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Planarian stem cell transcriptome

ABSTRACT: Many long-lived species of animals require the function of adult stem cells throughout their lives. However, the transcriptomes of stem cells in invertebrates and vertebrates have not been compared, and consequently ancestral regulatory circuits that control stem cell populations remain poorly defined. In this study, we have used data from high-throughput RNA sequencing (RNA-Seq) to compare the transcriptomes of pluripotent adult stem cells from planarians with the transcriptomes of human and mouse pluripotent embryonic stem cells. From a stringently-defined set of 4,432 orthologs shared between planarians, mice and humans, we identified 123 conserved genes that are ≥ 5-fold differentially expressed in stem cells from all three species. Guided by this gene set, we used RNAi screening in adult planarians to discover novel stem cell regulators, which we found to affect the stem cell-associated functions of tissue homeostasis, regeneration, and stem cell maintenance. Examples of genes that disrupted these processes included the orthologs of TBL3, PSD12, TTC27, and RACK1. From these analyses, we concluded that by comparing stem cell transcriptomes from diverse species, it is possible to uncover conserved factors that function in stem cell biology. These results provide insights into which genes composed the ancestral circuitry underlying the control of stem cell self-renewal and pluripotency.

ORGANISM(S): Schmidtea mediterranea

PROVIDER: GSE37910 | GEO | 2012/06/01

SECONDARY ACCESSION(S): PRJNA167022

REPOSITORIES: GEO

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Planarian stem cell transcriptome

Project description:Many long-lived species of animals require the function of adult stem cells throughout their lives. However, the transcriptomes of stem cells in invertebrates and vertebrates have not been compared, and consequently ancestral regulatory circuits that control stem cell populations remain poorly defined. In this study, we have used data from high-throughput RNA sequencing (RNA-Seq) to compare the transcriptomes of pluripotent adult stem cells from planarians with the transcriptomes of human and mouse pluripotent embryonic stem cells. From a stringently-defined set of 4,432 orthologs shared between planarians, mice and humans, we identified 123 conserved genes that are ≥ 5-fold differentially expressed in stem cells from all three species. Guided by this gene set, we used RNAi screening in adult planarians to discover novel stem cell regulators, which we found to affect the stem cell-associated functions of tissue homeostasis, regeneration, and stem cell maintenance. Examples of genes that disrupted these processes included the orthologs of TBL3, PSD12, TTC27, and RACK1. From these analyses, we concluded that by comparing stem cell transcriptomes from diverse species, it is possible to uncover conserved factors that function in stem cell biology. These results provide insights into which genes composed the ancestral circuitry underlying the control of stem cell self-renewal and pluripotency. Three planarian tissues were analyzed: stem cells, stem cell progeny, and differentiated tissues. For the manuscript: Labbe, RM, et. al., 2012, Stem Cells

2012-06-01 | E-GEOD-37910 | biostudies-arrayexpress

The DEAD-box helicase DDX56 is a conserved stemness regulator in normal and cancer stem cells

Project description:A common and shared biology across diverse animal species is that adult tissue homeostasis is ultimately regulated by stem cell proliferation, differentiation, and self-renewal. Aberrant activation of “stemness” programs is deleterious at organismal level, and commonly observed in human cancers. However, identifying key stemness genes in the milieu of thousands of genes dysregulated in a given human cancer is challenging. Here, using a comparative genomics approach between planarians and humans, we identify and functionally screen 76 highly conserved, putative stemness regulators in vivo that are also candidate drivers of stemness in human glioblastoma, a highly aggressive, stem-cell driven cancer with limited treatment options. We selected the helicase DDX56, and demonstrate a conserved role in regulating aspects of stemness across 4 normal and cancer stem cell systems: planarian adult stem cells; mouse embryonic neural stem cells; human glioma neural stem cells; and a fly model of glioblastoma. We demonstrate that DDX56 is required for self-renewal and survival of stem cells across the systems. Using planarians, we show that when DDX56 is lost, stem cells dysregulate expression of ribosomal RNAs and lose nucleolar integrity prior to stem cell death. Altogether, our study demonstrates the power of a comparative genomic approach to discover deeply conserved stemness regulators and actionable target genes relevant to human cancer.

