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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

SCAMPR, a single-cell automated multiplex pipeline for RNA quantification and spatial mapping.

Ramin Ali Marandi Ghoddousi^1,2, Valerie M Magalong¹, Anna K Kamitakahara^1,2,3

¹Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.

Cell Reports Methods

|October 31, 2022

Summary

We developed SCAMPR, a new pipeline for analyzing spatial gene expression in single neurons. This tool efficiently quantifies mRNA signals, aiding in understanding gene expression

Keywords:

HiPlex RNAscope bioinformatics heterogeneity in situ hybridization neuronal topography quantitative analysis segmentation spatial mapping spatial transcriptomics

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Last Updated: Aug 23, 2025

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Published on: July 6, 2022

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

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Published on: August 3, 2011

Area of Science:

Neuroscience
Molecular Biology
Genomics

Background:

Spatial gene expression analysis is crucial for understanding cell types in the nervous system.
Advanced techniques enable visualization of multiple mRNAs at single-cell resolution, but data analysis remains challenging.
High-dimensional datasets from multiplexed RNA visualization require efficient quantification methods.

Purpose of the Study:

To develop an automated pipeline for accurate segmentation and quantification of neuronal cell bodies and mRNA signals.
To facilitate the analysis of high-dimensional spatial gene expression data.
To demonstrate the utility of the pipeline in mapping gene expression in neuronal subtypes.

Main Methods:

Developed the single-cell automated multiplex pipeline for RNA (SCAMPR).
Utilized a dual immunohistochemistry-RNAscope protocol for cell body segmentation.
Employed open-source image processing and automated segmentation for mRNA quantification.
Applied SCAMPR to peripheral (vagal nodose) and central (visual cortex) neurons.

Main Results:

SCAMPR enables rapid and accurate segmentation of neuronal cell bodies.
The pipeline effectively quantifies both low- and high-abundance mRNA signals.
Demonstrated proof of principle for spatial mapping of gene expression in distinct neuronal populations.
Identified the impact of early life stress on gene expression in vagal neuron subtypes.

Conclusions:

SCAMPR provides an efficient and accurate method for analyzing spatial gene expression in single neurons.
The pipeline addresses challenges in quantifying high-dimensional multiplexed RNA data.
SCAMPR is effective for topographic phenotyping and linking gene expression to tissue topography.