Canonical and early lineage-specific stem cell types identified in planarian SirNeoblasts
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ABSTRACT:
PROVIDER: PRJNA666322 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12739020.fastq.gz | Fastqsanger.gz | |||
| SRR12739021.fastq.gz | Fastqsanger.gz |
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Project description:The pluripotent stem cells in planarians, a model for tissue and cellular regeneration, have yet to be definitively identified. We recently developed a method to enrich piwi-1+ cells in Schmidtea mediterranea, by staining cells with SiR-DNA and Cell Tracker Green, named SirNeoblasts that permits their propagation and subsequent functional study in vivo. Since traditional enrichment for planarian neoblasts by Hoechst 33342 staining, to generate X1 cells, blocks the cell cycle, inducing cytotoxicity, this method represents a substantive technological advance for functional investigation of cell fate and regeneration in basic and applied research questions. However, the similarities in heterogeneity of cell subtypes between SirNeoblasts and X1 remain unknown. In this work, we performed single cell RNA sequencing for SirNeoblasts for comparison with differential expression patterns in a publicly available X1 single cell RNA sequencing data. We found first that all of the lineage-specific progenitor cells in X1 were present in comparable proportions in SirNeoblasts. In addition, SirNeoblasts contain an early muscle progenitor unreported in X1. Analysis of new markers for putative pluripotent stem cells identified here, with subsequent sub-clustering analysis revealed earlier lineages of epidermal, muscular, intestinal, and pharyngeal progenitors than have been observed in X1. Using the ski-3 and GCM markers, we also identified a pluripotent cell population at higher resolution than that provided by tgs-1. The use of SirNeoblast will enable broad experimental advances in regeneration and cell fate specification, given the possibility for propagation and transplantation of recombinant and mutagenized pluripotent stem cells not previously afforded to this rapid and versatile model system.
2021-03-23 | GSE158706 | GEO
Project description:BackgroundThe pluripotent stem cells in planarians, a model for tissue and cellular regeneration, remain further identification. We recently developed a method to enrich piwi-1+ cells in Schmidtea mediterranea, by staining cells with SiR-DNA and Cell Tracker Green, named SirNeoblasts that permits their propagation and subsequent functional study in vivo. Since traditional enrichment for planarian neoblasts by Hoechst 33342 staining generates X1 cells, blocking the cell cycle and inducing cytotoxicity, this method by SiR-DNA and Cell Tracker Green represents a complementary technological advance for functional investigation of cell fate and regeneration. However, the similarities in heterogeneity of cell subtypes between SirNeoblasts and X1 remain unknown.ResultsIn this work, we performed single cell RNA sequencing of SirNeoblasts for comparison with differential expression patterns in a publicly available X1 single cell RNA sequencing data. We found first that all of the lineage-specific progenitor cells in X1 were present in comparable proportions in SirNeoblasts. In addition, SirNeoblasts contain an early muscle progenitor that is unreported in X1. Analysis of new markers for putative pluripotent stem cells identified here, with subsequent sub-clustering analysis, revealed earlier lineages of epidermal, muscular, intestinal, and pharyngeal progenitors than have been observed in X1. Using the gcm as a marker, we also identified a cell subpopulation resided in previously identified tgs-1+ neoblasts. Knockdown of gcm impaired the neoblast repopulation, suggesting a function of gcm in neoblasts.ConclusionsIn summary, the use of SirNeoblasts will enable broad experimental advances in regeneration and cell fate specification, given the possibility for propagation and transplantation of recombinant and mutagenized pluripotent stem cells that are not previously afforded to this rapid and versatile model system.
| S-EPMC7979843 | biostudies-literature
Project description:The transcriptome of a cell dictates its unique cell-type biology. We used single-cell RNA sequencing to determine the transcriptomes for essentially every cell type of a complete animal: the regenerative planarian Schmidtea mediterranea. Planarians contain a diverse array of cell types, possess lineage progenitors for differentiated cells (including pluripotent stem cells), and constitutively express positional information, making them ideal for this undertaking. We generated data for 66,783 cells, defining transcriptomes for known and many previously unknown planarian cell types and for putative transition states between stem and differentiated cells. We also uncovered regionally expressed genes in muscle, which harbors positional information. Identifying the transcriptomes for potentially all cell types for many organisms should be readily attainable and is a powerful new approach to metazoan biology.
