Allometry of cell types in planarians by single cell transcriptomics
Ontology highlight
ABSTRACT:
ORGANISM(S): Schmidtea mediterranea
PROVIDER: GSE246681 | GEO | 2023/11/06
REPOSITORIES: GEO
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Project description:We used scRNA-seq to examine serotonergic function in asexual planarians. We profiled 47,292 single cell transcriptomes of planarian of 3 different RNAi categories: gfp(RNAi), lhx1/5-1(RNAi) and pitx(RNAi). We detected changes in cell type frequency and gene expression patterns in planarian of different knock-down conditions, capturing regulatory programs of distinct cell types in response to loss of serotonergic function.
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Project description:The planarian Dugesia japonica has amazing ability to regenerate a head from the anterior ends of the amputated stump with maintenance of the original anterior-posterior polarity. Although planarians present an attractive system for molecular investigation of regeneration and research has focused on clarifying the molecular mechanism of regeneration initiation in planarians, but proteomic studies are still in the early stages. Here, a global proteomics analysis of regenerating head fragments in planarians at 0h, 2h and 6h after amputation was performed using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics coupled with LC-MS/MS strategy. Then the significantly changed proteins were identified. The correlation betwwen protein expression profiles and signaling pathways/biological processes was analyzed by bioinformatics and systems biology.
2015-07-07 | PXD002100 | Pride
Project description:PIWI proteins utilize small RNAs called piRNAs to silence transposable elements, thereby protecting germline integrity. In planarian flatworms, PIWI proteins are essential for regeneration, which requires adult stem cells termed neoblasts. Here, we characterize planarian piRNAs and examine the roles of PIWI proteins in neoblast biology. We find that the planarian PIWI proteins SMEDWI-2 and SMEDWI-3 cooperate to degrade active transposons via the ping-pong cycle. Unexpectedly, we discover that SMEDWI-3 plays an additional role in planarian mRNA surveillance. While SMEDWI-3 degrades numerous neoblast mRNAs in a homotypic ping-pong cycle, it is also guided to another subset of neoblast mRNAs by antisense piRNAs and binds these without degrading them. Mechanistically, the distinct activities of SMEDWI-3 are primarily dictated by the degree of complementarity between target mRNAs and antisense piRNAs. Planarian PIWI proteins thus act as both nucleases and RNA-binding proteins, enabling planarians to repurpose piRNAs for critical roles in neoblast mRNA turnover.
2019-09-04 | GSE122199 | GEO
Project description:Regeneration requires the precise integration of cues that initiate proliferation, direct differentiation, and ultimately re-pattern tissues to the proper size and scale. Yet how these processes are integrated with wounding cues remains relatively unknown. The freshwater planarian, Schmidtea mediterranea, is an ideal model to study the stereotyped proliferative and transcriptional responses to injury due to its high capacity for regeneration. Here, we characterize the effector of the Hippo signalling cascade, yorkie, during planarian regeneration and its role in restricting early injury responses. In yki(RNAi) regenerating animals, wound responses are hyper-activated; the bimodal proliferation kinetics are heighted and prolonged, while the transcriptional injury responses are similarly augmented with dysregulated temporal patterns. We also uncovered novel wound-induced genes by RNAseq that are primarily associated with tissue patterning. Indeed, a high proportion of non-wound- and wound-induced patterning molecules are mis-expressed in yki(RNAi), which we demonstrate is in part due to an expanded muscle cell population. These altered injury responses have consequential effects on regenerative outcomes, specifically sensing the size of a given injury and appropriately scaling organ and tissue sizes. Taken together, our results suggest that yki functions as a key node to integrate the injury responses of proliferation, apoptosis, injury-induced transcription, and patterning to coordinate regeneration.
2017-06-20 | GSE97787 | GEO
Project description:Background: Freshwater planarians are well known for their regenerative abilities. Less well known is how planarians maintain spatial patterning in long-lived adult animals or how they re-pattern tissues during regeneration. HOX genes are good candidates to regulate planarian spatial patterning, yet the full complement or genomic clustering of planarian HOX genes has not yet been described, primarily because only a few have been detectable by in situ hybridization, and none have given morphological phenotypes when knocked down by RNAi. Results: Because the planarian Schmidtea mediterranea (S. med) is unsegmented, appendage-less, and morphologically simple, it has been proposed that it may have a simplified HOX gene complement. Here we argue against this hypothesis and show that S. med has a total of 13 HOX genes, which represent homologs to all major axial categories, and can be detected by whole-mount in situ hybridization using a highly-sensitive method. In addition, we show that planarian HOX genes do not cluster in the genome, yet 5/13 have retained aspects of axially-restricted expression. Finally, we confirm HOX gene axial expression by RNA-deep-sequencing 6 anterior-to-posterior “zones” of the animal, which we provide as a dataset to the community to discover other axially-restricted transcripts. Conclusions: Freshwater planarians have an unappreciated HOX gene complexity, with all major axial categories represented. However, we conclude based on adult expression patterns that planarians have a derived body plan and their asexual lifestyle may have allowed for large changes in HOX expression from the last common ancestor between arthropods, flatworms, and vertebrates. Using our in situ method and axial zone RNAseq data, it should be possible to further understand the pathways that pattern the anterior-posterior axis of adult planarians.
