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Related Experiment Video

Updated: Jul 23, 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

Protocol for profiling in vitro intratumor heterogeneity using spatially annotated single-cell sequencing.

Myrthe M Smit¹, Kate J Feller¹, Li You¹

¹Department of Molecular Genetics, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands; Erasmus MC Cancer Institute, 3000 CA Rotterdam, the Netherlands.

|July 15, 2023

Summary

This summary is machine-generated.

This study introduces a new protocol for spatially annotated single-cell sequencing, enabling detailed profiling of tumor heterogeneity at single-cell resolution. The method combines imaging and photochemistry for precise cell selection and genetic analysis.

Keywords:

Bioinformatics Cancer Microscopy RNAseq

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Last Updated: Jul 23, 2025

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

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Published on: July 6, 2022

Comparative Lesions Analysis Through a Targeted Sequencing Approach

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Published on: November 5, 2019

A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

Published on: October 25, 2018

Area of Science:

Molecular Biology
Genomics
Cancer Research

Background:

Intratumor heterogeneity poses challenges in cancer treatment.
Understanding spatial variations in tumors is crucial for effective therapies.
Current single-cell sequencing methods often lack spatial context.

Purpose of the Study:

To present a novel protocol for spatially annotated single-cell sequencing.
To enable high-resolution spatial profiling of intratumor heterogeneity.
To provide a method applicable to various cell lines and potentially tissue sections.

Main Methods:

Combining live-cell imaging with photopatterned illumination.
Identifying and labeling specific regions of interest within an in vitro tumor model using photoactivatable dyes.
Isolating labeled cells for subsequent deep single-cell RNA sequencing (scRNAseq).

Main Results:

Demonstration of a protocol for spatially resolved single-cell analysis.
Successful application in an in vitro tumor model.
Potential for adaptation to diverse cell lines and tissue samples.

Conclusions:

The developed protocol offers a powerful tool for dissecting tumor microenvironments.
Spatially annotated single-cell sequencing enhances the understanding of cancer biology.
This technique can advance precision oncology by revealing spatial heterogeneity.