YAP and TAZ Dictate Binary Pan-Cancer Superclasses [RNA-seq]
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ABSTRACT:
PROVIDER: PRJNA605470 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11044000_1.fastq.gz | Fastqsanger.gz | |||
| SRR11044000_2.fastq.gz | Fastqsanger.gz | |||
| SRR11044001_1.fastq.gz | Fastqsanger.gz | |||
| SRR11044001_2.fastq.gz | Fastqsanger.gz | |||
| SRR11044002_1.fastq.gz | Fastqsanger.gz |
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Project description:YAP and TAZ Dictate Binary Pan-Cancer Superclasses
| PRJNA605473 | ENA
Project description:YAP and TAZ Dictate Binary Pan-Cancer Superclasses [ChIP-seq]
| PRJNA605477 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below. We defined pan-cancer binary classes based on distinct expression of YAP (and its paralog TAZ/ WWTR1) and YAP-responsive adhesion regulators. Combining informatics with in vivo and in vitro gain- and loss-of-function studies across multiple murine and human tumor types, we showed that opposite pro- or anti-cancer YAP activity functionally defines binary YAPon or YAPoff cancer classes that express or silence YAP, respectively. Essentially all leukemia and lymphoma fall into the YAPoff class, as do multiple neural and neuroendocrine YAPoff solid cancers. YAPoff solid cancers are frequently RB1-/-, such as retinoblastoma, small cell lung cancer and neuroendocrine prostate cancer. YAP-silencing was intrinsic to the cell-of-origin, or acquired with lineage-switching and drug-resistance. The binary cancer groups exhibit distinct YAP-dependent adhesive behavior, and pharmaceutical vulnerabilities, underscoring clinical relevance. Mechanistically, whereas YAP induces cell cycle genes in YAPon cancers, extensive RNAseq data showed that forced YAP expression in YAPoff cancers instead activated adhesion genes that are normally co-silenced with YAP. YAP regulates both of these anti-cancer adhesive or pro-cancer cell cycle programs through the TEAD DNA binding family (TEAD1-4). YAP/TEAD targets AP1-bound enhancers in YAPon cancers, but Chipseq studies revealed that in YAPoff cancers, YAP/TEAD instead targeted elements co-bound with neural and neuroendocrine lineage-defining basic helix-loop-helix (bHLH) and Homeobox transcription factors (e.g. NEUROD, ASCL1, NKX2, OTX2). A CRISPR screen revealed that, among the adhesion regulators, ITGAV/ITGB5 pair are required for YAP induced cytostasis in YAPoff cancers. YAP is thus pivotal across all cancer, but in opposite pro- or anti-cancer ways, which define contrasting genetic and drug sensitivities.
2021-06-21 | GSE144975 | GEO
Project description:We defined pan-cancer binary classes based on distinct expression of YAP (and its paralog TAZ/ WWTR1) and YAP-responsive adhesion regulators. Combining informatics with in vivo and in vitro gain- and loss-of-function studies across multiple murine and human tumor types, we showed that opposite pro- or anti-cancer YAP activity functionally defines binary YAPon or YAPoff cancer classes that express or silence YAP, respectively. Essentially all leukemia and lymphoma fall into the YAPoff class, as do multiple neural and neuroendocrine YAPoff solid cancers. YAPoff solid cancers are frequently RB1-/-, such as retinoblastoma, small cell lung cancer and neuroendocrine prostate cancer. YAP-silencing was intrinsic to the cell-of-origin, or acquired with lineage-switching and drug-resistance. The binary cancer groups exhibit distinct YAP-dependent adhesive behavior, and pharmaceutical vulnerabilities, underscoring clinical relevance. Mechanistically, whereas YAP induces cell cycle genes in YAPon cancers, extensive RNAseq data showed that forced YAP expression in YAPoff cancers instead activated adhesion genes that are normally co-silenced with YAP. YAP regulates both of these anti-cancer adhesive or pro-cancer cell cycle programs through the TEAD DNA binding family (TEAD1-4). YAP/TEAD targets AP1-bound enhancers in YAPon cancers, but Chipseq studies revealed that in YAPoff cancers, YAP/TEAD instead targeted elements co-bound with neural and neuroendocrine lineage-defining basic helix-loop-helix (bHLH) and Homeobox transcription factors (e.g. NEUROD, ASCL1, NKX2, OTX2). A CRISPR screen revealed that, among the adhesion regulators, ITGAV/ITGB5 pair are required for YAP induced cytostasis in YAPoff cancers. YAP is thus pivotal across all cancer, but in opposite pro- or anti-cancer ways, which define contrasting genetic and drug sensitivities.
