What question did this study set out to answer?

The goal is to explore the limitations of 2D analyses in capturing the complex structure of gastric tumors using 3D spatial multi-omics.

April 5, 2026Cancer Research0 citations

Abstract 4179: Three-dimensional spatial multi-omics of gastric tumor sections reveal hidden features beyond 2D analyses

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IJInyeop JangVanderbilt University Medical Center SISoyoung Im MKMinji KimVanderbilt University Medical Center

Key Points

The goal is to explore the limitations of 2D analyses in capturing the complex structure of gastric tumors using 3D spatial multi-omics.
Utilized the G4X platform for in-situ RNA and protein readouts
Profiled serial FFPE sections to quantify targeted RNAs and proteins
Registered sections into a common 3D frame to reconstruct a volumetric atlas
Acquired label-free 3D holotomography for structural visualization
Applied AI-based single-cell segmentation for detailed cell type mapping.
Identified strong variability in cell-type compositions in 2D slices
Revealed a coherent exhausted T-cell domain only in 3D analyses
Confirmed continuity between T cells, extracellular matrix, and tumor cells using holotomography
Highlighted the potential for clinically relevant immune niches to be missed in single-section analyses
Demonstrated a practical workflow for volumetric tumor-immune profiling.

Abstract

Abstract Single-section spatial-omics frequently misses microanatomical context and is sensitive to sectioning variability. Recent 3D reconstruction studies highlight substantial heterogeneity within the tumor microenvironment obscuring true biology. Emerging platforms (e.g. Singular Genomics G4X) enable in-situ RNA/protein readouts at subcellular resolution on the same slide with fluorescent H Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 4179.

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Cite This Study

Jang et al. (2026) studied this question.

synapsesocial.com/papers/69d1fd62a79560c99a0a3650 https://doi.org/10.1158/1538-7445.am2026-4179

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April 5, 2026Cancer Research0 citations

Abstract 4179: Three-dimensional spatial multi-omics of gastric tumor sections reveal hidden features beyond 2D analyses

View Full Paper

IJInyeop JangVanderbilt University Medical Center SISoyoung Im MKMinji KimVanderbilt University Medical Center

Key Points

The goal is to explore the limitations of 2D analyses in capturing the complex structure of gastric tumors using 3D spatial multi-omics.
Utilized the G4X platform for in-situ RNA and protein readouts
Profiled serial FFPE sections to quantify targeted RNAs and proteins
Registered sections into a common 3D frame to reconstruct a volumetric atlas
Acquired label-free 3D holotomography for structural visualization
Applied AI-based single-cell segmentation for detailed cell type mapping.
Identified strong variability in cell-type compositions in 2D slices
Revealed a coherent exhausted T-cell domain only in 3D analyses
Confirmed continuity between T cells, extracellular matrix, and tumor cells using holotomography
Highlighted the potential for clinically relevant immune niches to be missed in single-section analyses
Demonstrated a practical workflow for volumetric tumor-immune profiling.

Abstract

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Cite This Study

Jang et al. (2026) studied this question.

synapsesocial.com/papers/69d1fd62a79560c99a0a3650 https://doi.org/10.1158/1538-7445.am2026-4179

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