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Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in HeLa cells upon Hippo Components Overexpression or Knockout

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in HeLa cells upon Hippo Components Overexpression or Knockout

PROVIDER: PRJNA662555 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12616705_1.fastq.gz	Fastqsanger.gz
	SRR12616705_2.fastq.gz	Fastqsanger.gz
	SRR12616706_1.fastq.gz	Fastqsanger.gz
	SRR12616706_2.fastq.gz	Fastqsanger.gz
	SRR12616707_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in HeLa cells upon Hippo Components Overexpression or Knockout

Project description:Purpose: The goals of this study are to compare and integrate NGS-derived transcriptome when Hippo components are manipulated in HeLa cells. Methods: Total RNAs from three replicates were extracted using TRIzol (Thermo Fisher Scientific) from HeLa cells. RNA quality was assessed using a bioanalyzer (Agilent Technologies). RNA-seq libraries were prepared according to the Illumina TruSeq protocol. Then were pooled for deep sequencing by using Illumina Hiseq Xten (2 × 150) platforms at the Omics Core of Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai, China. Raw read qualities were evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, v0.11.5). Adaptor sequences and read sequences on both ends with Phred quality scores below 30 were trimmed. Trimmed reads were then mapped with the Hisat2 algorithm (version 2.1.0) to target sequences. Gene expression levels were quantified by the software package HTSeq (v0.6.1p1). The list of differentially expressed genes were generated by DESeq2 with FC：1.5，and adjust p-value<0.05.The significant genes were then compared with each other. Results: We finally get 558 genes that have dramatical change in different groups. Conclusions: Our study shows many common genes that can be loyally regulated by Hippo signaling.

2020-09-10 | GSE157717 | GEO

USP22 Facilitates Gastric Cancer Progression via Hippo/YAP axis

Project description:USP22 Facilitates Gastric Cancer Progression via Hippo/YAP axis

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VCPIP1 facilitates pancreatic cancer progression via Hippo/YAP signaling

Project description:VCPIP1 facilitates pancreatic cancer progression via Hippo/YAP signaling

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Transcriptional targets of Hippo signaling in mammalian cells

Project description:The Hippo pathway is an emerging signaling cascade involved in the regulation of organ size control. It consists of evolutionally conserved protein kinases that are sequentially phosphorylated and activated. The active Hippo pathway subsequently phosphorylates a transcription coactivator, YAP, which precludes its nuclear localization and transcriptional activation. Identification of transcriptional targets of YAP in diverse cellular contexts is therefore critical to the understanding of the molecular mechanisms in which the Hippo pathway restricts tissue growth. We used microarrays to profile the gene expression patterns upon acute siRNA knockdown of Hippo pathway components in multiple mammalian cell lines and identified a set of genes representing immediate transcriptional targets of the Hippo/Yap signaling pathway. Three mammalian cell lines (HEK293T, HepG2, HaCaT) were transfected with scramble siRNA controls or siRNAs against NF2 and LATS2, two core components of the Hippo pathway, simultaneously. Total RNAs were harvested four days after transfection to reveal the gene expression pattern unsing microarry. YAP and TAZ siRNAs were also transfected along with NF2 and LATS2 siRNAs to identify YAP/TAZ-dependent transcriptional targets upon loss of NF2/LATS2.

2013-12-31 | E-GEOD-49384 | biostudies-arrayexpress

In vivo screen reveals specific roles of Hippo pathway components in development and regeneration

Project description:The Hippo signalling pathway is a major regulator of regeneration and development. However, the comparative importance and functional roles of individual Hippo pathway components in vivo is greatly unknown, particularly within the vertebrate lineage. To gain direct and comparable insights we took advantage of the zebrafish larvae model system. We generated individual and combined CRISPR/Cas9 F0 knockouts of a range of core Hippo pathway genes, including upstream regulators, the co-transcriptional regulators Yap1/Taz, and Yap1/Taz-target genes. We analysed and compared the resulting developmental and regenerative phenotypes. Our findings highlight that paralogues of core components have distinct, but in some instances overlapping, functions. Intriguingly, we find that Yap and Taz have differential roles during development and regeneration. In addition, we characterise and compare two tail fin regenerative paradigms: after both severe and mild injury. These injury paradigms are drastically different and elicit diverse resolution processes. We confirm critical roles of the immune system in the regenerative process and identify that macrophages are recruited to lesser extent in tail fin regeneration upon Yap1 and Taz loss, suggesting defective regenerative macrophage function. This defective macrophage involvement might therefore be one of the mediators of the deficient regeneration in these two Crispants. Overall, our analysis emphasises distinct requirements and responses of the Hippo pathway during development and across different regenerative paradigms.

