Dissecting human endoderm development through a genome-wide CRISPR screen in human embryonic stem cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE95729 | GEO | 2019/09/06
REPOSITORIES: GEO
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2011-09-30 | E-GEOD-19091 | biostudies-arrayexpress
Project description:Mitogen-activated protein kinase kinase 4 (MKK4) is a dual-specificity kinase activated by environmental stress, cytokines, and peptide growth factors that reportedly can promote or inhibit tumor cell growth and metastasis. Somatic mutations in the gene encoding MKK4 (MAP2K4) have been identified in various human cancers, but the consequences of these mutations on MKK4 function and the biology of tumor cells that have them have not been elucidated. Here we report that, of the eleven mutations within the MAP2K kinase domain described thus far, one had gain-of-function (Q142L) and six had loss-of-function. Three of the loss-of-function mutations are nonsense mutations that produced C-terminally-truncated proteins (I295fs*23, R304*, and W310*) that were highly ubiqitinated and rapidly degraded when introduced into cells, and three are missense mutations in the ATP-binding pocket (N234I), activation loop (S251N), or C-lobe (P326L). We modeled the consequences of MAP2K4 loss-of-function mutations on cells by introducing MKK4 short-hairpin RNA constructs and found that MKK4 depletion enhanced the ability of a weakly tumorigenic murine cancer cell to metastasize when injected into syngeneic mice but had no effect on primary tumor formation. MKK4-depleted cells exhibited an increased capacity to migrate across PET filters and to invade through matrigel but no change in anchorage-dependent or -independent proliferation. Transcriptional profiling of these cells revealed gene expression changes that promote epithelial-to-mesenchymal transition and angiogenesis. We conclude that MKK4 inactivation promoted metastasis but not primary tumor formation. Collectively, these findings implicate loss-of-function MAP2K4 somatic mutations in tumor metastasis and provide one of the few examples of a somatic mutation in cancer cells that exerts a metastasis-specific effect. Keywords: Two-group comparison.
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Project description:Faithful embryogenesis requires the precise coordination between embryonic and extraembryonic tissues. Although embryonic and extraembryonic stem cells have been derived from several mammalian species including humans, they are cultured in different conditions, which makes it difficult to study their intercommunication. Here, by simultaneously activating FGF, TGF-β and WNT pathways, we derived stable pluripotent stem cells (PSCs), trophoblast stem cells (TSCs) and extraembryonic endoderm stem cells (XENs) from mouse blastocysts under the same condition (FTW). Co-culture of PSCs and XENs in the same environment uncovered, among other interactions, a previously unrecognized control of proliferation of epiblast cells by extraembryonic endoderm cells. FTW condition also supported de novo derivation of XENs from cynomolgus monkey and human blastocysts, and enabled setting up co-culture of human iPSCs and XENs. Crosspieces comparison revealed conserved and divergent processes and genes regulating XENs and ligand-receptor interactions between pluripotent and extraembryonic endoderm cells. Our study establishes a unique stem cell co-culture strategy to examine embryonic and extraembryonic lineage crosstalk during early mammalian development, and opens the door for developing more faithful in vitro models and differentiation protocols.
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Project description:A conserved molecular pathway has emerged controlling endoderm formation in Xenopus zebrafish and mice. Key genes in this pathway include Nodal ligands and transcription factors of the Mix-like paired homeodomain class, Gata4-6 zinc finger factors and Sox17 HMG domain proteins. While a linear epistatic pathway has been proposed, the precise hierarchical relationships between these factors and their downstream targets are largely unresolved. Here we used a combination of microarray analysis and loss-of-function experiments to examine the global regulatory network controlling Xenopus endoderm formation. We identified over 300 transcripts enriched in the gastrula endoderm, including most of the known endoderm regulators as well as over a hundred uncharacterized genes. Surprisingly only 10% of the endoderm transcriptome is regulated as predicted by the current linear model. We find that Nodals, Mixer and Sox17 have both shared and distinct sets of downstream targets and that a number of unexpected autoregulatory loops exist between Sox17 and Gata4-6, Sox17 and Bix1, 2, 4 and between Sox17 and Xnr4. We find that Mixer does not function primarily via Sox17 as previously proposed. This data provides a new insight into the complexity of endoderm formation and will serve as valuable resource for establishing a complete endoderm gene regulatory network. Keywords: Embryonic, Development. Endoderm, Xenopus, nodal, Sox17, Mixer, microarray, gene regulatory network
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