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Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues.

Zhiliang Bai1, Dingyao Zhang2, Yan Gao3

  • 1Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.

Biorxiv : the Preprint Server for Biology
|February 19, 2024
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Summary

Patho-DBiT enables spatial full-coverage transcriptome sequencing in FFPE tissues, revealing RNA processing and variants. This method decodes RNA biology in archived human samples for disease research.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Spatial transcriptomics currently focuses on gene expression, limiting the study of complex RNA dynamics in tissues.
  • Formalin-fixed and paraffin-embedded (FFPE) tissues are crucial for human biology and disease research but challenging for detailed RNA analysis.
  • Understanding the full RNA life cycle spatially is essential for dissecting intricate RNA biology in complex tissues.

Approach:

  • Patho-DBiT combines in situ polyadenylation and deterministic barcoding for spatial full-coverage transcriptome sequencing.
  • The method is optimized for analyzing diverse RNA species within clinically archived FFPE samples.
  • It enables spatial co-profiling of gene expression and RNA processing, including splicing isoforms and RNA variants.

Key Points:

  • Patho-DBiT achieves high-sensitivity transcriptomic mapping in FFPE tumor tissues stored for up to five years.
  • It can capture genome-wide single nucleotide RNA variants to differentiate malignant and non-malignant cells, as demonstrated in human lymphomas.
  • The platform maps microRNA-mRNA regulatory networks and RNA splicing dynamics, providing insights into spatial tumorigenesis.
  • High-resolution, cellular-level analysis reveals spatial neighborhoods and spatiotemporal kinetics driving tumor progression.

Conclusions:

  • Patho-DBiT offers a transformative platform for exploring comprehensive RNA biology in FFPE tissues.
  • This technology enhances human tissue biology research and aids in clinical pathology evaluation.
  • It unlocks new possibilities for studying RNA processing, variants, and regulatory networks in archived clinical samples.