scholarly journals Single-cell analysis of cell fate bifurcation in the chordate Ciona

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Konner M. Winkley ◽  
Wendy M. Reeves ◽  
Michael T. Veeman
Keyword(s):  
Transcription Factor ◽  
Cell Fate ◽  
Enrichment Analysis ◽  
Cell Types ◽  
Mapk Signaling ◽  
Embryonic Cell ◽  
Regulatory State ◽  
Cell Stage ◽  
Tissue Specific ◽  
Neural Lineage

Abstract Background Inductive signaling interactions between different cell types are a major mechanism for the further diversification of embryonic cell fates. Most blastomeres in the model chordate Ciona robusta become restricted to a single predominant fate between the 64-cell and mid-gastrula stages. The deeply stereotyped and well-characterized Ciona embryonic cell lineages allow the transcriptomic analysis of newly established cell types very early in their divergence from sibling cell states without the pseudotime inference needed in the analysis of less synchronized cell populations. This is the first ascidian study to use droplet scRNAseq with large numbers of analyzed cells as early as the 64-cell stage when major lineages such as primary notochord first become fate restricted. Results and conclusions We identify 59 distinct cell states, including new subregions of the b-line neural lineage and the early induction of the tail tip epidermis. We find that 34 of these cell states are directly or indirectly dependent on MAPK-mediated signaling critical to early Ciona patterning. Most of the MAPK-dependent bifurcations are canalized with the signal-induced cell fate lost upon MAPK inhibition, but the posterior endoderm is unique in being transformed into a novel state expressing some but not all markers of both endoderm and muscle. Divergent gene expression between newly bifurcated sibling cell types is dominated by upregulation in the induced cell type. The Ets family transcription factor Elk1/3/4 is uniquely upregulated in nearly all the putatively direct inductions. Elk1/3/4 upregulation together with Ets transcription factor binding site enrichment analysis enables inferences about which bifurcations are directly versus indirectly controlled by MAPK signaling. We examine notochord induction in detail and find that the transition between a Zic/Ets-mediated regulatory state and a Brachyury/FoxA-mediated regulatory state is unexpectedly late. This supports a “broad-hourglass” model of cell fate specification in which many early tissue-specific genes are induced in parallel to key tissue-specific transcriptional regulators via the same set of transcriptional inputs.

scholarly journals A single-cell analysis of the molecular lineage of chordate embryogenesis

2020 ◽  
Author(s):  
Tengjiao Zhang ◽  
Yichi Xu ◽  
Kaoru Imai ◽  
Teng Fei ◽  
Guilin Wang ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Cell Types ◽  
Mapk Signaling ◽  
Modular Structure ◽  
Marker Genes ◽  
List Type ◽  
Cell Stage

SummaryIn multicellular organisms, a single zygote develops along divergent lineages to produce distinct cell types. What governs these processes is central to the understanding of cell fate specification and stem cell engineering. Here we used the protochordate model Ciona savignyi to determine gene expression profiles of every cell of single embryos from fertilization through the onset of gastrulation and provided a comprehensive map of chordate early embryonic lineage specification. We identified 47 cell types across 8 developmental stages up to the 110-cell stage in wild type embryos and 8 fate transformations at the 64-cell stage upon FGF-MAPK inhibition. The identities of all cell types were evidenced by in situ expression pattern of marker genes and expected number of cells based on the invariant lineage. We found that, for the majority of asymmetrical cell divisions, the bipotent mother cell shows predominantly the gene signature of one of the daughter fates, with the other daughter being induced by subsequent signaling. Our data further indicated that the asymmetric segregation of mitochondria in some of these divisions does not depend on the concurrent fate inducing FGF-MAPK signaling. In the notochord, which is an evolutionary novelty of chordates, the convergence of cell fate from two disparate lineages revealed modular structure in the gene regulatory network beyond the known master regulator T/Brachyury. Comparison to single cell transcriptomes of the early mouse embryo showed a clear match of cell types at the tissue level and supported the hypothesis of developmental-genetic toolkit. This study provides a high-resolution single cell dataset to understand chordate embryogenesis and the relationship between fate trajectories and the cell lineage.HighlightsTranscriptome profiles of 47 cell types across 8 stages in early chordate embryoBipotent mother in asymmetric division shows the default daughter fateModular structure of the notochord GRN beyond the known function of TInvariant lineage and manual cell isolation provide truth to trajectory analysis

