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

Ram Prakash Yadav, Pengwei Xing, Miao Zhao, Peter Hollander, Carina Strell, Minglu Xie, Maede Salehi, Emma Torell, Tobias Sjöblom, Gunilla Enblad, Rose-Marie Amini, Fredrik Johansson Swartling, Ingrid Glimelius, Patrick Micke, Mats Hellström and Xingqi Chen ()
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Ram Prakash Yadav: Uppsala University
Pengwei Xing: Uppsala University
Miao Zhao: Uppsala University
Peter Hollander: Uppsala University
Carina Strell: Uppsala University
Minglu Xie: Uppsala University
Maede Salehi: Uppsala University
Emma Torell: Uppsala University
Tobias Sjöblom: Uppsala University
Gunilla Enblad: Uppsala University
Rose-Marie Amini: Uppsala University
Fredrik Johansson Swartling: Uppsala University
Ingrid Glimelius: Uppsala University
Patrick Micke: Uppsala University
Mats Hellström: Uppsala University
Xingqi Chen: Uppsala University

Nature Communications, 2025, vol. 16, issue 1, 1-21

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-66170-4

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