Spatio-temporal mRNA tracking in the early zebrafish embryo

AbstractEarly stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development. We measure spatial localization of mRNA molecules within the one-cell stage embryo, which allows us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we establish a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enables us to follow the fate of individual maternal transcripts until gastrulation. This approach reveals that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquire spatial transcriptomes of two xenopus species and compare evolutionary conservation of localized genes as well as enriched sequence motifs.

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Spatio-temporal mRNA dynamics in the early zebrafish embryo

10.1101/2020.11.19.389809 ◽

2020 ◽

Author(s):

Karoline Holler ◽

Anika Neuschulz ◽

Philipp Drewe-Boß ◽

Janita Mintcheva ◽

Bastiaan Spanjaard ◽

...

Keyword(s):

Single Cell ◽

Temporal Dynamics ◽

Primordial Germ Cells ◽

Sequence Motifs ◽

Cell Stage ◽

Systematic Analysis ◽

Spatially Resolved ◽

Rna Labeling ◽

Vegetal Pole ◽

Spatio Temporal

SummaryEarly stages of embryogenesis depend heavily on subcellular localization and transport of maternally deposited mRNA. However, systematic analysis of these processes is currently hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combined spatially-resolved transcriptomics and single-cell RNA labeling to study the spatio-temporal dynamics of the transcriptome during the first few hours of zebrafish development. We measured spatial localization of mRNA molecules with sub-single-cell resolution at the one-cell stage, which allowed us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we established a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enabled us to follow the fate of individual maternal transcripts until gastrulation. This approach revealed that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquired spatial transcriptomes of two xenopus species, and we compared evolutionary conservation of localized genes as well as enriched sequence motifs. In summary, we established sub-single-cell spatial transcriptomics and single-cell RNA labeling to reveal principles of mRNA localization in early vertebrate development.

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The spatio-temporal landscape of lung pathology in SARS-CoV-2 infection

10.1101/2020.10.26.20219584 ◽

2020 ◽

Author(s):

André Figueiredo Rendeiro ◽

Hiranmayi Ravichandran ◽

Yaron Bram ◽

Steven Salvatore ◽

Alain Borczuk ◽

...

Keyword(s):

Single Cell ◽

Cell Types ◽

Alveolar Epithelial Cells ◽

Lung Damage ◽

Lung Pathology ◽

Alveolar Epithelial ◽

Spatially Resolved ◽

Injured Lung ◽

Spatio Temporal ◽

Cell Data

SummaryRecent studies have provided insights into the pathology and immune response to coronavirus disease 2019 (COVID-19)1–8. However thorough interrogation of the interplay between infected cells and the immune system at sites of infection is lacking. We use high parameter imaging mass cytometry9 targeting the expression of 36 proteins, to investigate at single cell resolution, the cellular composition and spatial architecture of human acute lung injury including SARS-CoV-2. This spatially resolved, single-cell data unravels the disordered structure of the infected and injured lung alongside the distribution of extensive immune infiltration. Neutrophil and macrophage infiltration are hallmarks of bacterial pneumonia and COVID-19, respectively. We provide evidence that SARS-CoV-2 infects predominantly alveolar epithelial cells and induces a localized hyper-inflammatory cell state associated with lung damage. By leveraging the temporal range of COVID-19 severe fatal disease in relation to the time of symptom onset, we observe increased macrophage extravasation, mesenchymal cells, and fibroblasts abundance concomitant with increased proximity between these cell types as the disease progresses, possibly as an attempt to repair the damaged lung tissue. This spatially resolved single-cell data allowed us to develop a biologically interpretable landscape of lung pathology from a structural, immunological and clinical standpoint. This spatial single-cell landscape enabled the pathophysiological characterization of the human lung from its macroscopic presentation to the single-cell, providing an important basis for the understanding of COVID-19, and lung pathology in general.

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A spatially resolved single cell atlas of human gastrulation

10.1101/2020.07.21.213512 ◽

2020 ◽

Cited By ~ 2

Author(s):

Richard C.V. Tyser ◽

Elmir Mahammadov ◽

Shota Nakanoh ◽

Ludovic Vallier ◽

Antonio Scialdone ◽

...

