TEMPOmap Spatiotemporal Transcriptomics Subcellular Resolution
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Solution Overview
Problem
Current methods for spatial transcriptomics only capture mRNAs as static pictures, failing to account for their dynamic nature and ignoring intracellular information, thus lacking the ability to study gene expression in a spatiotemporal context.
Innovation Solution
The TEMPOmap method, which incorporates temporal resolution into spatial transcriptomic workflows by metabolically labeling nucleic acids with nucleoside analogs and using oligonucleotide probes to track nascently transcribed RNAs at subcellular resolution, allowing for the study of intracellular activities and dynamic gene expression.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of information
If current spatial transcriptomics methods are used to detect mRNAs, then spatial distribution of genes can be visualized, but temporal dynamics of gene expression cannot be captured
Solution Approach 1:
The method incorporates temporal resolution by performing sequential labeling at different time points before the imaging step. Nucleoside analogs are administered to cells at specific time points to label nascent transcripts, and these labeled transcripts are then detected in the same spatial location, creating a temporal record without requiring temporal imaging.
Solution Approach 2:
Nucleoside analogs serve as intermediaries that carry temporal information into the spatial transcriptomics workflow. These analogs are incorporated into nascent RNA transcripts at specific time points and act as temporal markers that can be detected alongside spatial information, bridging the gap between temporal and spatial dimensions.
2Measurement precision
If pan-cellular level detection is used, then heterogeneous cell types can be identified, but intracellular spatial information is lost
Solution Approach 1:
The method segments the detection process into distinct components: temporal labeling with nucleoside analogs, spatial mapping through transcriptomics, and integration of both dimensions. This segmentation allows intracellular spatial information to be resolved while maintaining compatibility with existing spatial transcriptomics workflows.
Solution Approach 2:
The method adds a temporal dimension to the existing spatial transcriptomics framework. By incorporating time-point specific labeling with nucleoside analogs, the workflow transitions from 2D spatial mapping to 3D spatiotemporal analysis, enabling resolution of intracellular spatial dynamics over time.
3Reliability
If static imaging of mRNAs is performed, then spatial distribution is captured, but dynamic gene expression processes are obscured
Solution Approach 1:
The method uses periodic labeling with nucleoside analogs at different time points to capture dynamic gene expression. Instead of continuous imaging, discrete time-point labeling is performed, reducing material consumption while reliably capturing the temporal dynamics of transcriptional processes.
Solution Approach 2:
The method creates temporal copies of spatial information by labeling nascent transcripts at different time points with nucleoside analogs. Each time point generates a copy of the spatial transcriptome profile, allowing dynamic processes to be reconstructed from these temporal copies without requiring continuous material presence.
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 visualization and understanding of genomic information processing in both time and space, facilitating the study of gene expression dynamics and its role in disease development and progression.
Implementation Method 1
incubating a cell in the presence of a pool of nucleoside analogs for an amount of time t1 to metabolically label nucleic acids synthesized by the cell
Implementation Method 2
contacting the metabolically labeled nucleic acids with one or more pairs of oligonucleotide probes comprising a second oligonucleotide probe and a third oligonucleotide probe, wherein the third oligonucleotide probe comprises a portion that is complementary to a metabolically labeled nucleic acid of interest
Implementation Method 3
performing rolling circle amplification to amplify the circular oligonucleotide using the second oligonucleotide probe as a primer to produce one or more concatenated amplicons
Data Source
AI summary
The present disclosure provides methods for profiling spatiotemporal gene expression, including methods for profiling spatiotemporal gene expression in vivo in a subject. The present disclosure also provides methods for profiling the role of post-transcriptional modification in spatiotemporal gene expression, methods for studying the role of spatiotemporal gene expression in the development or progression of a disease or disorder, methods for screening for an agent capable of modulating spatiotemporal gene expression, methods for diagnosing a disease or disorder in a subject, and methods for treating a disease or disorder in a subject. Oligonucleotide probes useful in the methods described herein are also provided by the present disclosure. The present disclosure also provide kits comprising the oligonucleotide probes disclosed herein. Systems for profiling spatiotemporal gene expression are also provided by the present disclosure.