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Multiplexed spatial transcriptomics methods and the application of expansion microscopy.

Andra Fortner1,2, Octavian Bucur2,3

  • 1Medical School, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany.

Frontiers in Cell and Developmental Biology
|August 6, 2024
PubMed
Summary

Spatial transcriptomics methods like ISS, ISH, and NGS reveal cellular organization. Combining these with expansion microscopy (ExM) enhances RNA detection and advances biological and medical insights.

Keywords:
Ex-STExSeqFISSEQMERFISHVisiumexpansion microscopyspatial omicstranscriptomics

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Spatial transcriptomics revolutionizes cellular organization studies.
  • Numerous innovative transcriptomics methods have emerged, including in situ sequencing (ISS), in situ hybridization (ISH), and next-generation sequencing (NGS)-based region capture.
  • A key challenge is limited RNA detection due to optical crowding.

Purpose of the Study:

  • To review ISS, ISH, and NGS-based spatial transcriptomic protocols.
  • To explore how expansion microscopy (ExM) enhances these techniques.
  • To highlight the broader implications of transcriptomics in biology and medicine.

Main Methods:

  • Review of existing literature on spatial transcriptomics techniques (ISS, ISH, NGS).
  • Discussion of expansion microscopy (ExM) principles and applications.
  • Integration of ExM with spatial transcriptomics protocols.

Main Results:

  • ExM overcomes optical crowding and diffraction limits for improved RNA visualization.
  • Combining ExM with ISS, ISH, and NGS enhances RNA detection sensitivity and spatial resolution.
  • Spatial transcriptomics provides insights into gene expression, cell types, and disease mechanisms.

Conclusions:

  • Expansion microscopy significantly improves spatial transcriptomics performance.
  • These enhanced techniques offer deeper understanding of cellular organization and disease.
  • Spatial transcriptomics holds vast potential for biological and medical research breakthroughs.