Keyword(s):

Single Cell ◽

Primordial Germ Cells ◽

Embryonic Stem ◽

Experimental Models ◽

Model Systems ◽

Spatial Patterning ◽

Directed Differentiation ◽

Spatially Resolved ◽

Basic Body

ABSTRACTGastrulation is the fundamental process during the embryogenesis of all multicellular animals through which the basic body plan is first laid down. It is pivotal in generating cellular diversity coordinated with spatial patterning. Gastrulation in humans occurs in the third week following fertilization. Our understanding of this process in humans is extremely limited, and based almost entirely on experimental models. Here, we characterize in a spatially resolved manner the single cell transcriptional profile of an entire gastrulating human embryo approximately 16 to 19 days after fertilization. We used these data to provide the first unequivocal demonstration that human embryonic stem cells represent the early post implantation epiblast. We identified both primordial germ cells and red blood cells, which had never been characterized so early during human development. Comparison with mouse gastrula transcriptomes revealed many commonalities between the human and mouse but also several key differences, particularly in FGF signaling, that we validated experimentally. This unique dataset offers a unique glimpse into a central but generally inaccessible stage of our development, provides new context for interpreting experiments in other model systems and represents a valuable resource for guiding directed differentiation of human cells in vitro.

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The spatio-temporal program of liver zonal regeneration

10.1101/2021.08.11.455924 ◽

2021 ◽

Author(s):

Shani Ben-Moshe ◽

Tamar Veg ◽

Rita Manco ◽

Stav Dan ◽

Aleksandra A. Kolodziejczyk ◽

...

Keyword(s):

Liver Regeneration ◽

Single Cell ◽

Stellate Cell ◽

Cell Types ◽

Matrix Remodeling ◽

Spatially Resolved ◽

Single Cell Rna Sequencing ◽

Ability To Regenerate ◽

Spatio Temporal ◽

Macrophage Populations

The liver carries a remarkable ability to regenerate rapidly after acute zonal damage. Single-cell approaches are necessary to study this process, given the spatial heterogeneity of multiple liver cell types. Here, we use spatially-resolved single cell RNA sequencing (scRNAseq) to study the dynamics of mouse liver regeneration after acute acetaminophen (APAP) intoxication. We find that hepatocytes proliferate throughout the liver lobule, creating the mitotic pressure required to repopulate the necrotic pericentral zone rapidly. A subset of hepatocytes located at the regenerating front transiently up-regulate fetal-specific genes, including Afp and Cdh17, as they reprogram to a pericentral state. Zonated endothelial, hepatic-stellate cell (HSC) and macrophage populations are differentially involved in immune recruitment, proliferation and matrix remodeling. We observe massive transient infiltration of myeloid cells, yet stability of lymphoid cell abundance, in accordance with global decline in antigen presentation. Our study provides a resource for understanding the coordinated programs of zonal liver regeneration.

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Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

Nature Methods ◽

10.1038/s41592-021-01343-9 ◽

2022 ◽

Author(s):

Britta Velten ◽

Jana M. Braunger ◽

Ricard Argelaguet ◽

Damien Arnol ◽

Jakob Wirbel ◽

...

Keyword(s):

Factor Analysis ◽

Dimensionality Reduction ◽

Single Cell ◽

Cell Biology ◽

Multimodal Data ◽

Spatially Resolved ◽

Temporal And Spatial ◽

Spatio Temporal ◽

Personalized Health ◽

Analysis Models

AbstractFactor analysis is a widely used method for dimensionality reduction in genome biology, with applications from personalized health to single-cell biology. Existing factor analysis models assume independence of the observed samples, an assumption that fails in spatio-temporal profiling studies. Here we present MEFISTO, a flexible and versatile toolbox for modeling high-dimensional data when spatial or temporal dependencies between the samples are known. MEFISTO maintains the established benefits of factor analysis for multimodal data, but enables the performance of spatio-temporally informed dimensionality reduction, interpolation, and separation of smooth from non-smooth patterns of variation. Moreover, MEFISTO can integrate multiple related datasets by simultaneously identifying and aligning the underlying patterns of variation in a data-driven manner. To illustrate MEFISTO, we apply the model to different datasets with spatial or temporal resolution, including an evolutionary atlas of organ development, a longitudinal microbiome study, a single-cell multi-omics atlas of mouse gastrulation and spatially resolved transcriptomics.

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