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Related Experiment Video

Updated: Jun 16, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

Scalable spatial single-cell transcriptomics and translatomics in 3D thick tissue blocks.

Xin Sui^1,2,3, Jennifer A Lo^2,4,3, Shuchen Luo^1,2

¹Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.

Biorxiv : the Preprint Server for Biology

|August 16, 2024

Summary

This summary is machine-generated.

New 3D spatial profiling methods, Deep-STARmap and Deep-RIBOmap, enable gene and translation activity mapping in thick tissue blocks. This advances understanding of gene function in tissue structure and disease.

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Last Updated: Jun 16, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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Published on: January 10, 2019

Staining and High-Resolution Imaging of Three-Dimensional Organoid and Spheroid Models

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Published on: March 27, 2021

Area of Science:

Molecular Biology
Genomics
Biotechnology

Background:

Understanding gene expression in 3D tissue context is crucial for health and disease research.
Existing spatial profiling methods are limited to thin tissue sections (5-20 μm).

Purpose of the Study:

To develop novel 3D spatial profiling techniques for gene and translation activity quantification.
To enable analysis within thicker tissue blocks (up to 200 μm).

Main Methods:

Developed Deep-STARmap for 3D transcript quantification and Deep-RIBOmap for 3D translation activity mapping.
Utilized scalable probe synthesis, hydrogel embedding, and cDNA crosslinking.
Integrated with multicolor fluorescent protein imaging for cell typing and morphology tracing.

Main Results:

Achieved 3D in situ quantification of thousands of gene transcripts and translation activities in 200-μm thick tissue.
Successfully performed molecular cell typing and 3D neuron morphology tracing in mouse brain.
Demonstrated comprehensive analysis of tumor-immune interactions in human skin cancer.

Conclusions:

Deep-STARmap and Deep-RIBOmap overcome limitations of existing methods, enabling high-resolution 3D spatial profiling.
These techniques provide new avenues for studying gene function, tissue architecture, and disease mechanisms in 3D.
Facilitates quantitative analysis of complex biological systems like tumor microenvironments.