Spatio-temporal mRNA dynamics in the early zebrafish embryo

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.

Download Full-text

Spatio-temporal mRNA tracking in the early zebrafish embryo

Nature Communications ◽

10.1038/s41467-021-23834-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Karoline Holler ◽

Anika Neuschulz ◽

Philipp Drewe-Boß ◽

Janita Mintcheva ◽

Bastiaan Spanjaard ◽

...

Keyword(s):

Single Cell ◽

Primordial Germ Cells ◽

Temporal Analysis ◽

Sequence Motifs ◽

Cell Stage ◽

Systematic Analysis ◽

Spatially Resolved ◽

Rna Labeling ◽

Stage Embryo ◽

Spatio Temporal

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.

Download Full-text

STAB: a spatio-temporal cell atlas of the human brain

Nucleic Acids Research ◽

10.1093/nar/gkaa762 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D1029-D1037

Author(s):

Liting Song ◽

Shaojun Pan ◽

Zichao Zhang ◽

Longhao Jia ◽

Wei-Hua Chen ◽

...

Keyword(s):

Human Brain ◽

Single Cell ◽

Temporal Dynamics ◽

Cell Types ◽

Brain Regions ◽

Molecular Characteristics ◽

Great Effort ◽

Brain Functions ◽

Spatio Temporal ◽

The Brain

Abstract The human brain is the most complex organ consisting of billions of neuronal and non-neuronal cells that are organized into distinct anatomical and functional regions. Elucidating the cellular and transcriptome architecture underlying the brain is crucial for understanding brain functions and brain disorders. Thanks to the single-cell RNA sequencing technologies, it is becoming possible to dissect the cellular compositions of the brain. Although great effort has been made to explore the transcriptome architecture of the human brain, a comprehensive database with dynamic cellular compositions and molecular characteristics of the human brain during the lifespan is still not available. Here, we present STAB (a Spatio-Temporal cell Atlas of the human Brain), a database consists of single-cell transcriptomes across multiple brain regions and developmental periods. Right now, STAB contains single-cell gene expression profiling of 42 cell subtypes across 20 brain regions and 11 developmental periods. With STAB, the landscape of cell types and their regional heterogeneity and temporal dynamics across the human brain can be clearly seen, which can help to understand both the development of the normal human brain and the etiology of neuropsychiatric disorders. STAB is available at http://stab.comp-sysbio.org.

Download Full-text

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.

Download Full-text

Spatio-temporal dynamics of cerebral capillary segments with stalling red blood cells

Journal of Cerebral Blood Flow & Metabolism ◽

10.1177/0271678x17743877 ◽

2017 ◽

Vol 39 (5) ◽

pp. 886-900 ◽

Cited By ~ 20

Author(s):

Şefik Evren Erdener ◽

Jianbo Tang ◽

Amir Sajjadi ◽

Kıvılcım Kılıç ◽

Sreekanth Kura ◽

...

Keyword(s):

Temporal Dynamics ◽

Oct Angiography ◽

Label Free ◽

Systematic Analysis ◽

Volumetric Imaging ◽

Cerebral Capillary ◽

Spatio Temporal ◽

The Brain

Optical coherence tomography (OCT) allows label-free imaging of red blood cell (RBC) flux within capillaries with high spatio-temporal resolution. In this study, we utilized time-series OCT-angiography to demonstrate interruptions in capillary RBC flux in mouse brain in vivo. We noticed ∼7.5% of ∼200 capillaries had at least one stall in awake mice with chronic windows during a 9-min recording. At any instant, ∼0.45% of capillaries were stalled. Average stall duration was ∼15 s but could last over 1 min. Stalls were more frequent and longer lasting in acute window preparations. Further, isoflurane anesthesia in chronic preparations caused an increase in the number of stalls. In repeated imaging, the same segments had a tendency to stall again over a period of one month. In awake animals, functional stimulation decreased the observance of stalling events. Stalling segments were located distally, away from the first couple of arteriolar-side capillary branches and their average RBC and plasma velocities were lower than nonstalling capillaries within the same region. This first systematic analysis of capillary RBC stalls in the brain, enabled by rapid and continuous volumetric imaging of capillaries with OCT-angiography, will lead to future investigations of the potential role of stalling events in cerebral pathologies.

Download Full-text

Spatially resolved simulations of the spread of COVID-19 in three European countries

PLoS Computational Biology ◽

10.1371/journal.pcbi.1009090 ◽

2021 ◽

Vol 17 (7) ◽

pp. e1009090

Author(s):

Andrea Parisi ◽

Samuel P. C. Brand ◽

Joe Hilton ◽

Rabia Aziza ◽

Matt J. Keeling ◽

...

Keyword(s):

Temporal Dynamics ◽

European Countries ◽

Potential Candidate ◽

Middle Income ◽

Spatially Resolved ◽

Contact Patterns ◽

Containment Measures ◽

Spatio Temporal ◽

Using Data ◽

Temporal Spread

We explore the spatial and temporal spread of the novel SARS-CoV-2 virus under containment measures in three European countries based on fits to data of the early outbreak. Using data from Spain and Italy, we estimate an age dependent infection fatality ratio for SARS-CoV-2, as well as risks of hospitalization and intensive care admission. We use them in a model that simulates the dynamics of the virus using an age structured, spatially detailed agent based approach, that explicitly incorporates governmental interventions and changes in mobility and contact patterns occurred during the COVID-19 outbreak in each country. Our simulations reproduce several of the features of its spatio-temporal spread in the three countries studied. They show that containment measures combined with high density are responsible for the containment of cases within densely populated areas, and that spread to less densely populated areas occurred during the late stages of the first wave. The capability to reproduce observed features of the spatio-temporal dynamics of SARS-CoV-2 makes this model a potential candidate for forecasting the dynamics of SARS-CoV-2 in other settings, and we recommend its application in low and lower-middle income countries which remain understudied.