scholarly journals A single cell brain atlas in human Alzheimer’s disease

2019 ◽  
Author(s):  
Alexandra Grubman ◽  
Gabriel Chew ◽  
John F. Ouyang ◽  
Guizhi Sun ◽  
Xin Yi Choo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Single Cell ◽  
Cell Fate ◽  
Expression Patterns ◽  
Cell Types ◽  
Gene Expression Patterns ◽  
Cell Type ◽  
Web Resource ◽  
Cell Type Specific

AbstractAlzheimer’s disease (AD) is a heterogeneous disease that is largely dependent on the complex cellular microenvironment in the brain. This complexity impedes our understanding of how individual cell types contribute to disease progression and outcome. To characterize the molecular and functional cell diversity in the human AD brain we utilized single nuclei RNA- seq in AD and control patient brains in order to map the landscape of cellular heterogeneity in AD. We detail gene expression changes at the level of cells and cell subclusters, highlighting specific cellular contributions to global gene expression patterns between control and Alzheimer’s patient brains. We observed distinct cellular regulation of APOE which was repressed in oligodendrocyte progenitor cells (OPCs) and astrocyte AD subclusters, and highly enriched in a microglial AD subcluster. In addition, oligodendrocyte and microglia AD subclusters show discordant expression of APOE. Integration of transcription factor regulatory modules with downstream GWAS gene targets revealed subcluster-specific control of AD cell fate transitions. For example, this analysis uncovered that astrocyte diversity in AD was under the control of transcription factor EB (TFEB), a master regulator of lysosomal function and which initiated a regulatory cascade containing multiple AD GWAS genes. These results establish functional links between specific cellular sub-populations in AD, and provide new insights into the coordinated control of AD GWAS genes and their cell-type specific contribution to disease susceptibility. Finally, we created an interactive reference web resource which will facilitate brain and AD researchers to explore the molecular architecture of subtype and AD-specific cell identity, molecular and functional diversity at the single cell level.HighlightsWe generated the first human single cell transcriptome in AD patient brainsOur study unveiled 9 clusters of cell-type specific and common gene expression patterns between control and AD brains, including clusters of genes that present properties of different cell types (i.e. astrocytes and oligodendrocytes)Our analyses also uncovered functionally specialized sub-cellular clusters: 5 microglial clusters, 8 astrocyte clusters, 6 neuronal clusters, 6 oligodendrocyte clusters, 4 OPC and 2 endothelial clusters, each enriched for specific ontological gene categoriesOur analyses found manifold AD GWAS genes specifically associated with one cell-type, and sets of AD GWAS genes co-ordinately and differentially regulated between different brain cell-types in AD sub-cellular clustersWe mapped the regulatory landscape driving transcriptional changes in AD brain, and identified transcription factor networks which we predict to control cell fate transitions between control and AD sub-cellular clustersFinally, we provide an interactive web-resource that allows the user to further visualise and interrogate our dataset.Data resource web interface:http://adsn.ddnetbio.com

scholarly journals Understanding Tissue-specific Gene Regulation

2017 ◽  
Author(s):  
Abhijeet R. Sonawane ◽  
John Platig ◽  
Maud Fagny ◽  
Cho-Yi Chen ◽  
Joseph N. Paulson ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcriptional Control ◽  
Tissue Specificity ◽  
Enrichment Analysis ◽  
Tissue Expression ◽  
Gene Set Enrichment Analysis ◽  
Specific Gene ◽  
Tissue Specific ◽  
Network Nodes ◽  
Transcription Factor Expression

