Spatial Single-Cell Sequencing with In Situ Barcode Retention

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Solution Overview

Problem

Current single cell sequencing methods fail to provide spatial context and are limited by low capture efficiency, high cost, and complex spatial tagging, leading to loss of spatial information and restricted multiplexing capabilities.

Innovation Solution

A method for adding spatially addressed nucleic acid barcodes to cellular samples in situ, allowing for dissociation of cells while maintaining spatial tags, and analyzing them through single cell sequencing to provide spatially-resolved profiles.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Loss of information

If spatial tagging and in situ assays are combined, then spatial information is preserved, but device complexity increases and multiplexing capabilities are limited

Engineering Contradiction:

Improvespatial informationVSAvoidsystem complexity

Core Design Contradiction:

Loss of informationVSDevice complexity

Solution Approach 1:

The patent segments the spatial tagging system into two independent parts: (1) spatial hash tags that provide spatial location information, and (2) single cell barcodes that provide cell identity information. These are added separately and independently, allowing each component to be optimized without compromising the other, thereby reducing overall system complexity while maintaining spatial information.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The spatial hash tags serve multiple functions: they provide spatial location information, act as barcodes for digital recording, and can be detected through various methods (fluorescence, microscopy, sequencing). This multi-functionality reduces the need for separate specialized reagents and methods, simplifying the overall system.

Inventive Principle:

Principle #6Universality (Multi-functionality)

2Productivity

If array-based methods are used, then sequencing capability is provided, but capture efficiency decreases and spatial resolution is reduced

Engineering Contradiction:

Improvesequencing capabilityVSAvoidspatial resolution

Core Design Contradiction:

ProductivityVSMeasurement precision

Solution Approach 1:

The patent extracts the spatial information encoding into separate spatial hash tags that remain with the cells during dissociation. This allows single-cell sequencing to be performed without requiring the cells to be固定在 arrays, thereby maintaining high spatial resolution while enabling efficient sequencing through standard single-cell protocols.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

Instead of physically transferring RNA from tissue sections to arrays (which loses spatial information), the patent creates digital copies of spatial location through barcode sequences. These barcode copies are added to cells and maintained through dissociation, allowing spatial information to be preserved without physical array-based constraints.

Inventive Principle:

Principle #26Copying

3Productivity

If compartmentalization of single cells is performed, then single cell sequencing is enabled, but spatial context is removed

Engineering Contradiction:

Improvesingle cell sequencingVSAvoidspatial context

Core Design Contradiction:

ProductivityVSLoss of information

Solution Approach 1:

The patent performs preliminary action by adding spatial hash tags and single cell barcodes to cells before dissociation. This preliminary barcoding ensures that spatial and identity information are already encoded in the cells before they are separated, allowing single-cell sequencing to be performed while preserving spatial context through the pre-added barcodes.

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The spatial hash tags act as intermediaries that bridge the gap between spatial location and single-cell analysis. These tags are added to cells in situ, survive dissociation, and provide spatial information that can be mapped back to the original tissue location, thereby mediating between the need for single-cell resolution and spatial context preservation.

Inventive Principle:

Principle #24Intermediary (Mediator)

4Productivity

If barcoded arrays are used, then sequencing is enabled, but manufacturing cost increases and spatial resolution is limited

Engineering Contradiction:

Improvesequencing capabilityVSAvoidmanufacturing cost

Core Design Contradiction:

ProductivityVSEase of manufacture

Solution Approach 1:

The patent uses inexpensive, disposable spatial hash tags and single cell barcodes that can be synthesized through standard oligonucleotide methods. These short-lived molecular tags are added to cells and then discarded after providing their informational function, eliminating the need for expensive, complex barcoded arrays while maintaining sequencing capability.

Inventive Principle:

Principle #27Cheap short-living objects (Disposable)

Data Source

PatentUS20260028752A1Methods and compositions for spatially-resolved single cell sequencing

Publication Date: 2026.01.29 SCALE BIOSCIENCES INC

AI summary

Provided herein, among other things, is a method for spatial single cell analysis. In some embodiments, the method may comprise: obtaining a cellular sample comprising nucleic acid molecules, binding spatial tags to the sample, removing any unbound or unreacted spatial tags, determining the location and identity of the spatial tag, dissociating the sample into single cells, performing single cell sequencing, determine the spatial barcode for each single cell, and assigning the single cell sequencing reads to its spatial location.