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Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Spatial Transcriptomics, Proteomics, and Epigenomics as Tools in Tissue Engineering and Regenerative Medicine.

Mikko J Lammi1, Chengjuan Qu2

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Bioengineering (Basel, Switzerland)
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Summary

Innovative spatial transcriptomics, proteomics, and epigenomics reveal cellular functions and heterogeneity in tissues. Combining these powerful technologies enhances understanding of cell guidance in tissue engineering.

Keywords:
bioengineeringregenerative medicinesingle-cell RNA sequencingspatial multiomics

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Area of Science:

  • Multi-omics spatial technologies
  • Cellular and tissue analysis

Background:

  • Spatial transcriptomics, proteomics, and epigenomics offer high-resolution insights into cellular functions and interactions.
  • These techniques enable the study of gene and protein expression at the single-cell level, identifying cellular heterogeneity and rare cell populations.

Purpose of the Study:

  • To explore the capabilities and limitations of spatial transcriptomics, proteomics, and epigenomics.
  • To understand how these technologies can advance the study of bioengineered tissues and disease processes.
  • To highlight the potential of integrating these multi-omics approaches for improved tissue engineering.

Main Methods:

  • Spatial transcriptomics for mapping gene activity within tissue architecture.
  • Spatial proteomics for analyzing protein distribution.
  • Spatial epigenomics for understanding gene regulation in tissues.
  • Single-cell analysis to investigate cellular heterogeneity.

Main Results:

  • These methods allow simultaneous analysis of thousands of cells, providing deep transcriptomic views of complex tissues.
  • Spatial transcriptomics preserves tissue architecture, enabling mapping of gene activity across regions.
  • Spatial proteomics and epigenomics provide data on protein distribution and gene regulatory aspects, respectively.

Conclusions:

  • Despite limitations like technical noise and data interpretation challenges, these spatial multi-omics technologies are rapidly advancing.
  • Combining spatial transcriptomics, proteomics, and epigenomics promises a comprehensive understanding of cell function and tissue organization.
  • Integration of these techniques is expected to improve cell guidance in tissue-engineered constructs and enhance tissue technology products.