Spatial profiling technologies illuminate the tumor microenvironment

Cancer Cell, Год журнала: 2023, Номер 41(3), С. 404 - 420

Опубликована: Фев. 16, 2023

Язык: Английский

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Spatially resolved single-cell translatomics at molecular resolution

Science, Год журнала: 2023, Номер 380(6652)

Опубликована: Июнь 29, 2023

The precise control of messenger RNA (mRNA) translation is a crucial step in posttranscriptional gene regulation cellular physiology. However, it remains challenge to systematically study mRNA at the transcriptomic scale with spatial and single-cell resolution. Here, we report development ribosome-bound mapping (RIBOmap), highly multiplexed three-dimensional situ profiling method detect translatome. RIBOmap 981 genes HeLa cells revealed cell cycle-dependent translational colocalized functional modules. We mapped 5413 mouse brain tissues, yielding spatially resolved translatomic profiles for 119,173 revealing type-specific region-specific regulation, including remodeling during oligodendrocyte maturation. Our detected widespread patterns localized neuronal glial intact tissue networks.

Язык: Английский

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Benchmarking spatial clustering methods with spatially resolved transcriptomics data

Nature Methods, Год журнала: 2024, Номер 21(4), С. 712 - 722

Опубликована: Март 15, 2024

Язык: Английский

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Branched chemically modified poly(A) tails enhance the translation capacity of mRNA

Nature Biotechnology, Год журнала: 2024, Номер unknown

Опубликована: Март 22, 2024

Язык: Английский

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Spatiotemporal omics for biology and medicine

Cell, Год журнала: 2024, Номер 187(17), С. 4488 - 4519

Опубликована: Авг. 1, 2024

Язык: Английский

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Bento: a toolkit for subcellular analysis of spatial transcriptomics data

Genome biology, Год журнала: 2024, Номер 25(1)

Опубликована: Апрель 2, 2024

Abstract The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell–cell interactions, and expression patterns, they are limited to the multicellular scale. We present Bento, Python toolkit that takes advantage single-molecule information enable analysis at subcellular Bento ingests molecular coordinates segmentation boundaries perform three analyses: defining domains, annotating localization quantifying gene–gene colocalization. demonstrate MERFISH, seqFISH + , Molecular Cartography, Xenium datasets. part open-source Scverse ecosystem, enabling integration with other single-cell tools.

Язык: Английский

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Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues

Cell, Год журнала: 2024, Номер 187(23), С. 6760 - 6779.e24

Опубликована: Сен. 30, 2024

The capability to spatially explore RNA biology in formalin-fixed paraffin-embedded (FFPE) tissues holds transformative potential for histopathology research. Here, we present pathology-compatible deterministic barcoding tissue (Patho-DBiT) by combining situ polyadenylation and computational innovation spatial whole transcriptome sequencing, tailored probe the diverse species clinically archived FFPE samples. It permits co-profiling of gene expression processing, unveiling region-specific splicing isoforms, high-sensitivity transcriptomic mapping clinical tumor stored 5 years. Furthermore, genome-wide single-nucleotide variants can be captured distinguish malignant subclones from non-malignant cells human lymphomas. Patho-DBiT also maps microRNA regulatory networks dynamics, decoding their roles tumorigenesis. Single-cell level dissects spatiotemporal cellular dynamics driving clonal architecture progression. stands poised as a valuable platform unravel rich aid pathology evaluation.

Язык: Английский

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Genetic variation across and within individuals

Nature Reviews Genetics, Год журнала: 2024, Номер 25(8), С. 548 - 562

Опубликована: Март 28, 2024

Язык: Английский

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High-resolution spatially resolved proteomics of complex tissues based on microfluidics and transfer learning

Cell, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Despite recent advances in imaging- and antibody-based methods, achieving in-depth, high-resolution protein mapping across entire tissues remains a significant challenge spatial proteomics. Here, we present parallel-flow projection transfer learning omics data (PLATO), an integrated framework combining microfluidics with deep to enable of thousands proteins whole tissue sections. We validated the PLATO by profiling proteome mouse cerebellum, identifying 2,564 groups single run. then applied rat villus human breast cancer samples, resolution 25 μm uncovering proteomic dynamics associated disease states. This approach revealed spatially distinct tumor subtypes, identified key dysregulated proteins, provided novel insights into complexity microenvironment. believe that represents transformative platform for exploring regulation its interplay genetic environmental factors.

Язык: Английский

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Brainstem neuropeptidergic neurons link a neurohumoral axis to satiation

Cell, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

Язык: Английский

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