snCED-seq: high-fidelity cryogenic enzymatic dissociation of nuclei for single-nucleus RNA-seq of FFPE tissues

Abstract

Recent advances have shown that single-nucleus RNA sequencing (snRNA-seq) can be applied to formalin-fixed, paraffin-embedded (FFPE) tissues, opening avenues for transcriptomic analysis of archived specimens. Yet, isolating intact nuclei remains difficult due to RNA cross-linking. Here, we introduce a cryogenic enzymatic dissociation (CED) strategy for rapid, high-yield and fidelity nuclei extraction from FFPE samples and validate its utility with snRandom-seq (snCED-seq) using male C57/BL6 mice. Compared with conventional approaches, CED delivers a tenfold increase in nuclei yield with significantly reduced hands-on time, while minimizing secondary RNA degradation and preserving intranuclear transcripts. snCED-seq enhances gene detection sensitivity, lowers mitochondrial and ribosomal contamination, and increases overall gene expression quantification. In Alzheimer’s disease studies, it distinguished two astrocyte subpopulations, microglia, and oligodendrocytes, revealing cellular heterogeneity. Additionally, snCED-seq identify major cell types in a single 50 μm FFPE human lung section. Our results demonstrate that snCED-seq is robust for FFPE specimens and poised to enable multi-omics analyses of clinical samples.