scholarly journals Inferring and perturbing cell fate regulomes in human cerebral organoids

2021 ◽  
Author(s):  
Jonas S. Fleck ◽  
Sophie M.J. Jansen ◽  
Damian Wollny ◽  
Makiko Seimiya ◽  
Fides Zenk ◽  
...  
Keyword(s):  
Human Brain ◽  
Single Cell ◽  
Cell Fate ◽  
Brain Region ◽  
Zinc Finger Protein ◽  
Interaction Analysis ◽  
State Regulation ◽  
Model Systems ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Self-organizing cerebral organoids grown from pluripotent stem cells combined with single-cell genomic technologies provide opportunities to explore gene regulatory networks (GRNs) underlying human brain development. Here we acquire single-cell transcriptome and accessible chromatin profiling data over a dense time course covering multiple phases of organoid development including neuroepithelial formation, patterning, brain regionalization, and neurogenesis. We identify temporally dynamic and brain region-specific regulatory regions, and cell interaction analysis reveals emergent patterning centers associated with regionalization. We develop Pando, a flexible linear model-based framework that incorporates multi-omic data and transcription binding site predictions to infer a global GRN describing organoid development. We use pooled genetic perturbation with single-cell transcriptome readout to assess transcription factor requirement for cell fate and state regulation in organoid. We find that certain factors regulate the abundance of cell fates, whereas other factors impact neuronal cell states after differentiation. We show that the zinc finger protein GLI3 is required for cortical fate establishment in humans, recapitulating previous work performed in mammalian model systems. We measure transcriptome and chromatin accessibility in normal or GLI3-perturbed cells and identify a regulome central to the dorsoventral telencephalic fate decision. This regulome suggests that Notch effectors HES4/5 are direct GLI3 targets, which together coordinate cortex and ganglionic eminence diversification. Altogether, we provide a framework for how multi-brain region model systems and single-cell technologies can be leveraged to reconstruct human brain developmental biology.

scholarly journals Lifelong single-cell profiling of cranial neural crest diversification

2021 ◽  
Author(s):  
Peter Fabian ◽  
Kuo-Chang Tseng ◽  
Mathi Thiruppathy ◽  
Claire Arata ◽  
Hung-Jhen Chen ◽  
...  
Keyword(s):  
Neural Crest ◽  
Single Cell ◽  
Cell Fate ◽  
Intrinsic Property ◽  
Chromatin Accessibility ◽  
Specific Cell ◽  
List Type ◽  
Cranial Neural Crest ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractThe cranial neural crest generates a huge diversity of derivatives, including the bulk of connective and skeletal tissues of the vertebrate head. How neural crest cells acquire such extraordinary lineage potential remains unresolved. By integrating single-cell transcriptome and chromatin accessibility profiles of cranial neural crest-derived cells across the zebrafish lifetime, we observe region-specific establishment of enhancer accessibility for distinct fates. Neural crest-derived cells rapidly diversify into specialized progenitors, including multipotent skeletal progenitors, stromal cells with a regenerative signature, fibroblasts with a unique metabolic signature linked to skeletal integrity, and gill-specific progenitors generating cell types for respiration. By retrogradely mapping the emergence of lineage-specific chromatin accessibility, we identify a wealth of candidate lineage-priming factors, including a Gata3 regulatory circuit for respiratory cell fates. Rather than multilineage potential being an intrinsic property of cranial neural crest, our findings support progressive and region-specific chromatin remodeling underlying acquisition of diverse neural crest lineage potential.HighlightsSingle-cell transcriptome and chromatin atlas of cranial neural crestProgressive emergence of region-specific cell fate competencyChromatin accessibility mapping identifies candidate lineage regulatorsGata3 function linked to gill-specific respiratory programGraphical Abstract

scholarly journals Dissecting Transition Cells from Single-cell Transcriptome Data through Multiscale Stochastic Dynamics

