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2 Janelia Publications

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    Tillberg LabAguilera Castrejon LabStringer LabLiu (Zhe) LabScientific Computing
    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

    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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    Aguilera Castrejon Lab
    08/06/25 | Transgene-free generation of mouse post-gastrulation whole embryo models solely from naive ESCs and iPSCs.
    Yilmaz A, Gurhan G, Comar M, Viukov S, Serfaty I, Gayretli M, Golenchenko S, Lokshtanov D, Ashouokhi S, Polanco A, Berlad I, Ha T, Aguilera-Castrejon A, Tarazi S, Cohen M, Livnat N, Kumar K, Cholakkal H, Levy N, Yosef N, Khatib N, Kakun RR, Kedmi M, Nachman IB, Keren-Shaul H, Addadi Y, Orenbuch A, Korovin K, Molchadsky A, Hochedlinger K, Gafni O, Maza I, Novershtern N, Oldak B, Hanna JH
    Cell Stem Cell. 2025 Aug 06:. doi: 10.1016/j.stem.2025.07.005

    The generation of post-gastrulation stem cell-derived mouse embryo models (SEMs) exclusively from naive embryonic stem cells (nESCs) has underscored their ability to give rise to embryonic and extra-embryonic lineages. However, existing protocols for mouse SEMs rely on the separate induction of extra-embryonic lineages and on ectopic expression of transcription factors to induce nESC differentiation into trophectoderm (TE) or primitive endoderm (PrE). Here, we demonstrate that mouse nESCs and naive induced pluripotent stem cells (niPSCs) can be simultaneously co-induced, via signaling pathway modulation, to generate PrE and TE extra-embryonic cells that self-organize into embryonic day (E) 8.5-E8.75 transgene-free (TF) SEMs. We also devised an alternative condition (AC) naive media that in vitro stabilizes TF-SEM-competent OCT4+/NANOG+ nESC colonies that co-express antagonistic CDX2 and/or GATA6 extra-embryonic fate master regulators and self-renew while remaining poised for TE and PrE differentiation, respectively. These findings improve mouse SEM strategies and shed light on amplifying an inherent and dormant extra-embryonic plasticity of mouse naive pluripotent cells in vitro.

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