2018-04-17 | GSE111764 | GEO
Project description:Neoblasts are adult stem cells (ASCs) in planarians which sustain cell replacement during homeostasis and regeneration of any missing tissue. While numerous studies have examined genes underlying neoblast pluripotency, molecular pathways driving the postmitotic fate remain poorly defined. Here we used transcriptional profiling of irradiation-sensitive and -insensitive cell populations and RNA interference (RNAi) functional screening to uncover markers and regulators of postmitotic progeny. We identified 32 new markers, which distinguish two epithelial progenitor populations, and a planarian homolog to the MEX3 RNA-binding protein (Smed-mex3-1) as a key regulator of lineage progression. mex3-1 is required for generating progenitors of epithelial, neural, eye, pharyngeal, and protonephridial lineages, and restricting expansion of the stem cell compartment. We also demonstrate the utility of using mex3-1(RNAi) animals to identify additional progenitor markers. These results show that mex3-1 promotes differentiation in multiple, if not all, lineages, and maintains the balance between ASC self-renewal and commitment. Sorted and irradiated animals were collected as previously described (Labbe, et al., 2012) and RNAi conditions were triplicated, RNA was purified independently, then each replicate was pooled in equal amounts for sequencing at the timepoint: 1 feed day 12 for control RNAi and mex3-1 RNAi.
2015-06-15 | E-GEOD-68581 | biostudies-arrayexpress
Project description:The planarian epidermis provides an excellent model to explore adult stem cell (ASC) lineage development due to well-characterized and distinct spatiotemporal phases during lineage progression. Using flow cytometry-isolated cells enriched in epidermal progenitors, we performed transcriptional profiling and RNAi screening to uncover regulators of epidermal differentiation. We identified a MYB-type transcription factor (Smed-myb-1) required for specification of the first temporal phase of post-mitotic maturation. Knockdown of myb-1 abolished the early progenitor phase of differentiation without ceasing production of subsequent epidermal progenitors or homeostatic turnover and regeneration of the epidermis. Further examination revealed accelerated maturation of ASC descendants, with premature entry into subsequent progeny phases and ultimately the epidermis. These results demonstrate that a spatiotemporal shift in lineage progression occurs in the absence of the early progenitor state after myb-1 RNAi, and identify myb-1 as a critical regulator of the early temporal window in the step-wise specification during planarian epidermal differentiation.
