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Updated: Aug 19, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Assessment of spatial transcriptomics for oncology discovery.

Anna Lyubetskaya1, Brian Rabe1, Andrew Fisher1

  • 1Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.

Cell Reports Methods
|December 1, 2022
PubMed
Summary

Spatial transcriptomics (ST) aids oncology drug discovery by mapping tumor landscapes. This technology reveals key features like hypoxia and cell interactions, enabling new target identification.

Keywords:
biomarkerscancer biologycancer genomicsdigital pathologygenomicsoncologypancreatic cancerspatial genomicsspatial transcriptomicstumors

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Area of Science:

  • Oncology
  • Genomics
  • Biotechnology

Background:

  • Tumor heterogeneity presents a significant hurdle in oncology drug discovery and development.
  • Understanding the spatial tumor landscape is crucial for identifying novel therapeutic targets and effective preclinical models.

Purpose of the Study:

  • To evaluate the utility of spatial transcriptomics (ST) for advancing oncology discovery.
  • To profile diverse tissue types and sample formats using ST to capture spatial information.

Main Methods:

  • Profiling of 40 tissue sections and 80,024 capture spots using spatial transcriptomics.
  • Verification of ST accuracy and fidelity through matched pathology analysis.
  • Analysis of spatial data to identify tumor depth features and cell-type locations.

Main Results:

  • ST successfully captured key tumor depth features including hypoxia, necrosis, vasculature, and extracellular matrix variations.
  • Spatial context analysis revealed anti-correlation between tumor and immune cells in syngeneic cancer models.
  • Demonstrated target identification in pancreatic adenocarcinoma, highlighting tumor-intrinsic biomarkers and paracrine signaling.

Conclusions:

  • Spatial transcriptomics is a valuable tool for oncology discovery, providing insights into the tumor microenvironment.
  • ST facilitates the identification of novel biomarkers and therapeutic targets by analyzing spatial relationships within tumors.
  • This approach enhances the understanding of tumor heterogeneity and supports the development of more effective cancer therapies.