# scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples

## TL;DR

The paper introduces scFFPE-ATAC, a new method for studying chromatin accessibility in archived FFPE tissues, enabling insights into epigenetic changes in diseases like cancer.

## Contribution

The novel method scFFPE-ATAC enables high-throughput single-cell chromatin profiling in FFPE samples, overcoming DNA damage challenges.

## Key findings

- scFFPE-ATAC successfully profiles chromatin accessibility in FFPE mouse spleen and human lymph node samples.
- The method reveals distinct regulatory trajectories in lung cancer tissues between tumor center and invasive edge.
- Epigenetic dynamics associated with relapse and transformation are identified in archived lymphoma samples.

## Abstract

Formalin-fixed paraffin-embedded (FFPE) samples are the gold standard for tissue preservation in clinical and research settings. Current single-cell chromatin accessibility technologies cannot resolve cell-type-specific epigenetic profiles in FFPE tissues due to extensive DNA damage. We present scFFPE-ATAC, a high-throughput single-cell chromatin accessibility assay for FFPE samples that integrates an FFPE-adapted Tn5 transposase, ultra-high-throughput DNA barcoding (>56 million barcodes per run), T7 promoter-mediated DNA damage repair, and in vitro transcription. We benchmark scFFPE-ATAC on FFPE mouse spleen and validate its performance against fresh tissue. We apply it to human lymph node samples archived for 8–12 years and to lung cancer FFPE tissues, revealing distinct regulatory trajectories between tumor center and invasive edge. Analysis of archived follicular lymphoma and transformed diffuse large B-cell lymphoma samples identifies relapse- and transformation-associated epigenetic dynamics. scFFPE-ATAC enables retrospective, spatial, and mechanistic epigenetic studies in long-term archived specimens.

The study introduces scFFPE-ATAC, a high-throughput single-cell chromatin accessibility profiling method enabling profiling from clinically archived formalin-fixed paraffin-embedded (FFPE) tissues, unlocking retrospective epigenetic insights across cancer and human diseases.