2021-06-21 | GSE144973 | GEO
Project description:We defined pan-cancer binary classes based on distinct expression of YAP (and its paralog TAZ/ WWTR1) and YAP-responsive adhesion regulators. Combining informatics with in vivo and in vitro gain- and loss-of-function studies across multiple murine and human tumor types, we showed that opposite pro- or anti-cancer YAP activity functionally defines binary YAPon or YAPoff cancer classes that express or silence YAP, respectively. Essentially all leukemia and lymphoma fall into the YAPoff class, as do multiple neural and neuroendocrine YAPoff solid cancers. YAPoff solid cancers are frequently RB1-/-, such as retinoblastoma, small cell lung cancer and neuroendocrine prostate cancer. YAP-silencing was intrinsic to the cell-of-origin, or acquired with lineage-switching and drug-resistance. The binary cancer groups exhibit distinct YAP-dependent adhesive behavior, and pharmaceutical vulnerabilities, underscoring clinical relevance. Mechanistically, whereas YAP induces cell cycle genes in YAPon cancers, extensive RNAseq data showed that forced YAP expression in YAPoff cancers instead activated adhesion genes that are normally co-silenced with YAP. YAP regulates both of these anti-cancer adhesive or pro-cancer cell cycle programs through the TEAD DNA binding family (TEAD1-4). YAP/TEAD targets AP1-bound enhancers in YAPon cancers, but Chipseq studies revealed that in YAPoff cancers, YAP/TEAD instead targeted elements co-bound with neural and neuroendocrine lineage-defining basic helix-loop-helix (bHLH) and Homeobox transcription factors (e.g. NEUROD, ASCL1, NKX2, OTX2). A CRISPR screen revealed that, among the adhesion regulators, ITGAV/ITGB5 pair are required for YAP induced cytostasis in YAPoff cancers. YAP is thus pivotal across all cancer, but in opposite pro- or anti-cancer ways, which define contrasting genetic and drug sensitivities.
2021-06-21 | GSE144972 | GEO
Project description:The factors regulating cellular identity are critical for understanding the transition from health to disease and responses to therapies. Cell identity is generally assigned based on static phenotypes, like “omics” profiles. However, how such static features translate into dynamic responses to perturbations that determine cellular function is often unclear. We found that autophagy perturbation in different cell types can have opposite responses in growth-promoting oncogenic YAP/TAZ transcriptional signalling. These apparently contradictory responses can be resolved by a feedback loop where autophagy negatively regulates the levels of α-catenins LC3-interacting proteins, which inhibit YAP/TAZ, which, in turn, positively regulate autophagy. High basal levels of α-catenins enable autophagy induction to positively regulate YAP/TAZ, while low α-catenins cause YAP/TAZ activation upon autophagy inhibition. These data reveal how feedback loops enable post-transcriptional determination of cell identity and how levels of a single intermediary protein can dictate the direction of response to external or internal perturbations.
2021-03-19 | PXD023711 | Pride
Project description:The optic vesicle comprises a pool of bi-potential progenitor cells from which the retinal pigment epithelium (RPE) and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation, but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz-Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises, and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap (yap1) mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz (wwtr1) mutant alleles such that, when Yap and Taz are both absent, optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co-factor. In contrast to loss of Yap and Taz, overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall, this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.
