scholarly journals Reversed graph embedding resolves complex single-cell developmental trajectories

2017 ◽  
Author(s):  
Xiaojie Qiu ◽  
Qi Mao ◽  
Ying Tang ◽  
Li Wang ◽  
Raghav Chawla ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Developmental Trajectories ◽  
Single Cells ◽  
Graph Embedding ◽  
Developmental Trajectory ◽  
Loss Of Function ◽  
Cell Fate Decisions ◽  
Principal Graph ◽  
Cell Trajectories

AbstractOrganizing single cells along a developmental trajectory has emerged as a powerful tool for understanding how gene regulation governs cell fate decisions. However, learning the structure of complex single-cell trajectories with two or more branches remains a challenging computational problem. We present Monocle 2, which uses reversed graph embedding to reconstruct single-cell trajectories in a fully unsupervised manner. Monocle 2 learns an explicit principal graph to describe the data, greatly improving the robustness and accuracy of its trajectories compared to other algorithms. Monocle 2 uncovered a new, alternative cell fate in what we previously reported to be a linear trajectory for differentiating myoblasts. We also reconstruct branched trajectories for two studies of blood development, and show that loss of function mutations in key lineage transcription factors diverts cells to alternative branches on the a trajectory. Monocle 2 is thus a powerful tool for analyzing cell fate decisions with single-cell genomics.

scholarly journals High-throughput single-cell transcriptomics reveals the female germline differentiation trajectory in Arabidopsis thaliana

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Zhimin Hou ◽  
Yanhui Liu ◽  
Man Zhang ◽  
Lihua Zhao ◽  
Xingyue Jin ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Single Cell ◽  
Cell Fate ◽  
Single Cells ◽  
Expression Patterns ◽  
Cell Types ◽  
Developmental Time ◽  
Developmental Trajectory ◽  
Germline Differentiation ◽  
Female Germline

AbstractFemale germline cells in flowering plants differentiate from somatic cells to produce specialized reproductive organs, called ovules, embedded deep inside the flowers. We investigated the molecular basis of this distinctive developmental program by performing single-cell RNA sequencing (scRNA-seq) of 16,872 single cells of Arabidopsis thaliana ovule primordia at three developmental time points during female germline differentiation. This allowed us to identify the characteristic expression patterns of the main cell types, including the female germline and its surrounding nucellus. We then reconstructed the continuous trajectory of female germline differentiation and observed dynamic waves of gene expression along the developmental trajectory. A focused analysis revealed transcriptional cascades and identified key transcriptional factors that showed distinct expression patterns along the germline differentiation trajectory. Our study provides a valuable reference dataset of the transcriptional process during female germline differentiation at single-cell resolution, shedding light on the mechanisms underlying germline cell fate determination.

scholarly journals Multiplexed biochemical imaging reveals caspase activation patterns underlying single cell fate

2018 ◽  
Author(s):  
Maximilian W. Fries ◽  
Kalina T. Haas ◽  
Suzan Ber ◽  
John Saganty ◽  
Emma K. Richardson ◽  
...  
Keyword(s):  
Cell Death ◽  
Single Cell ◽  
Cell Fate ◽  
Genetic Heterogeneity ◽  
Cellular Response ◽  
Single Cells ◽  
Caspase Activation ◽  
Cell Fate Decisions ◽  
Network Activation ◽  
Biochemical Imaging

The biochemical activities underlying cell-fate decisions vary profoundly even in genetically identical cells. But such non-genetic heterogeneity remains refractory to current imaging methods, because their capacity to monitor multiple biochemical activities in single living cells over time remains limited1. Here, we deploy a family of newly designed GFP-like sensors (NyxBits) with fast photon-counting electronics and bespoke analytics (NyxSense) in multiplexed biochemical imaging, to define a network determining the fate of single cells exposed to the DNA-damaging drug cisplatin. By simultaneously imaging a tri-nodal network comprising the cell-death proteases Caspase-2, -3 and -92, we reveal unrecognized single-cell heterogeneities in the dynamics and amplitude of caspase activation that signify survival versus cell death via necrosis or apoptosis. Non-genetic heterogeneity in the pattern of caspase activation recapitulates traits of therapy resistance previously ascribed solely to genetic causes3,4. Chemical inhibitors that alter these patterns can modulate in a predictable manner the phenotypic landscape of the cellular response to cisplatin. Thus, multiplexed biochemical imaging reveals cellular populations and biochemical states, invisible to other methods, underlying therapeutic responses to an anticancer drug. Our work develops widely applicable tools to monitor the dynamic activation of biochemical networks at single-cell resolution. It highlights the necessity to resolve patterns of network activation in single cells, rather than the average state of individual nodes, to define, and potentially control, mechanisms underlying cellular decisions in health and disease.