2021 ◽  
Author(s):  
Peijie Zhou ◽  
Shuxiong Wang ◽  
Tiejun Li ◽  
Qing Nie
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Stochastic Dynamics ◽  
Multiple Scales ◽  
Coarse Grained ◽  
Rate Theory ◽  
Transcriptome Data ◽  
Stochastic Dynamical Systems ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractAdvances of single-cell technologies allow scrutinizing of heterogeneous cell states, however, analyzing transitions from snap-shot single-cell transcriptome data remains challenging. To investigate cells with transient properties or mixed identities, we present MuTrans, a method based on multiscale reduction technique for the underlying stochastic dynamical systems that prescribes cell-fate transitions. By iteratively unifying transition dynamics across multiple scales, MuTrans constructs the cell-fate dynamical manifold that depicts progression of cell-state transition, and distinguishes meta-stable and transition cells. In addition, MuTrans quantifies the likelihood of all possible transition trajectories between cell states using the coarse-grained transition path theory. Downstream analysis identifies distinct genes that mark the transient states or drive the transitions. Mathematical analysis reveals consistency of the method with the well-established Langevin equation and transition rate theory. Applying MuTrans to datasets collected from five different single-cell experimental platforms and benchmarking with seven existing tools, we show its capability and scalability to robustly unravel complex cell fate dynamics induced by transition cells in systems such as tumor EMT, iPSC differentiation and blood cell differentiation. Overall, our method bridges data-driven and model-based approaches on cell-fate transitions at single-cell resolution.

scholarly journals Differential Network Analysis Reveals Regulatory Patterns in Neural Stem Cell Fate Decision

2019 ◽  
Author(s):  
Jiang Xie ◽  
Fuzhang yang ◽  
Jiamin Sun ◽  
Jiao Wang
Keyword(s):  
Stem Cell ◽  
Single Cell ◽  
Cell Fate ◽  
Neural Stem Cell ◽  
Integrative Analysis ◽  
Cell Fate Decisions ◽  
Multi Stage ◽  
Gene Regulatory ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Abstract Background Neural stem cell (NSC) differentiation is one of many multi-stage lineage systems that require multiple cell fate decisions. Recent single-cell transcriptome datasets became available at individual differentiation, however, a systematic and integrative analysis of multiple datasets at multiple temporal points of NSC differentiation is lacking. Results Here we investigate five NSC differentiation paths by analyzing and comparing four different single-cell transcriptome datasets. By constructing gene regulatory networks for each cell type, we delineate their regulatory patterns via analyses of differential topology and network diffusion. Among the five NSC differentiation paths, we find 12 common differentially expressed genes, with one common three-gene regulatory pattern shared by all paths. The identified regulatory pattern, partly supported by previous experimental evidence, is found to be essential to all differentiation paths, however, plays a different role in each path when regulating other genes. Conclusions Together, our integrative analysis provides both common and specific regulatory mechanisms for each of the five NSC differentiation paths, and the approach can be applied to analyzing other complex multi-stage lineage systems.

scholarly journals Single Cell Transcriptome-Based Dissection of Lineage Fate Decisions in Myelopoiesis

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1395-1395
Author(s):  
Andre Olsson ◽  
H. Leighton Grimes ◽  
Virendra K Chaudhri ◽  
Philip Dexheimer ◽  
Bruce J Aronow ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Molecular Mechanisms ◽  
Conflicts Of Interest ◽  
Expression Patterns ◽  
Rna Seq ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Cell Data ◽  
Insight Into

Abstract In spite of tremendous advances in the analysis of hematopoietic progenitors and transcription factors that give rise to different lineages, molecular insight into the mechanisms that underlie cell fate choice at the level of individual cells is lacking. We utilized single-cell RNA sequencing of murine granulocyte-monocyte progenitors (GMPs) to analyze the molecular basis of cell fate choice. Over 200 libraries were generated with average read depths of 4 million per library and an expressed gene call of over 3,800 genes with FPKM >3. Our data reveal a varied but coherent spectrum of gene expression patterns in individual murine GMPs. The majority of cells could be clustered into ones expressing either granulocytic or monocytic genes, suggesting that they were primed for lineage determination. A minority of GMPs expressed a mixed-lineage pattern of genes. The single-cell data suggested an antagonistic transcription factor circuit involving Gfi1 and IRF8 that was validated with both loss- and gain-of-function experiments in GMPs. Our data highlight the utility of single cell RNA-Seq analysis to reveal molecular mechanisms controlling lineage fate decisions in hematopoiesis. Disclosures No relevant conflicts of interest to declare.

scholarly journals Single-cell transcriptome reveals the redifferentiation trajectories of the early stage of de novo shoot regeneration in Arabidopsis thaliana

2022 ◽  
Author(s):  
Guangyu Liu ◽  
Jie Li ◽  
Jiming Li ◽  
Zhiyong Chen ◽  
Peisi Yuan ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Shoot Regeneration ◽  
De Novo ◽  
Developmental Process ◽  
Early Stage ◽  
Cell Populations ◽  
Cell Heterogeneity ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

