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

Area of Science:

• Epigenetics
• Molecular Biology
• Genomics

Background:

• Formalin-fixed paraffin-embedded (FFPE) tissues are crucial for clinical and research applications.
• Existing single-cell chromatin accessibility assays struggle with DNA damage in FFPE samples, limiting cell-type-specific epigenetic profiling.

Purpose of the Study:

• To develop a novel high-throughput single-cell assay, scFFPE-ATAC, for analyzing chromatin accessibility in FFPE tissues.
• To enable epigenetic studies on long-term archived clinical specimens.

Main Methods:

• scFFPE-ATAC integrates an FFPE-adapted Tn5 transposase, ultra-high-throughput DNA barcoding, T7 promoter-mediated DNA damage repair, and in vitro transcription.
• The method was benchmarked on FFPE mouse spleen and validated against fresh tissue.
• Applied to archived human lymph node and lung cancer FFPE tissues.

Main Results:

• scFFPE-ATAC successfully profiled epigenetic landscapes in archived human FFPE tissues.
• Distinct regulatory trajectories were identified between tumor center and invasive edge in lung cancer.
• Epigenetic dynamics associated with relapse and transformation were observed in B-cell lymphoma samples.

Conclusions:

• scFFPE-ATAC overcomes limitations of previous technologies, enabling high-throughput single-cell epigenetic analysis of FFPE samples.
• The method facilitates retrospective, spatial, and mechanistic epigenetic studies on valuable archived specimens.
• Opens new avenues for understanding disease progression and therapeutic responses using historical samples.