REZCUE: Rescuing 3D spatial omics from archived FFPE tissue
- 1Stanford University
Abstract
Archived formalin-fixed, paraffin-embedded (FFPE) tissue represents a vast clinical resource, yet three-dimensional imaging and molecular profiling remain largely incompatible because current antigen retrieval and clearing can degrade nucleic acids. We developed REZCUE, a depth-invariant antigen retrieval chemistry based on in situ protein refolding that enables 3D multiplexed immunofluorescence imaging of intact FFPE tissue while preserving DNA, RNA, and protein for subsequent assays. REZCUE restores antigenicity in tissue archived for up to 30 years, supports 160 commercial antibodies across tissue types, and enables imaging to 4 mm depth. Imaging before destructive molecular profiling establishes a 3D spatial reference for registering molecular assays to intact tissue architecture. In a 25-year-archived breast cancer specimen, REZCUE integrated 3D image-guided clonal segmentation with spatial transcriptomics, mass spectrometry, miRNA sequencing, and whole-genome sequencing, identifying a luminalB/HER2-positive clone missed by conventional section-based spatial-omics. REZCUE transforms archived FFPE specimens into spatially registered substrates for sequential 3D multi-omic interrogation.
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BibTeX
@misc{zhang2026rezcue,
title = {{REZCUE: Rescuing 3D spatial omics from archived FFPE tissue}},
author = {L. Zhang and W. C.-S. Cho and J. J. X. Li and B. P. S. Pang and B. T. Y. Wong and E. P. L. Tsoi and Y. Tan and H.-M. Lai},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.06.757132},
url = {https://www.biorxiv.org/content/10.64898/2026.10.06.757132v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - REZCUE: Rescuing 3D spatial omics from archived FFPE tissue
AU - L. Zhang
AU - W. C.-S. Cho
AU - J. J. X. Li
AU - B. P. S. Pang
AU - B. T. Y. Wong
AU - E. P. L. Tsoi
AU - Y. Tan
AU - H.-M. Lai
PY - 2026
DA - 2026/10/06
PB - bioRxiv
DO - 10.64898/2026.10.06.757132
UR - https://www.biorxiv.org/content/10.64898/2026.10.06.757132v1
AB - Archived formalin-fixed, paraffin-embedded (FFPE) tissue represents a vast clinical resource, yet three-dimensional imaging and molecular profiling remain largely incompatible because current antigen retrieval and clearing can degrade nucleic acids. We developed REZCUE, a depth-invariant antigen retrieval chemistry based on in situ protein refolding that enables 3D multiplexed immunofluorescence imaging of intact FFPE tissue while preserving DNA, RNA, and protein for subsequent assays. REZCUE restores antigenicity in tissue archived for up to 30 years, supports 160 commercial antibodies across tissue types, and enables imaging to 4 mm depth. Imaging before destructive molecular profiling establishes a 3D spatial reference for registering molecular assays to intact tissue architecture. In a 25-year-archived breast cancer specimen, REZCUE integrated 3D image-guided clonal segmentation with spatial transcriptomics, mass spectrometry, miRNA sequencing, and whole-genome sequencing, identifying a luminalB/HER2-positive clone missed by conventional section-based spatial-omics. REZCUE transforms archived FFPE specimens into spatially registered substrates for sequential 3D multi-omic interrogation.
ER -