The emerging landscape of spatial profiling technologies

Nature Reviews Genetics, Journal Year: 2022, Volume and Issue: 23(12), P. 741 - 759

Published: July 20, 2022

Language: Английский

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An invasive zone in human liver cancer identified by Stereo-seq promotes hepatocyte–tumor cell crosstalk, local immunosuppression and tumor progression

Cell Research, Journal Year: 2023, Volume and Issue: 33(8), P. 585 - 603

Published: June 19, 2023

Abstract Dissecting and understanding the cancer ecosystem, especially that around tumor margins, which have strong implications for cell infiltration invasion, are essential exploring mechanisms of metastasis developing effective new treatments. Using a novel border scanning digitization model enabled by nanoscale resolution-SpaTial Enhanced REsolution Omics-sequencing (Stereo-seq), we identified 500 µm-wide zone centered in patients with liver cancer, referred to as “the invasive zone”. We detected immunosuppression, metabolic reprogramming, severely damaged hepatocytes this zone. also subpopulation increased expression serum amyloid A1 A2 (referred collectively SAAs) located close on paratumor side. Overexpression CXCL6 adjacent malignant cells could induce activation JAK-STAT3 pathway nearby hepatocytes, subsequently caused SAAs’ overexpression these hepatocytes. Furthermore, secretion SAAs lead recruitment macrophages M2 polarization, further promoting local potentially resulting progression. Clinical association analysis additional five independent cohorts primary secondary ( n = 423) showed had worse prognosis. Further vivo experiments using mouse models situ confirmed knockdown genes encoding decreased macrophage accumulation delayed growth. The identification characterization human not only add an important layer regarding invasion metastasis, but may pave way therapeutic strategies advanced other solid tumors.

Language: Английский

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Single-cell technologies: From research to application

The Innovation, Journal Year: 2022, Volume and Issue: 3(6), P. 100342 - 100342

Published: Oct. 18, 2022

Language: Английский

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Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

Nature Plants, Journal Year: 2023, Volume and Issue: 9(4), P. 515 - 524

Published: April 13, 2023

Language: Английский

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Single‐cell RNA‐seq reveals fate determination control of an individual fibre cell initiation in cotton (Gossypium hirsutum)

Plant Biotechnology Journal, Journal Year: 2022, Volume and Issue: 20(12), P. 2372 - 2388

Published: Aug. 29, 2022

Summary Cotton fibre is a unicellular seed trichome, and lint initials per as factor determines yield. However, the mechanisms controlling initiation from ovule epidermis are not understood well enough. Here, with single‐cell RNA sequencing (scRNA‐seq), total of 14 535 cells were identified cotton outer integument Xu142_LF line at four developmental stages (1.5, 1, 0.5 days before anthesis day anthesis). Three major cell types, fibre, non‐fibre pigment layer then verified by in situ hybridization. A comparative analysis on scRNA‐seq data between Xu142 its fibreless mutant fl further confirmed cluster definition. The trajectory was reconstructed, differentiated 1 anthesis. Gene regulatory networks revealed spatiotemporal pattern core transcription factors, MYB25‐like HOX3 demonstrated played key roles commanders differentiation tip‐biased diffuse growth respectively. model for early development single proposed here, which sheds light deciphering mechanism plant trichome improvement

Language: Английский

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Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2023, Volume and Issue: 50(9), P. 625 - 640

Published: March 27, 2023

The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology, from the invention of microscope 350 years ago recent emergence single-cell sequencing, which scientific community has been able visualize at an unprecedented resolution. Most recently, Spatially Resolved Transcriptomics (SRT) technologies have filled gap probing spatial or even three-dimensional organization molecular foundation behind mysteries life, including origin different cellular populations developed totipotent cells human diseases. In this review, we introduce progress challenges on SRT perspectives bioinformatic tools, as well representative applications. With currently fast-moving promising results early adopted research projects, can foresee bright future such new tools understanding most profound analytical level.

Language: Английский

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STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D1053 - D1061

Published: Nov. 11, 2023

Abstract Recent technological developments in spatial transcriptomics allow researchers to measure gene expression of cells and their locations at the single-cell level, generating detailed biological insight into processes. A comprehensive database could facilitate sharing transcriptomic data streamline acquisition process for researchers. Here, we present Spatial TranscriptOmics DataBase (STOmicsDB), a that serves as one-stop hub transcriptomics. STOmicsDB integrates 218 manually curated datasets representing 17 species. We annotated cell types, identified regions genes, performed cell-cell interaction analysis these datasets. features user-friendly interface rapid visualization millions cells. To further reusability interoperability data, developed standards archiving constructed system. Additionally, offer distinctive capability customizing dedicated sub-databases researchers, assisting them visualizing analyses. believe contribute research insights field, including archiving, sharing, analysis. is freely accessible https://db.cngb.org/stomics/.

Language: Английский

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Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap

Nature Plants, Journal Year: 2023, Volume and Issue: 9(7), P. 1026 - 1033

Published: June 12, 2023

Abstract Retrieving the complex responses of individual cells in native three-dimensional tissue context is crucial for a complete understanding functions. Here, we present PHYTOMap (plant hybridization-based targeted observation gene expression map), multiplexed fluorescence situ hybridization method that enables single-cell and spatial analysis whole-mount plant transgene-free manner at low cost. We applied to simultaneously analyse 28 cell-type marker genes Arabidopsis roots successfully identified major cell types, demonstrating our can substantially accelerate mapping defined RNA-sequencing datasets tissue.

Language: Английский

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Mapping cells through time and space with moscot

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: May 11, 2023

Abstract Single-cell genomics technologies enable multimodal profiling of millions cells across temporal and spatial dimensions. Experimental limitations prevent the measurement all-encompassing cellular states in their native dynamics or tissue niche. Optimal transport theory has emerged as a powerful tool to overcome such constraints, enabling recovery original context. However, most algorithmic implementations currently available have not kept up pace with increasing dataset complexity, so that current methods are unable incorporate information scale single-cell atlases. Here, we introduce multi-omics optimal (moscot), general scalable framework for applications genomics, supporting multimodality all applications. We demonstrate moscot’s ability efficiently reconstruct developmental trajectories 1.7 million mouse embryos 20 time points identify driver genes first heart field formation. The moscot formulation can be used dimensions well: To this, enrich transcriptomics datasets by mapping from profiles liver sample, align multiple coronal sections brain. then present moscot.spatiotemporal, new approach leverages gene expression uncover spatiotemporal embryogenesis. Finally, disentangle lineage relationships novel murine, time-resolved pancreas development using paired measurements chromatin accessibility, finding evidence shared ancestry between delta epsilon cells. Moscot is an easy-to-use, open-source python package extensive documentation at https://moscot-tools.org .

Language: Английский

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Spatial metatranscriptomics resolves host–bacteria–fungi interactomes

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 42(9), P. 1384 - 1393

Published: Nov. 20, 2023

The interactions of microorganisms among themselves and with their multicellular host take place at the microscale, forming complex networks spatial patterns. Existing technology does not allow simultaneous investigation between a multitude its colonizing microorganisms, which limits our understanding host-microorganism within plant or animal tissue. Here we present metatranscriptomics (SmT), sequencing-based approach that leverages 16S/18S/ITS/poly-d(T) multimodal arrays for transcriptome- microbiome-wide characterization tissues 55-µm resolution. We showcase SmT in outdoor-grown Arabidopsis thaliana leaves as model system, find tissue-scale bacterial fungal hotspots. By network analysis, study inter- intrakingdom well response to microbial provides an answering fundamental questions on host-microbiome interplay.

Language: Английский

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