De novo shoot regeneration from a callus plays a crucial role in both plant biotechnology and the fundamental research of plant cell totipotency. Recent studies have revealed many regulatory factors involved in this developmental process. However. our knowledge of the cell heterogeneity and cell fate transition during de novo shoot regeneration is still limited. Here, we performed time-series single-cell transcriptome experiments to reveal the cell heterogeneity and redifferentiation trajectories during the early stage of de novo shoot regeneration. Based on the single-cell transcriptome data of 35,669 cells at five-time points, we successfully determined seven major cell populations in this developmental process and reconstructed the redifferentiation trajectories. We found that all cell populations resembled root identities and undergone gradual cell-fate transitions. In detail, the totipotent callus cells differentiated into pluripotent QC-like cells and then gradually developed into less differentiated cells that have multiple root-like cell identities, such as pericycle-like cells. According to the reconstructed redifferentiation trajectories, we discovered that the canonical regeneration-related genes were dynamically expressed at certain stages of the redifferentiation process. Moreover, we also explored potential transcription factors and regulatory networks that might be involved in this process. The transcription factors detected at the initial stage, QC-like cells, and the end stage provided a valuable resource for future functional verifications. Overall, this dataset offers a unique glimpse into the early stages of de novo shoot regeneration, providing a foundation for a comprehensive analysis of the mechanism of de novo shoot regeneration.

scholarly journals Comparative analysis of human brain organoids of brainstem and midbrain at single-cell resolution

2020 ◽  
Author(s):  
Kaoru Kinugawa ◽  
Joachim Luginbühl ◽  
Takeshi K. Matsui ◽  
Nobuyuki Eura ◽  
Yoshihiko M. Sakaguchi ◽  
...  
Keyword(s):  
Human Brain ◽  
Single Cell ◽  
Neurological Diseases ◽  
Cell Types ◽  
Molecular Heterogeneity ◽  
The Difference ◽  
Brain Organoid ◽  
Cell Transcriptome ◽  
Unique Cell ◽  
Single Cell Transcriptome

ABSTRACTHuman brain organoids provide us the means to investigate human brain development and neurological diseases, and single-cell RNA-sequencing (scRNA-seq) technologies allow us to identify homologous cell types and the molecular heterogeneity between individual cells. Previously established human brain organoids of brainstem (hBSOs) and midbrain (hMBOs) were analyzed by scRNA-seq, but the difference in cellular composition between these organoids remains unclear. Here, we integrated and compared the single-cell transcriptome of hBSOs and hMBOs. Our analysis demonstrated that the hBSOs and hMBOs contain some unique cell types, including inflammatory and mesenchymal cells. Further comparison of the hBSOs and hMBOs with publicly available scRNA-seq dataset of human fetal midbrain (hMB) showed high similarity in their neuronal components. These results provide new insights into human brain organoid technologies.

scholarly journals Single-cell transcriptome profiling reveals dermal and epithelium cell fate decisions during embryonic hair follicle development

2019 ◽  
Author(s):  
Wei Ge ◽  
Shao-Jing Tan ◽  
Shan-He Wang ◽  
Lan Li ◽  
Xiao-Feng Sun ◽  
...  
Keyword(s):  
Single Cell ◽  
Hair Follicle ◽  
Cell Fate ◽  
Cell Lineage ◽  
Follicle Development ◽  
Cell Fate Decisions ◽  
Dermal Cell ◽  
Hair Follicle Development ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractCharacterization of the morphological structure during hair follicle development has been well documented, while the current understanding of the molecular mechanisms involved in follicle development remain limited. Here, using unbiased single-cell RNA sequencing, we analyzed 15,086 single cell transcriptome profiles from E13.5 and E16.5 fetal mice, and newborn mouse (postnatal day 0, P0) dorsal skin cells. Based on t-distributed Stochastic Neighbor Embedding (tSNE) clustering, we identified 14 cell clusters from skin cells and delineated their cell identity gene expression profiles. Pseudotime ordering analysis successfully constructed epithelium/dermal cell lineage differentiation trajectory and revealed sequential activation of key regulons involved during cell fate decisions. Along with this, intercellular communication between different cell populations were inferred based on a priori knowledge of ligand-receptor pairs. Together, our findings here provide a molecular landscape during hair follicle epithelium/dermal cell lineage fate decisions, and more importantly, recapitulate sequential activation of core regulatory transcriptional factors for different cell populations during hair follicle morphogenesis.

