Biology subjects

Li, J. J. X.

Publications and source records attributed to Li, J. J. X..

4 recordsLinked to original sources

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

COLOR-3D: a versatile tool for revealing novel 3D histological features

Hematoxylin and eosin (H&E) has been the fundamental method for visualising tissue morphology. Recent advances in tissue clearing and microscopy have enabled the observation of tissue morphology in 3D, but incomplete penetration of nucleic acid dyes has remained the bottleneck. To address this, we develop a new staining chemistry called Cyclodextrin and Organic solvent-assisted deep Labelling of ORgans in 3D (COLOR-3D), which attains the best penetration depth and homogeneity among state-of-the-art methods. We also demonstrate the scalability of COLOR-3D and its compatibility with other staining modalities. To bridge the gap between 3D histology and its wider application in biomedical research and histopathology, we develop a computational pipeline to convert 3D fluorescence images into bright-field H&E images, enabling the creation of a 3D atlas of both normal tissues and pathological specimens. Apart from qualitative observation of tissue morphology, COLOR-3D also enables quantitative analysis for studying biological phenomena. In the mouse liver, we discover rare populations of tetranuclear hepatocytes as well as m16n, t4n and t8n hepatocytes. We also propose the first structural model of the liver lobule based on 3D histology. With a more complete penetration, we reveal the following aging-related changes in tissue microarchitecture, including an increase in extreme nuclear polyploidy, and the disruption of vasculature and portal triad.

pathology↗

bioRxiv2024

Topologically distinct and equivalent multiple efferent arterioles in the human glomeruli

We revisit the assumption that the human glomerulus consists of a capillary network with one afferent arteriole and only one efferent arteriole. Using three-dimensional tissue imaging, we unambiguously demonstrate the existence of multiple efferent arterioles via total reconstruction of a full human glomerular capillary network. Through graph network analysis, we found these multiple efferent arterioles can be topologically distinct or equivalent with reference to the global glomerular capillary network, and were strategically positioned with respect to the afferent arteriole. We also found the extraglomerular connections between two efferent arterioles may have significant contributions to the redistribution of intraglomerular blood flow. These new findings can provide new paradigms in the regulation and dysfunction of glomerular ultrafiltration, the crosstalk between intra- and extraglomerular factors, and the cross-coupling between nephrons.

pathology↗

bioRxiv2024

INSIHGT: Accessible multimodal systems biology with quantitative molecular phenotyping in 3D

Biological systems are complex, encompassing intertwined spatial, molecular and functional features. However, methodological constraints always limit the completeness of information that can be extracted. Here, we report the development of INSIHGT, a minimally perturbative, accessible and cost-efficient three-dimensional (3D) spatial biology method utilizing superchaotropes and host-guest chemistry. This allows highly multiplexed and multi-modal readout of tissue biomolecules in biological systems up to centimeter scales, permitting radio-histological correlation of phosphorylated alpha-synuclein pathologies in human hemi-brainstem. The homogeneous penetration permits reliable semi-quantitative signals in 3D compared to reference signals. Diverse antigens, mRNA transcripts, neurotransmitters, and post-translational and epigenetic modifications, are well-preserved and visualized. INSIHGT also allows multi-round molecular probing for high-dimensional spatial biology and compatibility with downstream traditional histology. With INSIHGT, we mapped previously undescribed podocyte-to-parietal epithelial cell microfilaments and demonstrated their geodesic clustering in mouse glomeruli, and catalogued sparsely located neurofilament-intensive inclusion bodies in the human cerebellum, and identified NPY-proximal cell types defined by spatial morpho-proteomics in mouse hypothalamus. We anticipate INSIHGT can form the foundations for 3D spatial multi-omics technology development and holistic systems biology studies.

bioengineering↗