scholarly journals Single cell RNA-seq and ATAC-seq indicate critical roles of Isl1 and Nkx2-5 for cardiac progenitor cell transition states and lineage settlement

2017 ◽  
Author(s):  
Guangshuai Jia ◽  
Jens Preussner ◽  
Stefan Guenther ◽  
Xuejun Yuan ◽  
Michail Yekelchyk ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Regulatory Networks ◽  
Progenitor Cell ◽  
Marker Gene ◽  
Transitional Cell ◽  
Developmental Trajectory ◽  
Open Chromatin ◽  
Cardiac Progenitor Cell ◽  
Cell Fate Decisions

SUMMARYFormation and segregation of cell lineages building the vertebrate heart have been studied extensively by genetic cell tracing techniques and by analysis of single marker gene expression but the underlying gene regulatory networks driving cell fate transitions during early cardiogenesis are only partially understood. Here, we comprehensively characterized mouse cardiac progenitor cells (CPC) marked by Nkx2-5 and Isl1 expression from E7.5 to E9.5 using single-cell RNA sequencing. By leveraging on cell-to-cell heterogeneity, we identified different previously unknown cardiac sub-populations. Reconstruction of the developmental trajectory revealed that Isl1+ CPC represent a transitional cell population maintaining a prolonged multipotent state, whereas extended expression of Nkx2-5 commits CPC to a unidirectional cardiomyocyte fate. Furthermore, we show that CPC fate transitions are associated with distinct open chromatin states, which critically depend on Isl1 and Nkx2-5. Our data provide a model of transcriptional and epigenetic regulations during cardiac progenitor cell fate decisions at single-cell resolution.

scholarly journals Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis

2020 ◽  
Author(s):  
T. Lohoff ◽  
S. Ghazanfar ◽  
A. Missarova ◽  
N. Koulena ◽  
N. Pierson ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Single Cell ◽  
Cell Fate ◽  
Target Genes ◽  
Single Cells ◽  
Spatial Context ◽  
Sequencing Data ◽  
Cell Fate Decisions ◽  
Spatially Resolved

AbstractTranscriptional and epigenetic profiling of single-cells has advanced our knowledge of the molecular bases of gastrulation and early organogenesis. However, current approaches rely on dissociating cells from tissues, thereby losing the crucial spatial context that is necessary for understanding cell and tissue interactions during development. Here, we apply an image-based single-cell transcriptomics method, seqFISH, to simultaneously and precisely detect mRNA molecules for 387 selected target genes in 8-12 somite stage mouse embryo tissue sections. By integrating spatial context and highly multiplexed transcriptional measurements with two single-cell transcriptome atlases we accurately characterize cell types across the embryo and demonstrate how spatially-resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain-hindbrain boundary and the developing gut tube. Our spatial atlas uncovers axes of resolution that are not apparent from single-cell RNA sequencing data – for example, in the gut tube we observe early dorsal-ventral separation of esophageal and tracheal progenitor populations. In sum, by computationally integrating high-resolution spatially-resolved gene expression maps with single-cell genomics data, we provide a powerful new approach for studying how and when cell fate decisions are made during early mammalian development.

scholarly journals Ultra-multiplexed analysis of single-cell dynamics reveals logic rules in differentiation

2019 ◽  
Vol 5 (4) ◽  
pp. eaav7959 ◽  
Author(s):  
Ce Zhang ◽  
Hsiung-Lin Tu ◽  
Gengjie Jia ◽  
Tanzila Mukhtar ◽  
Verdon Taylor ◽  
...  
Keyword(s):  
Stem Cell ◽  
Cell Differentiation ◽  
Single Cell ◽  
Cell Fate ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Critical Role ◽  
Stem Cell Differentiation ◽  
Cell Fate Decisions ◽  
Cellular Microenvironments

