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Related Experiment Video

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Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Feasibility Study Utilizing NanoString's Digital Spatial Profiling (DSP) Technology for Characterizing the Immune

Qurat-Ul-Ain1, Nicola F Frei2, Amir M Khoshiwal2

  • 1Department of Pathology, University of California, San Francisco, CA 94143, USA.

Cancers
|December 23, 2023
PubMed
Summary

Investigating the microenvironment of Barrett's esophagus (BE) using spatial profiling reveals key protein differences in patients who progress to esophageal adenocarcinoma (EAC). This study identifies potential biomarkers for BE progression.

Keywords:
Barrett’s esophagusesophageal adenocarcinomaimmune profilingspatial proteomicsspatial transcriptomicstumor microenvironment

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Area of Science:

  • Gastroenterology
  • Oncology
  • Molecular Biology

Background:

  • Barrett's esophagus (BE) progression to esophageal adenocarcinoma (EAC) is poorly understood.
  • The tumor microenvironment's role in BE progression requires further investigation.
  • Novel diagnostics and therapies for EAC are needed.

Purpose of the Study:

  • To assess the feasibility of multiplex spatial profiling on FFPE BE biopsies.
  • To identify immune cells and pathways involved in BE progression to EAC.
  • To discover potential biomarkers for predicting BE progression.

Main Methods:

  • Spatial proteomic analysis of 49 proteins using NanoString GeoMx digital spatial profiling (GeoMax DSP) on FFPE biopsies.
  • RNA analysis of 1812 cancer-related transcripts from BE, dysplasia, and EAC tissues.
  • Comparison of protein expression in non-progressing vs. progressing non-dysplastic BE (NDBE) patients.

Main Results:

  • GeoMx DSP profiling yielded high-quality data with distinct epithelium and stroma signals.
  • Several proteins showed increased expression in NDBE biopsies from patients who later progressed.
  • Differences in protein expression suggest potential roles in BE progression.

Conclusions:

  • Multiplex spatial profiling is effective for analyzing the BE microenvironment in FFPE samples.
  • Specific protein expression patterns in NDBE may predict progression to EAC.
  • Further research is warranted to validate these findings and develop diagnostic/therapeutic strategies.