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Related Experiment Video

Updated: Jun 19, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Spatial transcriptomic profiling of isolated microregions in tissue sections utilizing laser-induced forward

Kaiqiang Ye1, Wanqing Chang1, Jitao Xu1

  • 1State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China.

Plos One
|July 25, 2024
PubMed
Summary

We developed LIFT-seq, a new method for isolating specific tissue regions for spatial transcriptomics. This technique reliably profiles gene expression in microregions of interest, advancing our understanding of cell fates.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Neuroscience

Background:

  • Understanding cell fates in multicellular organisms requires gene expression profiling that preserves spatial information.
  • Current methods for isolating microregions of interest (mROIs) for spatial transcriptomics are limited in flexibility and simplicity.
  • Spatial transcriptomics is crucial for mapping gene expression within complex biological tissues.

Purpose of the Study:

  • To present a novel and efficient method for isolating microregions of interest (mROIs) for spatial transcriptomics.
  • To demonstrate the capability of the new method in profiling region-specific gene expression.
  • To validate the identified marker genes using established techniques.

Main Methods:

  • Development of a laser-induced forward transfer (LIFT)-based method.
  • Integration of LIFT with a full-length mRNA-sequencing protocol, termed LIFT-seq.
  • Application of LIFT-seq to profile gene expression in microregions from adjacent tissue sections of mouse brain (cortex and hippocampus).

Main Results:

  • LIFT-seq successfully and sensitively detected gene expression in selected mROIs from adjacent tissue sections.
  • The method accurately identified region-specific mROIs in the mouse cortex and hippocampus.
  • Marker genes specific to different cortical layers were identified and their expression patterns validated using in situ hybridization (ISH).

Conclusions:

  • LIFT-seq offers a valuable and efficient technique for spatial transcriptome profiling.
  • The method enables reliable isolation and analysis of microregions of interest for gene expression studies.
  • LIFT-seq has broad applicability for profiling spatial transcriptomes across various tissues.