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Related Experiment Video

Updated: Jul 12, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections.

Hailey Sounart1, Enikő Lázár1,2, Yuvarani Masarapu1

  • 1Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden.

Genome Biology
|October 20, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces a spatial transcriptomics method for analyzing host and pathogen gene expression in formalin-fixed paraffin-embedded (FFPE) tissues. The approach reveals key insights into host responses during SARS-CoV-2 infection in lung cells.

Keywords:
Colocalization analysisFormalin-fixed paraffin-embedded (FFPE) tissuesHost–pathogen interactionsSpatial transcriptomics

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Area of Science:

  • Infectious Diseases
  • Molecular Biology
  • Genomics

Background:

  • Localized host-pathogen interactions are critical for understanding infection dynamics but are challenging to study.
  • Existing technologies often lack the resolution or scope to simultaneously analyze host and pathogen molecular responses within tissue microenvironments.

Purpose of the Study:

  • To develop and validate a novel spatial transcriptomics approach for simultaneous, high-resolution transcriptome-wide analysis of both host and pathogen in FFPE tissue sections.
  • To investigate the spatial landscape of host-pathogen interactions during SARS-CoV-2 infection in human lung tissue.

Main Methods:

  • Development of a spatial transcriptomics technique enabling simultaneous transcriptome-wide gene expression profiling of host and pathogen.
  • Application of the method to formalin-fixed paraffin-embedded (FFPE) human lung tissue samples from COVID-19 patients.
  • Validation of spatial SARS-CoV-2 detection using RNAScope and in situ sequencing.

Main Results:

  • The methodology successfully captured spatial gene expression data for both host and SARS-CoV-2 at near single-cell resolution in FFPE lung tissues.
  • Spatial colocalization analysis identified potential host factors modulating SARS-CoV-2 infection.
  • Validation confirmed the accuracy of the spatial detection of the virus.

Conclusions:

  • This novel spatial transcriptomics approach offers unprecedented insights into the complex interplay between hosts and pathogens at a spatial level within FFPE tissues.
  • The technique facilitates unbiased, simultaneous detection of two transcriptomes, advancing the study of infectious diseases and host responses.
  • Findings contribute to understanding the host response to SARS-CoV-2 infection and may guide therapeutic strategies.