Dynamical control of cellular microenvironments is highly desirable to study complex processes such as stem cell differentiation and immune signaling. We present an ultra-multiplexed microfluidic system for high-throughput single-cell analysis in precisely defined dynamic signaling environments. Our system delivers combinatorial and time-varying signals to 1500 independently programmable culture chambers in week-long live-cell experiments by performing nearly 106 pipetting steps, where single cells, two-dimensional (2D) populations, or 3D neurospheres are chemically stimulated and tracked. Using our system and statistical analysis, we investigated the signaling landscape of neural stem cell differentiation and discovered “cellular logic rules” that revealed the critical role of signal timing and sequence in cell fate decisions. We find synergistic and antagonistic signal interactions and show that differentiation pathways are highly redundant. Our system allows dissection of hidden aspects of cellular dynamics and enables accelerated biological discovery.

scholarly journals Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis

2021 ◽  
Author(s):  
T. Lohoff ◽  
S. Ghazanfar ◽  
A. Missarova ◽  
N. Koulena ◽  
N. Pierson ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Target Genes ◽  
Single Cells ◽  
Cell Types ◽  
Spatial Context ◽  
Cell Fate Decisions ◽  
Spatially Resolved ◽  
Regulatory Processes ◽  
Cell Transcriptome

AbstractMolecular profiling of single cells has advanced our knowledge of the molecular basis of development. However, current approaches mostly rely on dissociating cells from tissues, thereby losing the crucial spatial context of regulatory processes. Here, we apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes in tissue sections of mouse embryos at the 8–12 somite stage. By integrating spatial context and multiplexed transcriptional measurements with two single-cell transcriptome atlases, we characterize cell types across the embryo and demonstrate that spatially resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain–hindbrain boundary (MHB) and the developing gut tube. We uncover axes of cell differentiation that are not apparent from single-cell RNA-sequencing (scRNA-seq) data, such as early dorsal–ventral separation of esophageal and tracheal progenitor populations in the gut tube. Our method provides an approach for studying cell fate decisions in complex tissues and development.

scholarly journals Cell-to-cell heterogeneity in p38-mediated cross-inhibition of JNK causes stochastic cell death

2017 ◽  
Author(s):  
Haruko Miura ◽  
Yohei Kondo ◽  
Michiyuki Matsuda ◽  
Kazuhiro Aoki
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Stress Responses ◽  
Imaging System ◽  
Single Cells ◽  
High Specificity ◽  
Cellular Heterogeneity ◽  
Cell Fate Decisions ◽  
Specificity And Sensitivity ◽  
Cross Inhibition

AbstractThe stress activated protein kinases (SAPKs), c-Jun N-terminal kinase (JNK) and p38, are important players in cell fate decisions in response to environmental stress signals. Crosstalk signaling between JNK and p38 is emerging as an important regulatory mechanism in the inflammatory and stress responses. However, it is still unknown how this crosstalk affects signaling dynamics, cell-to-cell variation, and cellular responses at the single-cell level. To address these questions, we established a multiplexed live-cell imaging system based on kinase translocation reporters to simultaneously monitor JNK and p38 activities with high specificity and sensitivity at single-cell resolution. Various stresses, such as anisomycin, osmotic stress, and UV irradiation, and pro-inflammatory cytokines activated JNK and p38 with various dynamics. In all cases, however, p38 suppressed JNK activity in a cross-inhibitory manner. We demonstrate that p38 antagonizes JNK through both transcriptional and post-translational mechanisms. This cross-inhibition of JNK appears to generate cellular heterogeneity in JNK activity after stress exposure. Our data indicate that this heterogeneity in JNK activity plays a role in fractional killing in response to UV stress. Our highly sensitive multiplexed imaging system enables detailed investigation into the p38-JNK interplay in single cells.One Sentence SummaryCross-inhibition by p38 generates cell-to-cell variability in JNK activity.

scholarly journals Developmental switching inPhysarum polycephalum: Petri net analysis of single cell trajectories of gene expression indicates responsiveness and genetic plasticity of the Waddington quasipotential landscape

2017 ◽  
Author(s):  
Britta Werthmann ◽  
Wolfgang Marwan
Keyword(s):  
Gene Expression ◽  
Petri Nets ◽  
Single Cell ◽  
Cell Fate ◽  
Petri Net ◽  
Single Cells ◽  
Cell Fate Decision ◽  
Stimulus Pulse ◽  
Fate Decision ◽  
Cell Trajectories