Although all human tissues carry out common processes, tissues are distinguished by gene expres-sion patterns, implying that distinct regulatory programs control tissue-specificity. In this study, we investigate gene expression and regulation across 38 tissues profiled in the Genotype-Tissue Expression project. We find that network edges (transcription factor to target gene connections) have higher tissue-specificity than network nodes (genes) and that regulating nodes (transcription factors) are less likely to be expressed in a tissue-specific manner as compared to their targets (genes). Gene set enrichment analysis of network targeting also indicates that regulation of tissue-specific function is largely independent of transcription factor expression. In addition, tissue-specific genes are not highly targeted in their corresponding tissue-network. However, they do assume bottleneck positions due to variability in transcription factor targeting and the influence of non-canonical regulatory interactions. These results suggest that tissue-specificity is driven by context-dependent regulatory paths, providing transcriptional control of tissue-specific processes.

scholarly journals Consistent apparent Young’s modulus of human embryonic stem cells and derived cell types stabilized by substrate stiffness regulation promotes lineage specificity maintenance

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Anqi Guo ◽  
Bingjie Wang ◽  
Cheng Lyu ◽  
Wenjing Li ◽  
Yaozu Wu ◽  
...  
Keyword(s):  
Stem Cell ◽  
Cell Fate ◽  
Cell Expansion ◽  
Embryonic Stem ◽  
Cell Types ◽  
Substrate Stiffness ◽  
Cell Stage ◽  
Cytoskeletal Organization ◽  
Lineage Specificity

Abstract Background Apparent Young’s modulus (AYM), which reflects the fundamental mechanical property of live cells measured by atomic force microscopy and is determined by substrate stiffness regulated cytoskeletal organization, has been investigated as potential indicators of cell fate in specific cell types. However, applying biophysical cues, such as modulating the substrate stiffness, to regulate AYM and thereby reflect and/or control stem cell lineage specificity for downstream applications, remains a primary challenge during in vitro stem cell expansion. Moreover, substrate stiffness could modulate cell heterogeneity in the single-cell stage and contribute to cell fate regulation, yet the indicative link between AYM and cell fate determination during in vitro dynamic cell expansion (from single-cell stage to multi-cell stage) has not been established. Results Here, we show that the AYM of cells changed dynamically during passaging and proliferation on substrates with different stiffness. Moreover, the same change in substrate stiffness caused different patterns of AYM change in epithelial and mesenchymal cell types. Embryonic stem cells and their derived progenitor cells exhibited distinguishing AYM changes in response to different substrate stiffness that had significant effects on their maintenance of pluripotency and/or lineage-specific characteristics. On substrates that were too rigid or too soft, fluctuations in AYM occurred during cell passaging and proliferation that led to a loss in lineage specificity. On a substrate with ‘optimal’ stiffness (i.e., 3.5 kPa), the AYM was maintained at a constant level that was consistent with the parental cells during passaging and proliferation and led to preservation of lineage specificity. The effects of substrate stiffness on AYM and downstream cell fate were correlated with intracellular cytoskeletal organization and nuclear/cytoplasmic localization of YAP. Conclusions In summary, this study suggests that optimal substrate stiffness regulated consistent AYM during passaging and proliferation reflects and contributes to hESCs and their derived progenitor cells lineage specificity maintenance, through the underlying mechanistic pathways of stiffness-induced cytoskeletal organization and the downstream YAP signaling. These findings highlighted the potential of AYM as an indicator to select suitable substrate stiffness for stem cell specificity maintenance during in vitro expansion for regenerative applications.

scholarly journals Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation

2019 ◽  
Author(s):  
Jonathan E. Valencia ◽  
Roberto Feuda ◽  
Dan O. Mellott ◽  
Robert D. Burke ◽  
Isabelle S. Peter
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Sea Urchin ◽  
Cell Types ◽  
Pigment Cells ◽  
Current Evidence ◽  
Regulatory State ◽  
Developmental Context ◽  
Immotile Cilia ◽  
Retinal Determination