2015-08-06 | E-GEOD-71681 | biostudies-arrayexpress
Project description:The two effector proteins of the Hippo signaling pathway, YAP and TAZ, play a pivotal role in the cellular homeostasis of podocytes and in the pathogenesis of focal segmental glomerulosclerosis (FSGS). We aim to unravel the unique and redundant functions of YAP and TAZ in the podocyte by identifying podocyte-specific interactors. We generated stable heat sensitive mouse podocytes (hsMPs) carrying a single copy integration of a transgenic construct expressing a flagged version of mouse Yap (3XFLAG.YAP), Taz (3XFLAG.TAZ) or Ruby (3XFLAG.RUBY) in the Rosa26 locus. To explore the interactome of YAP and TAZ in podocytes we immunoprecipitated the tagged proteins and characterized the co-immunoprecipitated protein complexes by mass spectrometry. Within the interactome analyses of the hsMPs, we identified shared and non-shared interacting proteins between YAP and TAZ. Among these identified proteins many well established interactors of YAP and TAZ were included, like proteins of the Tead family, different angiomotins or large tumor suppressor kinase 1 (Lats1). Strikingly, among the shared proteins were numerous proteins of the nuclear shuttling machinery, like importins (Ipo), exportins (Xpo), transportins (Tnpo) and nucleoporins (Nup) that form the nuclear pore complex (NPC), such as NUP107, NUP133, NUP205 and XPO5.
2024-01-26 | PXD040448 | Pride
Project description:The Hippo pathway plays a crucial in organ size control during development and tissue homeostasis in adult life. To examine a role for Hippo signaling in the intestinal epithelium, we analyzed gene expression patterns in the mouse intestinal epithelilum transfected with siRNAs or expression plasmids for shRNAs targeting the Hippo pathway effectors, YAP and TAZ. We performed two independent series of experiments (siGFP (n=3) vs siYAP/siTAZ (n=3), and shLacZ (n=1) vs shYAP/shTAZ (n=1)). Control siRNA (siGFP), YAP/TAZ siRNAs, or expression plasmids for control shRNA (shLacZ) or YAP/TAZ shRNAs were introduced into the mouse intestinal epithelium by the newly-developed in vivo transfection method. Four days after transfection, intestinal epithelial cells were isolated from the tissues and total RNA was extracted.
2014-07-18 | E-GEOD-45155 | biostudies-arrayexpress
Project description:Oral squamous cell carcinoma (OSCC) is a prevalent form of cancer that develops from the epithelium of the oral cavity. OSCC is on the rise worldwide, and death rates associated with the disease are particularly high. Despite progress in understanding of the mutational and expression landscape associated with OSCC, advances in deciphering these alterations for the development of therapeutic strategies have been limited. Further insight into the molecular cues that contribute to OSCC is therefore required. Here we show that the transcriptional regulators YAP (YAP1) and TAZ (WWTR1), which are key effectors of the Hippo pathway, drive pro-tumorigenic signals in OSCC. Regions of pre-malignant oral tissues exhibit aberrant nuclear YAP accumulation, suggesting that dysregulated YAP activity contributes to the onset of OSCC. Supporting this premise, we determined that nuclear YAP and TAZ activity drives OSCC cell proliferation, survival, and migration in vitro, and is required for OSCC tumor growth and metastasis in vivo. Global gene expression profiles associated with YAP and TAZ knockdown revealed changes in the control of gene expression implicated in pro-tumorigenic signaling, including those required for cell cycle progression and survival. Notably, the transcriptional signature regulated by YAP and TAZ significantly correlates with gene expression changes occurring in human OSCCs identified by The Cancer Genome Atlas (TCGA), emphasizing a central role for YAP and TAZ in OSCC biology. Expression profiling was conducted following the repression of the transcriptional regulators TAZ and YAP (YAP/TAZ) in human SCC2 oral cancer cells. Human SCC2 oral cancer cells were transfected with control siRNA, or siRNAs targeting TAZ, YAP, or YAP/TAZ for 48 hours. Total RNA from three independent experiments carried out on separate days was isolated and purified and the samples were then profiled on Affymetrix Human Gene 2.0 Chips at the Boston University Microarray Core. The expression profiles were processed and normalized using the Robust Multi-array Average (RMA) procedure (23) based on a custom Brainarray CDF (24). For each of the siRNA experiments, signatures of genes differentially expressed between treatment and corresponding siRNA control with an FDR q-value ?0.05 and a fold change ?2 were identified as either activated (up-regulated in control) or repressed (up-regulated in treatment). The overlap between the differentially expressed gene signatures was evaluated by Fisher test. Hierarchical gene and sample clustering was performed on the top 3000 genes with highest median absolute deviation (MAD; a robust version of the variance) across 12 samples, using “ward” as the agglomeration rule, and 1 minus Pearson correlation and Euclidean as the distance measures for genes and samples, respectively.
2015-05-26 | E-GEOD-66949 | biostudies-arrayexpress