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Project description:Freshwater planarian flatworms possess uncanny regenerative capacities mediated by abundant and collectively totipotent adult stem cells. Key functions of these cells during regeneration and tissue homeostasis have been shown to depend on PIWI, a molecule required for piRNA expression in planarians. Nevertheless, the full complement of piRNAs, and microRNAs (miRNAs) in this organism has yet to be defined. Here, we report on the large scale cloning and sequencing of small RNAs from the planarian Schmidtea mediterranea, yielding altogether millions of sequenced unique small RNAs. We show that piRNAs are in part organized in genomic clusters and that they share characteristic features with mammalian and fly piRNAs. We further identify 61 novel miRNA genes and thus double the number of known planarian miRNAs. Sequencing, as well as quantitative PCR of small RNAs uncovered ten miRNAs enriched in planarian stem cells. These miRNAs are down-regulated in animals in which stem cells have been abrogated by irradiation, and thus constitute miRNAs likely associated with specific stem cell functions. Altogether, we present the first comprehensive small RNA analysis in animals belonging to the third animal superphylum, the Lophotrochozoa, and single out a number of miRNAs that may function in regeneration. Several of these miRNAs are deeply conserved in animals. Small RNAs were sequenced from FACS-sorted neoblast stem cells, untreated planarians and irradiated planarians, depleted of neoblasts
2009-06-30 | E-GEOD-16159 | biostudies-arrayexpress
Project description:Background: The planarian, Schmidtea mediterranea, is a master regenerator with a large adult stem cell compartment. The lack of transgenic labeling techniques in this animal have hindered the study of lineage progression and has made understanding the mechanisms of tissue replacement during regeneration a challenge. However, recent advances in single cell transcriptomics and analysis methods may allow for the discovery of novel cell lineages as differentiation progresses from stem cell to terminally differentiated cell. Here we apply Waterfall analysis and single cell transcriptomics to identify adult stem cells belonging to specific cellular lineages and identify novel candidate genes for future in vivo lineage studies. Results: Single-cell-RNA-deep sequencing (scRNAseq) of 168 purified single stem and progeny cells from the planarian head was used to identify a molecularly distinct, neural stem cell population (νNeoblasts). Hierarchical clustering revealed 10 distinct subgroups and pseudotime analysis with Waterfall predicted a neural lineage trajectory as well as a novel alternative lineage. Previously undescribed neural lineage genes identified in silico were characterized in vivo and were shown to have neural expression patterns. Using the predicted νNeoblast markers, we demonstrate that a novel piwi-2+piwi-1lo stem cell population exists adjacent to the brain and immediately takes up BrdU. Conclusions: scRNAseq coupled with in silico lineage analysis offers a new approach for studying lineage progression in planarians. The lineages identified here were extracted from a highly heterogeneous dataset with minimal prior knowledge of planarian lineages, demonstrating that lineage purification by transgenic labelling is not a prerequisite for this approach. The identification of the νNeoblast lineage demonstrates the usefulness of the planarian system for computationally predicting cellular lineages in an adult context coupled with in vivo verification.
2016-04-08 | GSE79866 | GEO
Project description:Epimorphic regeneration commonly relies on the activation of quiescent stem cells to drive new cell production. The planarian Schmidtea mediterranea is among the best regenerators in nature, thanks to its large population of adult stem cells, called neoblasts. While neoblasts have long been known to drive regeneration, whether a subset of neoblasts is reserved for this purpose is unknown. Here, we revisited the idea of reserved neoblasts by approaching neoblast heterogeneity from a regulatory perspective. By implementing a new fluorescence-activated cell sorting strategy in planarians, we identified a population of neoblasts defined by low transcriptional activity. These RNAlow neoblasts are relatively slow-cycling at homeostasis and undergo a morphological regeneration response characterized by cell growth at 48 hours post-amputation. At this time, RNAlow neoblasts proliferated in a TOR-dependent manner. Additionally, knockdown of the tumour suppressor Lrig-1, which is enriched in RNAlow neoblasts, resulted in RNAlow neoblast growth and hyperproliferation at homeostasis, and ultimately delayed regeneration. We propose that slow-cycling RNAlow neoblasts represent a regeneration-reserved neoblast population.
2020-12-31 | GSE157860 | GEO
Project description:Nkx2.2 is an intestine-enriched transcription factor required for regeneration in planarians. The goal of this study was to identify differentially expressed transcripts in uninjured nkx2.2(RNAi) planarians.
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Project description:Transcriptional profiling of Schmidtea mediterranea planarians that have been amputated transversely and left to regenerate for different time points (UNIRR); the same experiment was performed on irradiated - neoblast depleted animals (IRR). The purpose of this experiment was to identify transcriptional changes that are induced within the first 12h following amputation. In order to distinguish between gene expression changes in the differentiated tissue and the neoblasts, a second set of time course data was created from irradiated animals Two-color experiment, 3 replicates per condition (including 10 animals/replica)
2012-04-29 | E-GEOD-36945 | biostudies-arrayexpress