2018-08-18 | GSE118674 | GEO
Project description:<p>During development of the human brain, multiple cell types with diverse regional identities are generated. Here we report a system to generate early human brain forebrain and mid/hindbrain cell types from human embryonic stem cells (hESCs), and infer and experimentally confirm a lineage tree for the generation of these types based on single-cell RNA-Seq analysis. We engineered <i>SOX2<sup>Cit/+</sup></i> and <i>DCX<sup>Cit/Y</sup></i> hESC lines to target progenitors and neurons throughout neural differentiation for single-cell transcriptomic profiling, then identified discrete cell types consisting of both rostral (cortical) and caudal (mid/hindbrain) identities. Direct comparison of the cell types were made to primary tissues using gene expression atlases and fetal human brain single-cell gene expression data, and this established that the cell types resembled early human brain cell types, including preplate cells. From the single-cell transcriptomic data a Bayesian algorithm generated a unified lineage tree, and predicted novel regulatory transcription factors. The lineage tree highlighted a prominent bifurcation between cortical and mid/hindbrain cell types, confirmed by clonal analysis experiments. We demonstrated that cell types from either branch could preferentially be generated by manipulation of the canonical Wnt/beta-catenin pathway. In summary, we present an experimentally validated lineage tree that encompasses multiple brain regions, and our work sheds light on the molecular regulation of region-specific neural lineages during human brain development.</p>
| phs001205 | dbGaP
Project description:Neoblasts are adult stem cells (ASCs) in planarians which sustain cell replacement during homeostasis and regeneration of any missing tissue. While numerous studies have examined genes underlying neoblast pluripotency, molecular pathways driving the postmitotic fate remain poorly defined. Here we used transcriptional profiling of irradiation-sensitive and -insensitive cell populations and RNA interference (RNAi) functional screening to uncover markers and regulators of postmitotic progeny. We identified 32 new markers, which distinguish two epithelial progenitor populations, and a planarian homolog to the MEX3 RNA-binding protein (Smed-mex3-1) as a key regulator of lineage progression. mex3-1 is required for generating progenitors of epithelial, neural, eye, pharyngeal, and protonephridial lineages, and restricting expansion of the stem cell compartment. We also demonstrate the utility of using mex3-1(RNAi) animals to identify additional progenitor markers. These results show that mex3-1 promotes differentiation in multiple, if not all, lineages, and maintains the balance between ASC self-renewal and commitment.
2015-06-15 | GSE68581 | GEO
Project description:Proper function and repair of the digestive system are vital to most animals. Deciphering the mechanisms involved in these processes requires an atlas of gene expression and cell types. Here, we applied laser-capture microdissection (LCM) and RNA-seq to characterize the intestinal transcriptome of Schmidtea mediterranea, a planarian flatworm that can regenerate all organs, including the gut. We identified hundreds of genes with intestinal expression undetected by previous approaches. Systematic analyses revealed extensive conservation of digestive physiology and cell types with other animals, including humans. Furthermore, spatial LCM enabled us to uncover previously unappreciated regionalization of gene expression in the planarian intestine along the medio-lateral axis, especially among intestinal goblet cells. Finally, we identified two intestine-enriched transcription factors that specifically regulate regeneration (hedgehog signaling effector gli-1) or maintenance (RREB2) of goblet cells. Altogether, this work provides resources for further investigation of mechanisms involved in gastrointestinal function, repair and regeneration.
2020-03-20 | GSE135351 | GEO
Project description:The head-regeneration transcriptome of the planarian Schmidtea mediterranea
2011-07-15 | E-MTAB-607 | biostudies-arrayexpress
Project description:Background: In the Lophotrochozoan superphylum, few organisms have the capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planarian. The species Schmidtea mediterranea in particular has become a powerful model to study adult stem cell biology and mechanisms of regeneration. Despite this, systematic attempts to define gene complements and their annotations are lacking, restricting comparative analyses that detail the conservation of biochemical pathways and identify lineage-specific innovations. Results: In this study we compare several transcriptomes and define a robust set of 35,232 transcripts. From this, we perform systematic gene annotations and undertake a genome-scale metabolic reconstruction for S. mediterranea. Cross-species comparisons of gene content identify both conserved, lineage-specific, and expanded gene families, which may contribute to the regenerative properties of planarians. In particular, we find that TRAF and cadherin gene families have been greatly expanded in planarians. We further provide a single-cell RNA-sequencing analysis of 2000 cells, revealing both known and novel cell-types defined by unique signatures of gene expression. Amongst these were a novel mesenchymal cell population as well as a cell type involved in eye regeneration. Integration of our metabolic reconstruction further reveals the extent to which a given cell types have adapted energy and nucleotide biosynthetic pathways to support their specialized roles. Conclusions: In general, S. mediterranea displays a high level of gene and pathways conservation with other model systems, rendering it as a viable model to study the roles of these pathways in stem cell biology and regeneration.
2018-08-01 | GSE115280 | GEO