach 1:
The localization tag acts as an intermediary that bridges spatial information and protein identity. By attaching this tag to proteins within cells, the system captures both the spatial context (which cell the protein is in) and the protein identity (through sequencing), thereby preserving cellular features information while maintaining high throughput.
Solution Approach 2:
The method replaces traditional imaging-based mechanical observation with a molecular tagging and sequencing approach. Instead of visually imaging cells to identify features, the system uses molecular tags and sequencing assays to extract both spatial and cellular feature information, achieving higher throughput without information loss.
3Measurement precision
If traditional protein analysis methods are used, then protein identification is achieved, but spatial context is lost
Solution Approach 1:
The method performs preliminary tagging of proteins with localization tags before any protein extraction or analysis. This preliminary action captures the spatial context while the protein is still in its native spatial arrangement, ensuring that spatial information is preserved throughout subsequent protein identification steps.
Data Source
AI summary
Provided herein are methods and compositions for spatial analysis of macromolecules (e.g., proteins, polypeptides, or peptides). In some embodiments, the methods are for analyzing a macromolecule or a plurality of macromolecules, (e.g., peptides, polypeptides, and proteins) including determining spatial information and sequencing the macromolecule. In some embodiments, the analysis employs barcoding and nucleic acid encoding of molecular recognition events, and/or detectable labels. Also provided are compositions, e.g., kits, containing components for performing the provided methods for analysis of the macromolecule.