ABSTRACTOne of the signatures of evolutionarily related cell types is the expression of similar combinations of transcription factors in distantly related animals. Here we present evidence that sea urchin larvae possess bilateral clusters of ciliary photoreceptors that are positioned in the oral/anterior apical neurogenic domain and associated with pigment cells. The expression of synaptotagmin indicates that the photoreceptors are neurons. Immunostaining shows that the sea urchin photoreceptors express an RGR/GO-opsin, opsin3.2, which co-localizes with tubulin on immotile cilia on the cell surface. Furthermore, orthologs of several transcription factors expressed in vertebrate photoreceptors are expressed in sea urchin ciliary photoreceptors, including Otx, Six3, Tbx2/3, and Rx, a transcription factor typically associated with ciliary photoreceptors. Analysis of gene expression during sea urchin development indicates that the photoreceptors derive from the anterior apical neurogenic domain. Thus, based on location, developmental origin, and transcription factor expression, sea urchin ciliary photoreceptors are likely homologous to vertebrate rods and cones. However, we found that genes typically involved in eye development in many animals, including pax6, six1/2, eya, and dac, are not expressed in sea urchin ciliary photoreceptors. Instead, all four genes are co-expressed in the hydropore canal, indicating that these genes operate as a module in an unrelated developmental context. Thus, based on current evidence, we conclude that at least within deuterostomes, ciliary photoreceptors share a common evolutionary origin and express a shared regulatory state that includes Rx, Otx, and Six3, but not transcription factors that are commonly associated with the retinal determination circuit.

Modifications of cell fate specification in equal-cleaving nemertean embryos: alternate patterns of spiralian development

Development ◽  
1995 ◽  
Vol 121 (10) ◽  
pp. 3175-3185 ◽  
Author(s):  
M.Q. Martindale ◽  
J.Q. Henry
Keyword(s):  
Cell Fate ◽  
Cell Lineage ◽  
Cell Types ◽  
Embryonic Cell ◽  
Specific Cell ◽  
Cell Fate Specification ◽  
Cell Fates ◽  
Developmental Potential ◽  
Fate Specification ◽  
Symmetry Properties

The nemerteans belong to a phylum of coelomate worms that display a highly conserved pattern of cell divisions referred to as spiral cleavage. It has recently been shown that the fates of the four embryonic cell quadrants in two species of nemerteans are not homologous to those in other spiralian embryos, such as the annelids and molluscs (Henry, J. Q. and Martindale, M. Q. (1994a) Develop. Genetics 15, 64–78). Equal-cleaving molluscs utilize inductive interactions to establish quadrant-specific cell fates and embryonic symmetry properties following fifth cleavage. In order to elucidate the manner in which cell fates are established in nemertean embryos, we have conducted cell isolation and deletion experiments to examine the developmental potential of the early cleavage blastomeres of two equal-cleaving nemerteans, Nemertopsis bivittata and Cerebratulus lacteus. These two species display different modes of development: N. bivittata develops directly via a non-feeding larvae, while C. lacteus develops to form a feeding pilidium larva which undergoes a radical metamorphosis to give rise to the juvenile worm. By examining the development of certain structures and cell types characteristic of quadrant-specific fates for each of these species, we have shown that isolated blastomeres of the indirect-developing nemertean, C. lacteus, are capable of generating cell fates that are not a consequence of that cell's normal developmental program. For instance, dorsal blastomeres can form muscle fibers when cultured in isolation. In contrast, isolated blastomeres of the direct-developing species, N. bivittata do not regulate their development to the same extent. Some cell fates are specified in a precocious manner in this species, such as those that give rise to the eyes. Thus, these findings indicate that equal-cleaving spiralian embryos can utilize different mechanisms of cell fate and axis specification. The implications of these patterns of nemertean development are discussed in relation to experimental work in other spiralian embryos, and a model is presented that accounts for possible evolutionary changes in cell lineage and the process of cell fate specification amongst these protostome phyla.