Download Full-text

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.

Download Full-text

Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord

10.1101/472415 ◽

2018 ◽

Cited By ~ 1

Author(s):

Julien Delile ◽

Teresa Rayon ◽

Manuela Melchionda ◽

Amelia Edwards ◽

James Briscoe ◽

...

Keyword(s):

Gene Expression ◽

Spinal Cord ◽

Single Cell ◽

Neural Tube ◽

Temporal Dynamics ◽

Regulation Of Gene Expression ◽

Cell Types ◽

Neuronal Diversity ◽

Systematic Analysis ◽

Neural Tube Development

ABSTRACTThe coordinated spatial and temporal regulation of gene expression in the vertebrate neural tube determines the identity of neural progenitors and the function and physiology of the neurons they generate. Progress has been made deciphering the gene regulatory programmes responsible for this process, however, the complexity of the tissue has hampered the systematic analysis of the network and the underlying mechanisms. To address this, we used single cell mRNA sequencing to profile cervical and thoracic regions of the developing mouse neural tube between embryonic days (e)9.5-e13.5. We confirmed the data accurately recapitulates neural tube development, allowing us to identify new markers for specific progenitor and neuronal populations. In addition, the analysis highlighted a previously underappreciated temporal component to the mechanisms generating neuronal diversity and revealed common features in the sequence of transcriptional events that lead to the differentiation of specific neuronal subtypes. Together the data provide a compendium of gene expression for classifying spinal cord cell types that will support future studies of neural tube development, function, and disease.

Download Full-text

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.

Download Full-text

TMOD-15. IDENTIFYING THE SPATIAL AND TEMPORAL DYNAMICS OF GLIOBLASTOMA SUBPOPULATIONS WITHIN INDIVIDUAL PATIENTS

Neuro-Oncology ◽

10.1093/neuonc/noz175.1114 ◽

2019 ◽

Vol 21 (Supplement_6) ◽

pp. vi265-vi266

Author(s):

Bethan Morris ◽

Lee Curtin ◽

Andrea Hawkins-Daarud ◽

Bernard Bendok ◽

Maciej Mrugala ◽

...

Keyword(s):

Treatment Response ◽

Temporal Dynamics ◽

Dynamic Information ◽

Treatment Regimes ◽

Spatially Resolved ◽

Spatial And Temporal Dynamics ◽

Genetic Features ◽

Spatio Temporal ◽

Insight Into

Abstract Glioblastomas (GBMs) are known to be complex tumors comprising multiple subpopulations of genetically-distinct cancer cells; it is thought that this genetic variation is a major factor in the lack of observed survival benefit of treatment regimes that target one of these subpopulations. The field of radiogenomics seeks to study correlations between MRI patterns and genetic features of GBM tumors. Spatial radiogenomic maps produced using machine-learning (ML) methods that are trained against information from image-localized patient biopsies identify regions where particular cancer sub-populations are predicted to occur within a GBM, thus non-invasively characterizing the regional genetic variability of these tumors. These tumor subpopulations may also interact with one another, in ways which may be of a competitive or cooperative nature to varying degrees. It is important to ascertain the nature of these interactions, as they may have implications for treatment response to targeted therapies, and characterization of the spatio-temporal dynamics of these co-evolving sub-populations will shed light on why some therapies fail. Here we combine mathematical modeling techniques and spatially-resolved radiogenomic maps to study the nature of these interactions between molecularly-distinct GBM subpopulations. We model the interactions between cell populations using a partial differential equation based formalism. The model is parameterized using radiogenomic ML maps from which we infer the nature of interactions between subpopulations. Furthermore, using maps as inputs, the model turns static maps into dynamic information, thus providing insight into how these subpopulations composing the tumor change over time and the effect this has on observed treatment response for individual patients.

Download Full-text

scSLAM-seq reveals core features of transcription dynamics in single cells

10.1101/486852 ◽

2019 ◽

Cited By ~ 2

Author(s):

Florian Erhard ◽

Marisa A.P. Baptista ◽

Tobias Krammer ◽

Thomas Hennig ◽

Marius Lange ◽

...

Keyword(s):

Single Cell ◽

Temporal Dynamics ◽

Single Cells ◽

Transcriptional Response ◽

Gene Promoter ◽

Viral Gene Expression ◽

Viral Gene ◽

Stochastic Nature ◽

Rna Labeling ◽

Induced Changes

AbstractCurrent single-cell RNA sequencing approaches gives a snapshot of a cellular phenotype but convey no information on the temporal dynamics of transcription. Moreover, the stochastic nature of transcription at molecular level is not recovered. Here, we present single-cell SLAM-seq (scSLAM-seq), which integrates metabolic RNA labeling, biochemical nucleoside conversion and single-cell RNA-seq to directly measure total transcript levels and transcriptional activity by differentiating newly synthesized from pre-existing RNA for thousands of genes per single cell. scSLAM-seq recovers the earliest virus-induced changes in cytomegalovirus infection and reveals a so far hidden phase of viral gene expression comprising promiscuous transcription of all kinetic classes. It depicts the stochastic nature of transcription and demonstrates extensive gene-specific differences. These range from stable transcription rates to on-off dynamics which coincide with gene-/promoter-intrinsic features (Tbp-TATA-box interactions and DNA methylation). Gene but not cell-specific features thus explain the heterogeneity in transcriptomes between individual cells and the transcriptional response to perturbations.

Download Full-text