scholarly journals Single cell analysis of spondyloarthritis regulatory T cells identifies distinct synovial gene expression patterns and clonal fates

2021 ◽  
Author(s):  
Davide Simone ◽  
Frank Penkava ◽  
Anna Ridley ◽  
Stephen Nicholas Sansom ◽  
Hussein Mohamed Al-Mossawi ◽  
...  
Keyword(s):  
T Cells ◽  
Regulatory T Cells ◽  
Single Cell ◽  
Cell Fate ◽  
Single Cell Analysis ◽  
Expression Patterns ◽  
Treg Subset ◽  
Inflammatory Site ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Regulatory T cells (Tregs) play an important role in controlling inflammation and limiting autoimmunity, but their phenotypes at inflammatory sites in human disease are poorly understood. We here analyze the single-cell transcriptome of >16,000 Tregs obtained from peripheral blood and synovial fluid of two patients with HLA-B27+ ankylosing spondylitis and three patients with psoriatic arthritis, closely related forms of inflammatory spondyloarthritis. We identify multiple Treg clusters with distinct transcriptomic profiles, including, among others, a regulatory CD8+ subset expressing cytotoxic markers/genes, and a Th17-like RORC+ Treg subset characterized by IL-10 and LAG-3 expression. Synovial Tregs show upregulation of interferon signature and TNF receptor superfamily genes, and marked clonal expansion, consistent with tissue adaptation and antigen contact respectively. Individual synovial Treg clones map to different clusters indicating cell fate divergence. Finally, we demonstrate that LAG-3 directly inhibits IL-12/23 and TNF secretion by patient-derived monocytes, a mechanism with translational potential in SpA. Our detailed characterization of Tregs at an important inflammatory site illustrates the marked specialization of Treg subpopulations.

scholarly journals Defining Epidermal Stem Cell Fate Infidelity and Immunogenicity in Hidradenitis Suppurativa at the Single-Cell Resolution

2020 ◽  
Author(s):  
Meaghan Marohn ◽  
Meng-ju Lin ◽  
Wei-wen Yu ◽  
Ciara Mae Mendoza ◽  
Juliana Remark ◽  
...  
Keyword(s):  
Stem Cell ◽  
Single Cell ◽  
Cell Fate ◽  
Hidradenitis Suppurativa ◽  
Unique Feature ◽  
Inflammatory Skin Disease ◽  
Stem Cell Fate ◽  
Apocrine Sweat Gland ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractHidradenitis suppurativa (HS) is a severe chronic inflammatory skin disease affecting human apocrine sweat gland-bearing skin regions. One unique feature of HS is the development of keratinized sinus tracts that grow extensively deep in the dermis and are highly immunogenic. Here, we demonstrated that the stem cell fate infidelity exists in the HS sinus tracts, which exhibit features of both surface epidermis and appendages. Using single cell transcriptome analyses, we finely dissected different compartments of the HS epithelium and identified their respective changes in cytokine expression during disease progression and the critical interactions with the immune cells. Together, our work provides advanced understanding of the pathological epidermal remodeling and important implications for HS therapeutics.

scholarly journals Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Isabelle Bergiers ◽  
Tallulah Andrews ◽  
Özge Vargel Bölükbaşı ◽  
Andreas Buness ◽  
Ewa Janosz ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Endothelial Cell ◽  
Single Cell ◽  
Cell Fate ◽  
Regulatory Networks ◽  
Hematopoietic Stem ◽  
Stem And Progenitor Cells ◽  
Cell Transcriptome ◽  
Dynamical Function ◽  
Single Cell Transcriptome

Recent advances in single-cell transcriptomics techniques have opened the door to the study of gene regulatory networks (GRNs) at the single-cell level. Here, we studied the GRNs controlling the emergence of hematopoietic stem and progenitor cells from mouse embryonic endothelium using a combination of single-cell transcriptome assays. We found that a heptad of transcription factors (Runx1, Gata2, Tal1, Fli1, Lyl1, Erg and Lmo2) is specifically co-expressed in an intermediate population expressing both endothelial and hematopoietic markers. Within the heptad, we identified two sets of factors of opposing functions: one (Erg/Fli1) promoting the endothelial cell fate, the other (Runx1/Gata2) promoting the hematopoietic fate. Surprisingly, our data suggest that even though Fli1 initially supports the endothelial cell fate, it acquires a pro-hematopoietic role when co-expressed with Runx1. This work demonstrates the power of single-cell RNA-sequencing for characterizing complex transcription factor dynamics.

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