Expression analysis of primary mouse mebryonic fibroblasts lacking the POLE4 and P53 tumour suppressors genes
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ABSTRACT:
PROVIDER: PRJNA824790 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18685542.fastq.gz | Fastqsanger.gz | |||
| SRR18685543.fastq.gz | Fastqsanger.gz | |||
| SRR18685544.fastq.gz | Fastqsanger.gz | |||
| SRR18685545.fastq.gz | Fastqsanger.gz | |||
| SRR18685546.fastq.gz | Fastqsanger.gz |
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Project description:Mouse embryonic fibroblasts lacking the POLE4 subunit of Pol Epsilon show signs of replication stress and DNA damage. Strikingly this phenotype is lost upon deletion of the Trp53 gene. In order to reveal the mechanism responsible for this phenotype we carried oud bulk RNA sequencing from primary mouse embryonic fibroblast WT or KO for POLE4, in a p53 knock-out genetic background or in the presence of one of 2 copies of the wt allele
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Project description:The maintenance of genome stability relies on the coordinated control of origin activation and replication fork progression. How the interplay between these processes impacts human genetic disease and cancer remains incompletely characterized. Here we initially show that mouse cells lacking Pole4 and featuring Pole instability exhibit impaired genome-wide activation of DNA replication origins, in a origin location-independent manner. Lack of POLE4 leads to proteasome-dependent Pole degradation prior to CMG (CDC45/MCM2-7/GINS) helicase formation and origin activation. Strikingly, Trp53 ablation in primary Pole4 knock-out cells increased Pole levels and origin activation and reduced DNA damage levels in a transcription-dependent manner. Transcriptome analysis of primary Trp53 knock out cells revealed that the TRP53-CDKN1A/P21 axis maintains appropriate levels of replication initiation factors and CDK activity during unchallenged S-phase. Loss of this control mechanism deregulates origin activation, perturbs genome-wide replication fork progression and induces fork stalling and DNA damage. Thus, while our data support an impaired origin activation model for genetic diseases affecting CMG formation, we propose that loss of the TRP53-CDKN1A/P21 tumour suppressor axis induces inappropriate origin activation and deregulates genome wide fork progression. This phenomenon has broad implications for genetic instability and therapeutic targeting in cancer.
2022-05-16 | GSE200331 | GEO
Project description:Increased activity of the epigenetic modifier EZH2 has been associated with different cancers. However, evidence for a functional role of EZH2 in tumourigenesis in vivo remains poor, in particular in metastasising solid cancers. Here we reveal central roles of EZH2 in promoting growth and metastasis of cutaneous melanoma. In a melanoma mouse model, conditional Ezh2 ablation as much as treatment with the preclinical Ezh2 inhibitor GSK503 stabilises the disease through inhibition of growth and virtually abolishes metastases formation without affecting normal melanocyte biology. Comparably, in human melanoma cells, EZH2 inactivation impairs proliferation and invasiveness, accompanied by re-expression of tumour suppressors connected to increased patient survival. These EZH2 target genes suppress melanoma growth and prevent EMT / metastasis in vivo revealing the dual function of EZH2 in promoting tumour progression. Thus, EZH2-mediated epigenetic repression is highly relevant especially during advanced melanomagenesis, which makes EZH2 a promising target for novel melanoma therapies.
2014-11-12 | GSE63165 | GEO
Project description:Microarray expression data generated to determine the impact of defined p53 mutations on lung cancer cell phenotypes, and on the tumour supressive responses induced by WT p53 restoration. In murine models of lung cancer, the therapeutic benefit of WT p53 restoration has been demonstrated in p53-deficient tumours (Juntilla et al, 2010; Feldser et al, 2010). However, it remains unknown if the restoration of WT p53 function is beneficial in p53 mutant tumours. Thus, to determine the impact of p53-targeted therapy in mutant p53 lung cancer, we analysed cells from murine lung tumours of distinct p53 genotypes. Utilising the well characterised p53-ER allele (Christophorou et al, 2005; Martins et al, 2006; Juntilla et al, 2010) we carried out transcriptional profiling of KrasG12D/+ cell lines isolated from advanced lung tumours with defined p53 status: p53Fx/ER (null), p53R270H/ER and p53R172H/ER in the absence (p53 WT OFF) or presence (p53 WT ON) of 4-hydroxytamoxifen (4-OHT). The temporal specificity of p53-ER restoration allowed us to utilised two timepoints to determine both the immediate (2hr) and sustained (8hr) impact of WT p53 function.
