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Updated: Jul 29, 2026
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An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
Published on: April 5, 2018
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Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues
Pengfei Guo1, Yufan Chen2, Liran Mao3,4,5
1Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. pengfei.guo@pennmedicine.upenn.edu.
Nature Communications
|July 2, 2025
Summary
A new spatial epigenomic technique, FFPE-ATAC-seq, analyzes chromatin accessibility in archived formalin-fixed paraffin-embedded (FFPE) tissues. This method maps gene regulation and cell types in intact tissues, unlocking vast research potential.
Area of Science:
- Epigenomics
- Molecular Biology
- Genomics
Background:
- Formalin-fixed paraffin-embedded (FFPE) tissues are abundant but underutilized in epigenomic research due to limited molecular tools.
- Existing methods struggle to analyze chromatin accessibility in FFPE samples while preserving spatial information.
Purpose of the Study:
- To introduce spatial FFPE-ATAC-seq, a novel method for in situ chromatin accessibility profiling in archived FFPE tissues.
- To overcome challenges associated with formalin crosslinking for high-resolution epigenomic analysis.
Main Methods:
- Spatial FFPE-ATAC-seq was developed to profile chromatin accessibility directly within FFPE tissue sections.
- The method was applied to mouse and human tissues (brain, thymus) and human melanoma samples.
- Integration with single-cell RNA sequencing (scRNA-seq) was used for validation.
Main Results:
- Spatial FFPE-ATAC-seq successfully mapped chromatin landscapes with high resolution, preserving tissue architecture.
- Distinct cell types and spatial organization were identified in various tissues, aligning with morphology.
- The method precisely identified cell types and regulatory elements, validated by scRNA-seq integration.
- Chromatin accessibility was comprehensively characterized in tumor and non-tumor regions of human melanoma.
Conclusions:
- Spatial FFPE-ATAC-seq significantly expands the toolkit for epigenomic research on archived FFPE samples.
- The method enables the study of gene regulation and disease mechanisms with unprecedented spatial context.
- This approach unlocks the potential of vast FFPE archives for discovery in various biological and disease contexts.
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