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Aguilera Castrejon Lab - Team Members

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Alejandro Aguilera Castrejon

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02/20/25 | Deep-tissue transcriptomics and subcellular imaging at high spatial resolution

Gandin V, Kim J, Yang L, Lian Y, Kawase T, Hu A, Rokicki K, Fleishman G, Tillberg P, Aguilera Castrejon A, Stringer C, Preibisch S, Liu ZJ

Science. 2025 Feb 20:. doi: 10.1126/science.adq2084

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Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens. Here, we introduce cycle Hybridization Chain Reaction (HCR), a method that integrates multicycle DNA barcoding with HCR to overcome this limitation. cycleHCR enables highly multiplexed imaging of RNA and proteins using a unified barcode system. Whole-embryo transcriptomics imaging achieved precise three-dimensional gene expression and cell fate mapping across a specimen depth of ~310 μm. When combined with expansion microscopy, cycleHCR revealed an intricate network of 10 subcellular structures in mouse embryonic fibroblasts. In mouse hippocampal slices, multiplex RNA and protein imaging uncovered complex gene expression gradients and cell-type-specific nuclear structural variations. cycleHCR provides a quantitative framework for elucidating spatial regulation in deep tissue contexts for research and potentially diagnostic applications.

bioRxiv preprint: 10.1101/2024.05.17.594641

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