Stem cell differentiation trajectories in Hydra resolved at single cell resolution
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ABSTRACT:
PROVIDER: PRJNA497876 | ENA |
REPOSITORIES: ENA
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Project description:The adult Hydra polyp continuously renews all of its cells using three separate stem cell populations but the genetic pathways enabling these dynamic tissue properties are not well understood. We used Drop-seq to sequence 24,985 Hydra cells and identified the molecular signatures of a broad spectrum of cell states, from stem cells to terminally differentiated cells. We constructed differentiation trajectories for each cell lineage and identified the transcription factors expressed along these trajectories, thus creating a comprehensive map of all developmental lineages in the adult animal. We unexpectedly found that neuron and gland cell differentiation transits through a common progenitor state, suggesting a shared evolutionary history for these secretory cell types. Finally, we have built the first gene expression map of the Hydra nervous system. By producing a comprehensive molecular description of the adult Hydra polyp, we have generated a resource for addressing fundamental questions regarding the evolution of developmental processes and nervous system function.
2018-11-02 | GSE121617 | GEO
Project description: Not available
| S-EPMC7104783 | biostudies-literature
Project description:Positional RNA-sequencing of isolated Hydra body pieces and RNA-sequencing of fully regenerated Hydra animal was combined with RNA-sequencing of actively regenerating spheroids (see submission E-MTAB-9672) in order to elucidate the role of tissue stretching on regeneration and body pattern formation.
2022-10-13 | E-MTAB-9676 | biostudies-arrayexpress
Project description:Hydra has long been studied for its remarkable ability to regenerate its head. Previous studies focusing on molecular mechanisms of axial patterning and head regeneration using a candidate gene approach have revealed a central role for the canonical Wnt pathway. We performed a global gene expression analysis during Hydra magnipapillata head regeneration using RNA-seq to identify additional genes that are transcriptionally regulated during the regeneration of the head organizer in hydra. Differential expression analysis revealed a set of 4,978 genes with significant changes during a 48-hour head regeneration time-course that includes many key genes in the Wnt, TGF-M-NM-2/BMP and MAP kinase pathways. We observed the differential regulation of several genes that are part of the epithelial-to-mesenchymal transition in bilaterians such as Snail. We assembled 806 novel putative lincRNAs with 176 of these are differentially expressed during the time course. We observed the coordinated transcriptional regulation of several factors that regulate the effective pool of free M-NM-2-catenin that together synergize to increase the amount of M-NM-2-catenin available for transcriptional regulation of downstream genes. The differential expression of Snail and some of its interacting regulators and downstream targets suggests that a partial-EMT-like response is involved in hydra head regeneration. This time-course is a valuable resource for the study of the transcriptional dynamics of head regeneration in hydra. mRNA profiling of regenerating head from 6 time points post bisection of Hydra head (H. magnipapillata), generated by deep sequencing, in duplicates, using Illumina HiSeq2500.
2014-12-13 | E-GEOD-64127 | biostudies-arrayexpress
Project description:Immune cells sense their environment and adapt their state. Deciphering cellular trajectories unfolding over time is fundamental for understanding biology. Empirical in vivo genomic technologies measuring both cell state and time are lacking. Here, we present Zman-seq, a single-cell technology tracking transcriptomic dynamics across time by introducing fluorescent time stamps into immune cells. We applied Zman-seq to resolve immune cell state-transitions of the dysfunctional tumor immune microenvironment (TME) of glioblastoma (GBM). By measuring the exposure time of infiltrating immune cells in the TME, Zman-seq defines the cellular and molecular trajectories underlying immune incompetence in GBM. Within 24 hours, cytotoxic NK cells transitioned to a dysfunctional program regulated by Tgfb1, while monocytes differentiated into immunosuppressive macrophages in 36-48 hours. Anti-TREM2 antagonistic antibody reshaped the TME by redirecting monocytes to pro-inflammatory macrophages. Zman-seq is a broadly applicable technology enabling empirical measurements of differentiation trajectories guiding the development of more efficacious immunotherapies.
2023-12-21 | GSE232040 | GEO
Project description:The molecular nature of malignant tumors is well studied in vertebrates, while their evolutionary origin remains unknown. In particular, there is no evidence for naturally occurring malignant tumors in pre-bilaterian animals, such as sponges and cnidarians. This is somewhat surprising given that recent computational studies have predicted that all metazoans are prone to develop tumors. Here we provide first evidence for naturally occurring tumors in Hydra oligactis. Histological, cellular and molecular data reveal that these tumors are transplantable and caused by differentiation arrest of female gametes. Growth of tumor cells is independent from the cellular environment. Tumor bearing polyps have significantly reduced fitness. In addition, Hydra tumors show a greatly altered transcriptome that mimics expression shifts in vertebrate cancers. Therefore, this study shows, that invasive tumors have deep roots in animal phylogeny, and that early branching animals may be informative in revealing the fundamental mechanisms of tumorigenesis. We compared four samples of Hydra oligactis tumor-bearing animals to three samples of female polyps undergoing oogenesis and six samples of female asexual control polyps
2014-06-24 | E-GEOD-56287 | biostudies-arrayexpress
Project description:A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution
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Project description:The blueprint of lineage segregation of early mouse embryo is established during gastrulation in which progenitors of various cell fates are regionalized and patterned in specific embryo locations. Despite the central importance of this period of mammalian development, we currently lack a comprehensive understanding of the underlying developmental trajectories and molecular processes, principally because research efforts either employed in vitro systems, focused on small numbers of genes, or limited the number of developmental stages or cell types that were studied. Here, we study the regulatory landscape of gastrulation by combining single-cell RNA-seq (A total of ~35,000 single cells isolated at E6.5, E6.75, E7.0, E7.25, E7.5) and geographical position sequencing (Geo-seq) technique, and we report a de novo identification of spatial signatures and a method to enable retrospective locating of single cells to their origins. Our work provides insights into the exit from pluripotency and priming for differentiation, and the emergence of regulatory networks associated with cell fate decisions. Finally, we reconstruct the spatio-temporal roadmap of gastrula mouse embryo in single-cell resolution. This result uncovers the cell migration trajectories and molecular processes associated with lineage segregation.
2023-08-15 | GSE171588 | GEO
Project description:Single-Cell Resolution of Lineage Trajectories in the Arabidopsis Stomatal Lineage and Developing Leaf
| PRJNA703045 | ENA