Spatial Gene Expression Capture Probes for Live-Tissue Activity Tracking

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Solution Overview

Problem

Existing spatial gene expression technologies fail to provide concurrent spatio-temporal measurements of gene expression and cellular activity, particularly in live tissues, limiting the understanding of cellular behavior and drug effects.

Innovation Solution

A method using a perfusion chamber or multi-well plate system with capture probes that include spatial barcodes and capture domains to record cellular activity and gene expression, allowing for simultaneous spatio-temporal measurements by sequencing the spatial barcode and analyte sequences.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If spatial gene expression technology is used to capture gene transcripts from frozen or fixed tissues, then spatial positioning of gene transcripts is maintained, but temporal aspect of gene expression cannot be studied in live cells

Engineering Contradiction:

Improvespatial positioning accuracyVSAvoidtemporal measurement capability

Core Design Contradiction:

Measurement precisionVSAdaptability or versatility

Solution Approach 1:

The system segments the measurement process into two independent components: spatial positioning (handled by the capture probe array) and temporal/dynamic measurement (handled by the perfusion chamber with live cells). This allows each component to optimize for its specific function without compromising the other.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The capture probe array is designed to serve multiple functions: it provides spatial positioning information, captures gene expression data, and is compatible with both fixed and live tissue samples. The perfusion chamber adds the capability for temporal measurement and pharmacological manipulation, making the overall system universally applicable to various research questions.

Inventive Principle:

Principle #6Universality (Multi-functionality)

2Loss of information

If spatial gene expression arrays are used to detect gene expression, then spatial information is obtained, but cellular activity cannot be tracked in live tissues

Engineering Contradiction:

Improvespatial information retentionVSAvoidcellular activity tracking capability

Core Design Contradiction:

Loss of informationVSAdaptability or versatility

Solution Approach 1:

The invention merges the spatial gene expression array technology with a perfusion chamber system that maintains live cells. This combination allows simultaneous acquisition of spatial information (from the array) and temporal/dynamic information (from the live cell perfusion chamber), eliminating the need to choose between the two measurement types.

Inventive Principle:

Principle #5Merging (Combining)

Solution Approach 2:

The perfusion chamber enables continuous measurement of cellular activity in live cells over time, while the spatial array provides continuous spatial mapping. Both measurements can be performed concurrently and continuously, maintaining the viability of cells throughout the experiment.

Inventive Principle:

Principle #20Continuity of useful action

3Measurement precision

If frozen and fixed samples are used for spatial gene expression, then spatial positioning is maintained, but pharmacological manipulations cannot be performed

Engineering Contradiction:

Improvespatial positioning accuracyVSAvoidpharmacological manipulation capability

Core Design Contradiction:

Measurement precisionVSAdaptability or versatility

Solution Approach 1:

The system transitions from static frozen/fixed samples to dynamic live cell systems in the perfusion chamber. This allows the samples to remain alive and responsive to pharmacological manipulations while maintaining spatial positioning capability through the capture probe array.

Inventive Principle:

Principle #15Dynamics

Solution Approach 2:

The system changes the physical state parameter of the samples from frozen/fixed to live/viable. This parameter change enables pharmacological manipulations to be performed while the spatial array continues to provide positioning information through the capture probes.

Inventive Principle:

Principle #35Parameter changes

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 concurrent detection of gene expression and cellular activity in live tissues, providing comprehensive spatio-temporal data for drug screening and understanding tissue responses.

Implementation Method 1

hybridizing the analyte to the capture domain of the capture probe

Methodology Applied

Scientific EffectHybridization:

Implementation Method 2

extending the capture probe using the analyte as a template, thereby generating an extended capture probe

Methodology Applied

Scientific EffectTemplate-directed synthesis:

Implementation Method 3

amplifying the extended capture probe to produce a plurality of extended capture probes

Methodology Applied

Scientific EffectAmplification:

Implementation Method 4

sequencing (i) the spatial barcode, or a complement thereof, and (ii) all or part of the sequence of the analyte

Methodology Applied

Scientific EffectSequencing:

Data Source

PatentEP4414459B1Simultaneous spatio-temporal measurement of gene expression and cellular activity

Publication Date: 2025.09.03 10X GENOMICS INC

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AI summary

Provided herein are methods for simultaneous spatio-temporal measurement of gene expression and cellular activity.