A systemic transcriptome analysis reveals the regulation of neural stem cell maintenance by an E2F1–miRNA feedback loop

Palm, Thomas; Hemmer, Kathrin; Winter, Julia; Fricke, Inga B.; Tarbashevich, Katsiaryna; Shakib, Fereshteh Sadeghi; Rudolph, Ina-Maria; Hillje, Anna-Lena; Luca, Paola De; Bahnassawy, Lamia A; Madel, Rabea J; Viel, Thomas; Siervi, Adriana De; Jacobs, Andréas H.; Diederichs, Sven; Schwamborn, Jens Christian

doi:10.1093/nar/gkt070

Cited by 26 publications

(37 citation statements)

References 55 publications

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“…Cluster 1 was defined by genes primarily associated with proliferation and neurogenesis, including genes involved in chromosome and DNA packing (for example, Mtfhfd1), replication (for example, Mybl2, Pcna) and cell cycle regulation (for example, Ccna2, Cdc73). This cluster was also characterized by the expression of transcription factor E2f1 and cyclin D1 (Ccnd1), with well established functions in the control of cell cycle [19][20][21]. Cluster 2 was defined by GO terms related to interneuron differentiation, cell morphogenesis and forebrain development, suggesting that this cluster contains interneuron precursors that have left the cell cycle and become postmitotic.…”

Section: Resultsmentioning

confidence: 99%

Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially-resolved RNA-seq

Zechel¹,

Zając²,

Lönnerberg³

et al. 2014

Genome Biol

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Background: Cortical interneurons originating from the medial ganglionic eminence, MGE, are among the most diverse cells within the CNS. Different pools of proliferating progenitor cells are thought to exist in the ventricular zone of the MGE, but whether the underlying subventricular and mantle regions of the MGE are spatially patterned has not yet been addressed. Here, we combined laser-capture microdissection and multiplex RNA-sequencing to map the transcriptome of MGE cells at a spatial resolution of 50 μm. Results: Distinct groups of progenitor cells showing different stages of interneuron maturation are identified and topographically mapped based on their genome-wide transcriptional pattern. Although proliferating potential decreased rather abruptly outside the ventricular zone, a ventro-lateral gradient of increasing migratory capacity was identified, revealing heterogeneous cell populations within this neurogenic structure.

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Section: Resultsmentioning

confidence: 99%

Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially-resolved RNA-seq

Zechel¹,

Zając²,

Lönnerberg³

et al. 2014

Genome Biol

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“…In line with the promoter analysis, E2F1 expression and its target genes were found to be downregulated upon ENPP1 knockdown. Although a stem cell relevant role of E2F1 was so far not investigated in GSCs, E2F1 was shown to be of particular importance in the maintenance of neural stem cells 41 and human pluripotent stem cells 42 as well as in a transcriptional regulatory network governing the maintenance of embryonic stem cells. 43 Given the central role of E2F1 in the regulation of cell cycle progression, it is reasonable to assume that the observed reduced proliferation and accumulation of cells in G1 cell cycle phase in E-NPP1-deficient GSCs is mediated by a decreased transcriptional function of E2F1.…”

Section: Discussionmentioning

confidence: 99%

Stem cell characteristics in glioblastoma are maintained by the ecto-nucleotidase E-NPP1

