Pang, B. P. S. | Search bioRxiv

bioRxiv2026

REZCUE: Rescuing 3D spatial omics from archived FFPE tissue

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.

bioengineering↗

bioRxiv2026

Universal nucleic acid preservation in biological fluids with boron clusters

Nucleic acid preservation remains a critical bottleneck for diagnostics and therapeutics, with small molecule inhibitors such as EDTA showing limited spectrum against diverse nucleases, while protein-based alternatives requiring costly cold-chain storage. Here, we report dodecaborate cluster [B12H12]2- as a novel class of pan-nuclease inhibitor with a fundamentally different mechanism--preventing protein-nucleic acid interactions rather than targeting cofactor dependencies. [B12H12]2- inhibited all six DNases and ten RNases tested, making it the broadest spectrum nuclease inhibitor known. Remarkably, its inhibition is reversible via {gamma}-cyclodextrin complexation. We demonstrate that [B12H12]2- preserved a physiological range of DNA for 14 days and that of RNA for 3-7 days at room temperature in human plasma and urine, achieving up to 323,972-fold better RNA retention than controls. A newly developed blood collection tube using [B12H12]2- enables whole-blood circulating cell-free RNA sequencing after 7 days of room-temperature storage, with preserved transcript integrity. Mechanistic studies suggest [B12H12]2- binds to nuclease active sites and creates electrostatic barriers that prevent substrate binding. This chemically stable, indefinitely shelf-stable inhibitor enables cold-chain-free biological sample transport, potentially transforming accessibility of nucleic acid-based diagnostics worldwide. Graphical abstract

bioengineering↗