2021-03-01 | GSE159880 | GEO

RNA Seq analysis of sorted Schmidtea mediterranea X1 and Xins cells to identify factors specific to neoblasts

Project description:Adult stem cells are tissue-specific cells with the capacity to self-renew and differentiate to continually replace cells lost to normal physiological turnover or injury. Neoblasts, the planarian stem cells, are widely distributed throughout the body mesenchyme, driving constitutive renewal of tissues during homeostasis and endowing planarians with the remarkable capacity to regenerate wholly from tiny tissue fragments. Neoblasts are the only dividing cells in planarians and are believed to be collectively comprised of both a heterogeneous population of pluripotent cells with broad differentiation potential and also lineage-committed progenitor cells that give rise to specific tissues. Recent technology has allowed one to isolate stem cells so we used a well-established method to isolate planarian stem cells by Hoechst blue staining and flow cytometry. To understand the molecular mechanisms underlying neoblast differentiation, we performed an RNA-Seq analysis of X1 and Xins cells looking at the differentially expressed genes between the two populations. Examine gene expression profiles of adult flatwormâ??s X1 and Xins cell types. The experiment was performed in quadruplicate yielding a total of 8 samples.

2015-12-17 | E-GEOD-73027 | biostudies-arrayexpress

Expression Profiles of Planarain Stem Cells and their Immediate Division Progeny

Project description:Throughout adulthood, the replacement of cells lost to physiological turnover or injury in planarians is sustained by the proliferation and differentiation of adult stem cells known as neoblasts. Because neoblasts are the only known mitotic cells in asexual planarians, they can be efficiently eliminated by irradiation without significantly affecting post-mitotic differentiated cells. We uncovered a cohort of transcripts specific to the stem cells and their division progeny by defining the expression profiles of wild type and irradiated animals at different time points after irradiation. RNA from wild type animals, or from animals 24 hours or seven days after exposure to radiation, were compared to a common reference.

2008-09-12 | E-GEOD-11503 | biostudies-arrayexpress

Planarians recruit piRNAs for mRNA turnover in adult stem cells

Project description:Planarians recruit piRNAs for mRNA turnover in adult stem cells

| PRJNA503908 | ENA

Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identifies major cell types and pathway conservation

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

Polysome purified mRNA in control and RACK1 silenced in human hepatocarcinoma cells

Project description:Fighting viral infections is hampered by the scarcity of viral targets and their variability resulting in development of resistance. Viruses depend on cellular molecules for their life cycle, which are attractive alternative targets, provided that they are dispensable for normal cell functions. Using the model organism Drosophila melanogaster, we identify the ribosomal protein RACK1 as a cellular factor required for infection by internal ribosome entry site (IRES)-containing viruses. We further show that RACK1 is an essential determinant for hepatitis C virus translation and infection indicating that its function is conserved among distantly related human and fly viruses. Inhibition of RACK1 does not affect Drosophila or human cell viability and proliferation, and RACK1-silenced adult flies are viable, indicating that this protein is not essential for general translation. Our findings demonstrate a specific function for RACK1 in selective mRNA translation and uncover a new target for the development of broad antiviral intervention. 4 Controls 4 RACK1 silenced cells

2015-05-14 | E-GEOD-60374 | biostudies-arrayexpress

454 Life Sciences/Roche and Illumina sequencing of small RNAs from planarian samples

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

Expression Profiles of Planarain Stem Cells and their Immediate Division Progeny

2008-09-12 | GSE11503 | GEO

Smed-hippo(RNAi) RNA-Seq

Project description:The Hippo pathway plays a key role in regulating cell turnover in adult tissues, and abnormalities are consistently associated with human cancers. Initially related with the control of cell proliferation and death, hippo inhibition is commonly linked to an expansion of stem cells and progenitors, which leads to larger organs and tumors. To understand the mechanism through which Hippo directs cell renewal and promotes stemness, we studied its function in planarians, a stem cell-based organism that allows analysis of the complex cellular events underlying tissue renewal in the whole organism. We show that hippo inhibition in planarians decreases cell death, produces cell cycle arrest, and promotes the dedifferentiation of post-mitotic cells. Thus, hippo (RNAi) planarians have extensive undifferentiated areas and overgrowths with no effects on size or cell number. We propose an essential role for hippo in restricting cell plasticity and ensuring genomic stability, and thus in preventing tumoral transformation.

2018-01-23 | GSE95130 | GEO

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