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

Author

Listed:
  • Ram Prakash Yadav

    (Uppsala University)

  • Pengwei Xing

    (Uppsala University)

  • Miao Zhao

    (Uppsala University)

  • Peter Hollander

    (Uppsala University)

  • Carina Strell

    (Uppsala University
    University of Bergen)

  • 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)

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.

Suggested Citation

  • 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 Swartl, 2025. "scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples," Nature Communications, Nature, vol. 16(1), pages 1-21, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-66170-4
    DOI: 10.1038/s41467-025-66170-4
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