et al. 2014

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Glioblastomas are highly aggressive brain tumours and are characterised by substantial cellular heterogeneity within a single tumour. A sub-population of glioblastoma stem-like cells (GSCs) that shares properties with neural precursor cells has been described, exhibiting resistance to therapy and therefore being considered responsible for the high recurrence rate in glioblastoma. To elucidate the underlying cellular processes we investigated the role of phosphatases in the GSC phenotype, using an in vitro phosphatome-wide RNA interference screen. We identified a set of genes, the knockdown of which induces a significant decrease in the glioma stem cell marker CD133, indicating a role in the glioblastoma stem-like phenotype. Among these genes, the ecto-nucleotidase ENPP1 (ectonucleotide pyrophosphatase/phosphodiesterase 1) was found to be highly expressed in GSCs compared with normal brain and neural stem cells. Knockdown of ENPP1 in cultured GSCs resulted in an overall downregulation of stem cell-associated genes, induction of differentiation into astrocytic cell lineage, impairment of sphere formation, in addition to increased cell death, accumulation of cells in G1/G0 cell cycle phase and sensitisation to chemotherapeutic treatment. Genome-wide gene expression analysis and nucleoside and nucleotide profiling revealed that knockdown of ENPP1 affects purine and pyrimidine metabolism, suggesting a link between ENPP1 expression and a balanced nucleoside-nucleotide pool in GSCs. The phenotypic changes in E-NPP1-deficient GSCs are assumed to be a consequence of decreased transcriptional function of E2F1. Together, these results reveal that E-NPP1, by acting upstream of E2F1, is indispensable for the maintenance of GSCs in vitro and hence required to keep GSCs in an undifferentiated, proliferative state. Glioblastoma, classified by the WHO (World Health Organization) as grade IV astrocytoma, 1 is the most common primary malignant brain tumour in adults. Despite progress in surgical resection, radiation and chemotherapy, glioblastoma remains a deadly disease with a median survival time of about 1 year. 2 One particular therapeutic challenge for glioblastoma treatment is posed by their remarkable intratumoural cellular heterogeneity. Several studies indicate the existence of a highly tumourigenic, sub-population of cancer cells with stemlike characteristics. [3][4][5] There is substantial evidence that these so-called cancer stem cells have inherent chemotherapy and radiation resistance. 6,7 These findings suggest that cancer cells harbouring stem cell-like characteristics are responsible for ineffective therapy, explaining high recurrence rates despite significant reduction in tumour volume. Glioblastoma stem-like cells (GSCs) share properties with neural precursor cells, such as a capacity for self-renewal, differentiation and maintained proliferation, as well as stem cell marker expression. 4,5,8,9 GSCs were originally defined by expression of CD133 (Prominin-1) and its extracellular AC133 epitope. 4 Although recent...

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“…By performing a high-throughput mRNA and miRNA profiling, the researchers revealed that neuronal differentiation of NSCs induces drastic changes in the transcriptomic profile. These changes include the activation of numerous miRNAs [27]. QPCR results indicated that 3D culture environments contribute to maintain the self-renewal ability of NSCs.…”

Section: Figmentioning

confidence: 96%

The miR-7 Identified from Collagen Biomaterial-Based Three-Dimensional Cultured Cells Regulates Neural Stem Cell Differentiation

Cui

Xiao

Chen

et al. 2014

Stem Cells and Development

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Increasing evidence suggests that three-dimensional (3D) cultures provide more appropriate microenvironments to control stem cell response compared with traditional two-dimensional (2D) cultures. However, the molecular mechanism involved in 3D cultured stem cells is not well known. Several microRNAs whose target genes involved in the regulation of self-renewal and differentiation of stem cells were found to be downregulated in 3D cultured PA-1 cells. Among them, miR-7 was predicted to target Kruppel-like factor 4 (Klf4), a key gene for self-renewal of neural stem cells (NSCs). We showed that the differentiation of NSCs was inhibited in 3D collagen scaffolds compared with 2D cultured cells. The quantitative real-time PCR (qPCR) analysis indicated that the expression of miR-7 and Klf4 changed significantly in 2D cultures, whereas the expression stability of miR-7 and Klf4 was detected in 3D cultures. Using luciferase assay and western blot, Klf4 was identified as a target of miR-7 indicating that miR-7 plays a critical role in maintaining the selfrenewal capacity through a Klf4-dependent mechanism in 3D cultured cells. Thus, the collagen scaffold-based 3D cell cultures may provide a platform to reveal the regulatory mechanism of cell regulators, which are difficult to find in traditional 2D cell cultures.

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A systemic transcriptome analysis reveals the regulation of neural stem cell maintenance by an E2F1–miRNA feedback loop

Cited by 26 publications

References 55 publications

Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially-resolved RNA-seq

Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially-resolved RNA-seq

Stem cell characteristics in glioblastoma are maintained by the ecto-nucleotidase E-NPP1

The miR-7 Identified from Collagen Biomaterial-Based Three-Dimensional Cultured Cells Regulates Neural Stem Cell Differentiation

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