Stem cells and lineage development in the mammalian blastocyst

2007 ◽  
Vol 19 (1) ◽  
pp. 111 ◽  
Author(s):  
Janet Rossant
Keyword(s):  
Stem Cells ◽  
Cell Fate ◽  
Es Cells ◽  
Mammalian Species ◽  
Embryonic Stem ◽  
Cell Types ◽  
Mouse Cell ◽  
Embryonic Cell ◽  
Primitive Endoderm ◽  
Key Factors

The mammalian blastocyst is the source of the most pluripotent stem cells known: embryonic stem (ES) cells. However, ES cells are not totipotent; in mouse chimeras, they do not contribute to extra-embryonic cell types of the trophectoderm (TE) and primitive endoderm (PrE) lineages. Understanding the genetic pathways that control pluripotency v. extra-embryonic lineage restriction is key to understanding not only normal embryonic development, but also how to reprogramme adult cells to pluripotency. The trophectoderm and primitive endoderm lineages also provide the first signals that drive patterned differentiation of the pluripotent epiblast cells of the embryo. My laboratory has produced permanent mouse cell lines from both the TE and the PrE, termed trophoblast stem (TS) and eXtra-embryonic ENdoderm (XEN) cells. We have used these cells to explore the genetic and molecular hierarchy of lineage restriction and identify the key factors that distinguish the ES cell v. the TS or XEN cell fate. The major molecular pathways of lineage commitment defined in mouse embryos and stem cells are probably conserved across mammalian species, but more comparative studies of lineage development in embryos of non-rodent mammals will likely yield interesting differences in terms of timing and details.

scholarly journals Single-cell analysis of cell fate bifurcation in the chordate Ciona

2020 ◽  
Author(s):  
Konner M. Winkley ◽  
Wendy M. Reeves ◽  
Michael T. Veeman
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Single Cell Analysis ◽  
Cell Types ◽  
Embryonic Cell ◽  
Major Mechanism ◽  
Divergent Gene ◽  
Distinct Cell ◽  
Hourglass Model ◽  
Almost All

AbstractInductive signaling interactions between different cell types are a major mechanism for the further diversification of embryonic cell fates. Most blastomeres in the model chordate Ciona robusta become restricted to a single predominant fate between the 64-cell and mid-gastrula stages. We used single-cell RNAseq spanning this period to identify 53 distinct cell states, 25 of which are dependent on a MAPK-mediated signal critical to early Ciona patterning. Divergent gene expression between newly bifurcated sibling cell types is dominated by upregulation in the induced cell type. These upregulated genes typically include numerous transcription factors and not just one or two key regulators. The Ets family transcription factor Elk1/3/4 is upregulated in almost all the putatively direct inductions, indicating that it may act in an FGF-dependent feedback loop. We examine several bifurcations in detail and find support for a ‘broad-hourglass’ model of cell fate specification in which many genes are induced in parallel to key tissue-specific transcriptional regulators via the same set of transcriptional inputs.

The winged-helix transcription factor Foxd3 suppresses interneuron differentiation and promotes neural crest cell fate

Development ◽  
2001 ◽  
Vol 128 (21) ◽  
pp. 4127-4138 ◽  
Author(s):  
Mirella Dottori ◽  
Michael K. Gross ◽  
Patricia Labosky ◽  
Martyn Goulding
Keyword(s):  
Transcription Factor ◽  
Neural Crest ◽  
Cell Fate ◽  
Neural Tube ◽  
Neural Crest Cell ◽  
Neural Crest Cells ◽  
Cell Types ◽  
Winged Helix ◽  
Multiple Cell ◽  
Winged Helix Transcription Factor

The neural crest is a migratory cell population that gives rise to multiple cell types in the vertebrate embryo. The intrinsic determinants that segregate neural crest cells from multipotential dorsal progenitors within the neural tube are poorly defined. In this study, we show that the winged helix transcription factor Foxd3 is expressed in both premigratory and migratory neural crest cells. Foxd3 is genetically downstream of Pax3 and is not expressed in regions of Pax3 mutant mice that lack neural crest, implying that Foxd3 may regulate aspects of the neural crest differentiation program. We show that misexpression of Foxd3 in the chick neural tube promotes a neural crest-like phenotype and suppresses interneuron differentiation. Cells that ectopically express Foxd3 upregulate HNK1 and Cad7, delaminate and emigrate from the neural tube at multiple dorsoventral levels. Foxd3 does not induce Slug and RhoB, nor is its ability to promote a neural crest-like phenotype enhanced by co-expression of Slug. Together these results suggest Foxd3 can function independently of Slug and RhoB to promote the development of neural crest cells from neural tube progenitors.

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