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Related Experiment Video

Updated: Aug 10, 2025

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Published on: September 2, 2013

Genome-wide spatial expression profiling in formalin-fixed tissues.

Eva Gracia Villacampa¹, Ludvig Larsson¹, Reza Mirzazadeh¹

¹Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, 17165 Stockholm, Sweden.

|February 13, 2023

Summary

This summary is machine-generated.

This study introduces a new method for genome-wide spatial mRNA analysis in formalin-fixed paraffin-embedded (FFPE) tissues. This technique enables detailed molecular mapping of anatomical regions and heterogeneous clinical samples.

Keywords:

COVID-19 FFPE PFA SARS-CoV-2 Visium genome-wide mouse brain organoids ovarian carcinosarcoma spatial transcriptomics

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Area of Science:

Molecular Biology
Genomics
Histopathology

Background:

Formalin-fixed paraffin embedding (FFPE) is the standard for long-term tissue preservation.
Analyzing spatial gene expression in FFPE tissues is crucial for understanding tissue architecture and disease mechanisms.
Existing methods may have limitations in scalability or resolution for FFPE samples.

Purpose of the Study:

To develop and validate a genome-wide spatial mRNA analysis method for FFPE tissue sections.
To demonstrate the utility of this method for cell type mapping and molecular delineation of anatomical structures.
To showcase its application in analyzing heterogeneous clinical samples and organoids.

Main Methods:

Utilized commercially available imaging and spatial barcoding techniques.
Employed barcoded oligo(dT) probes to capture the 3' end of mRNA molecules in FFPE tissue sections.
Performed genome-wide expression profiling on various FFPE biospecimens.

Main Results:

Successfully mapped gene expression and delineated anatomical regions in mouse brain sections.
Characterized transcriptomic signatures in ovarian carcinosarcoma samples, revealing molecular insights into heterogeneity.
Demonstrated applicability to human organoids and FFPE lung biopsy specimens, including those infected with SARS-CoV-2.

Conclusions:

The developed method provides a powerful tool for genome-wide spatial mRNA analysis in FFPE tissues.
This approach facilitates retrospective analysis of biobanked samples for longitudinal studies and biomarker discovery.
It holds significant potential for advancing research in various fields, from neuroscience to oncology and infectious diseases.