AbstractThe developmental switch to sporulation inPhysarum polycephalumis a phytochrome-mediated far-red light-induced cell fate decision that synchronously encompasses the entire multinucleate plasmodial cell and is associated with extensive reprogramming of the transcriptome. By repeatedly taking samples of single cells after delivery of a light stimulus pulse, we analysed differential gene expression in two mutant strains and in a heterokaryon of the two strains all of which display a different propensity for making the cell fate decision. Multidimensional scaling of the gene expression data revealed individually different single cell trajectories eventually leading to sporulation. Characterization of the trajectories as walks through states of gene expression discretized by hierarchical clustering allowed the reconstruction of Petri nets that model and predict the observed behavior. Structural analyses of the Petri nets indicated stimulus- and genotype-dependence of both, single cell trajectories and of the quasipotential landscape through which these trajectories are taken. The Petri net-based approach to the analysis and decomposition of complex cellular responses and of complex mutant phenotypes may provide a scaffold for the data-driven reconstruction of causal molecular mechanisms that shape the topology of the quasipotential landscape.

scholarly journals Single-cell transcriptomic resolution of stem cells and their developmental trajectories in the hippocampus reveals epigenetic control of cell state perseverance

2021 ◽  
Author(s):  
Adrián Salas-Bastos ◽  
Martin Treppner ◽  
Josip S. Herman ◽  
Dimitrios Koutsogiannis ◽  
Harald Binder ◽  
...  
Keyword(s):  
Single Cell ◽  
Developmental Trajectories ◽  
Loss Of Function ◽  
Epigenetic Factor ◽  
Proliferation And Differentiation ◽  
Cornu Ammonis ◽  
Stem Cell Populations ◽  
Cell Trajectories ◽  
Conceptual Research ◽  
Radial Axis

Despite conceptual research on hippocampus development and the application of single-cell-resolved technologies, the nature and maturation of its diverse progenitor populations are unexplored. The chromatin modifier DOT1L balances progenitor proliferation and differentiation, and conditional loss-of-function mice featured impaired hippocampus development. We applied single-cell RNA sequencing on DOT1L-mutant mice and explored cell trajectories in the E16.5 hippocampus. We resolved in our data five distinct neural stem cell populations with the developmental repertoire to specifically generate the cornu ammonis (CA) 1 field and the dentate gyrus (DG). Within the two developing CA1- and CA3-fields, we identified two distinct maturation states and we thus propose CA1- and CA3-differentiation along the radial axis. In the developing hippocampus, DOT1L is primarily involved in the proper development of CA3 and the DG, and it serves as a state-preserving epigenetic factor that orchestrates the expression of several important transcription factors that impact neuronal differentiation and maturation.

Single cell chromatin accessibility reveals regulatory elements and developmental trajectories in the embryonic forebrain

2021 ◽  
Author(s):  
Christopher T. Rhodes ◽  
Apratim Mitra ◽  
Dongjin R. Lee ◽  
Daniel J. Lee ◽  
Yajun Zhang ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Developmental Trajectories ◽  
Transcript Abundance ◽  
Regulatory Elements ◽  
Brain Regions ◽  
Chromatin Accessibility ◽  
Embryonic Cells ◽  
Embryonic Mouse ◽  
Cell Fate Decisions

SUMMARYWhile epigenetic modifications are critical for cell state changes throughout development, a detailed characterization of chromatin accessibility during neurogenesis has not been explored. We collected single-cell chromatin accessibility profiles from four distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many restricted to distinct progenitor cell types or brain regions. Integrating snATAC-Seq and transcriptome data, we characterized changes of chromatin accessibility at enhancers and promoters that were tightly coupled to transcript abundance during neurodevelopment. Integrating chromatin accessibility profiles from embryonic and adult interneurons with the iPSYCH2012 dataset revealed several disease-associated polymorphisms overlapped with accessible regions in embryonic cells. These findings highlight a diverse chromatin landscape in embryonic neural progenitors, extensive coordination between chromatin accessibility and gene expression during neuron fate determination, and open the door for future studies to define critical enhancer-promoter interactions that direct cell fate decisions.

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