2025-12-16 | GSE311765 | GEO

DEK binds to pre-mRNAs and regulated alternative splicing of Hippo signaling genes in HeLa cell [RNA-seq]

Project description:Purpose: Explore how DEK genome widely bind RNA and affect the alternative splicing in cancer Methods: DEK was overexpressed by transfecting HeLa cells with a DEK-overexpressing plasmid and RNA_seq was used to analyze gene expression profile and splicing pattern of DEK overexpression and control cells. Then, an improved RIP-seq was conducted to explore genome-widely binding characteristic of DEK in HeLa cell. Bioinformatics analysis and qPCR/RIP-PCR were performed to identify and validate the bound and regulated targets of DEK, respectively Results:The results showed DEK overexpression did not affect transcript level expression of those high expressed genes (with FPKM > 1), but splicing pattern of 411 genes (RASGs) was regulated by DEK in HeLa cells, which were enriched in Hippo signaling pathway. Moreover, DEK broadly bind the RNA of a total of 11, 112 genes, with a biased binding the GGUAA motifs at the CDS and intronic regions Conclusions: our results indicated DEK could broadly bind and regulate the pre-mRNA splicing process, which provide new insights of mechanisms that DEK functions in various biological processes including cancer

2025-03-19 | GSE141565 | GEO

DEK binds to pre-mRNAs and regulated alternative splicing of Hippo signaling genes in HeLa cell [RIP-seq]

2025-03-19 | GSE141566 | GEO

In vivo screen reveals specific roles of Hippo pathway components in development and regeneration

Project description:In vivo screen reveals specific roles of Hippo pathway components in development and regeneration

| PRJNA1370883 | ENA

USP22 Facilitates Gastric Cancer Progression via Hippo/YAP axis

Project description:Gastric cancer (GC) is one of the most common malignancies in the digestive system. Previous studies demonstrated that the dysregulation of the Hippo pathway and hyperactivation of the YAP/TEAD transcriptional axis played important roles in GC progression, although the underlying mechanisms remain incompletely understood. Our study demonstrated that the deubiquitinase USP22 plays a pivotal role in regulating the Hippo pathway in GC, where its inhibition markedly suppresses YAP/TEAD activity and tumor progression. Mechanistically, USP22 interacts with YAP and inhibits its K48-linked polyubiquitination, thereby enhancing YAP protein stability and Hippo/YAP axis activity in GC. Intriguingly, YAP can transcriptionally upregulate USP22 by binding to its promoter region, establishing a positive feedback loop that promotes gastric cancer progression. Collectively, our findings reveal a reciprocal activation mechanism between USP22 and the Hippo pathway in gastric tumorigenesis, identifying USP22 as a promising novel therapeutic target.

2026-06-01 | GSE319116 | GEO

Merlin/NF2-loss Driven Tumorigenesis Linked to CRL4(DCAF1)-Mediated Inhibition of the Hippo Pathway Components Lats1 and 2

Project description:Studies in drosophila have suggested that Merlin/NF2 suppresses tumorigenesis by activating upstream components of the Hippo pathway at or near the plasma membrane. In contrast, studies of Merlin-deficient tumor cells have indicated that Merlin suppresses tumorigenesis by entering into the nucleus where it inhibits the E3 ubiquitin ligase CRL4DCAF1. We found that CRL4DCAF1 promotes YAP and TEAD-dependent transcription by ubiquitylating and thereby inhibiting Lats1 and 2 in the nucleus. Genetic epistasis experiments and analysis of tumor-derived missense mutations indicate that this signaling connection sustains the oncogenicity of Merlin-deficient tumor cells. Analysis of clinical samples confirms that this pathway operates in NF2 mutant mesotheliomas, schwannomas and meningiomas. We conclude that de-repressed CRL4DCAF1 controls the output of the Hippo pathway by inhibiting Lats1 and 2 in the nucleus.

2014-07-15 | GSE56157 | GEO

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