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Project description:p53 is a pivotal tumor suppressor and a major barrier against cancer. We now report that silencing of the Hippo pathway tumor suppressors LATS1 and LATS2 in non-transformed mammary epithelial cells reduces p53 phosphorylation and increases its association with the p52 NF-κB subunit. Moreover, it partly shifts p53’s conformation and transcriptional output towards a state resembling cancer-associated p53 mutants, and endow p53 with the ability to promote cell migration. Notably, LATS1 and LATS2 are frequently downregulated in breast cancer; we propose that such downregulation might benefit cancer by converting p53 from a tumor suppressor into a tumor facilitator.
2018-10-25 | PXD003120 | Pride
Project description:Tumor suppressors are mostly defined by inactivating somatic mutations in tumors, yet little is known about their epigenetic features in normal cells. Here, through integrative analysis of 1,134 genome-wide epigenetic profiles and mutations from >8,200 tumor-normal pairs, we discovered broad H3K4me3 (wider than 4 kb) as the first epigenetic signature for tumor suppressors in normal cells. Broad H3K4me3 is associated with increased transcription elongation and enhancer activity together leading to exceptionally high gene expression, and is distinct from other broad epigenetic features, such as super enhancers. Broad H3K4me3 conserved across normal cells represents core tumor suppressors, such as P53 and PTEN, whereas cell-type-specific broad H3K4me3 may indicate cell-identity genes and cell-type-specific tumor suppressors. Furthermore, widespread shortening of broad H3K4me3 in cancers is strongly associated with repression of tumor suppressors. Together, the broad H3K4me3 epigenetic signature we reported here may provide a new direction for the discovery and characterization of novel tumor suppressors. H3K4me3 ChIP-Seq was conducted in 1) liver tumor and matched tissue, 2) lung tumor and matched tissue, 3) cell line A549 grown under normal and flavopiridol treatment conditions.
2015-07-29 | E-GEOD-67471 | biostudies-arrayexpress
Project description:FOXQ1 transcription factors is highly induced in several types of carcinomas where it promotes tumour growth and metastasis, however, the molecular mechanisms leading to FOXQ1 deregulation in cancer are incompletely understood. Here, we used a CRISPR/Cas9-based genomic locus proteomics (GLoPro) to discover transcriptional regulators of FOXQ1 and identified the tumour suppressor p53 as a transcriptional repressor of FOXQ1 expression. ChIP-qPCR as well as complementary gain and loss-of-function assays in model cell lines indicated that p53 has multiple binding sites close to the transcription start site of the FOXQ1 promoter, and that it suppresses FOXQ1 expression in various cell types. Consistently, pharmacological activation of p53 using nutlin-3 or doxorubicin reduced FOXQ1 mRNA and protein levels in colorectal cancer cell lines harboring wild type p53. In conclusion, these results suggest that mutational loss-of-function of p53, a hallmark feature of many types of cancer, de-represses FOXQ1, which accelerates tumour progression.
2024-05-13 | PXD047868 | Pride
Project description:Tumor suppressors are mostly defined by inactivating somatic mutations in tumors, yet little is known about their epigenetic features in normal cells. Here, through integrative analysis of 1,134 genome-wide epigenetic profiles and mutations from >8,200 tumor-normal pairs, we discovered broad H3K4me3 (wider than 4 kb) as the first epigenetic signature for tumor suppressors in normal cells. Broad H3K4me3 is associated with increased transcription elongation and enhancer activity together leading to exceptionally high gene expression, and is distinct from other broad epigenetic features, such as super enhancers. Broad H3K4me3 conserved across normal cells represents core tumor suppressors, such as P53 and PTEN, whereas cell-type-specific broad H3K4me3 may indicate cell-identity genes and cell-type-specific tumor suppressors. Furthermore, widespread shortening of broad H3K4me3 in cancers is strongly associated with repression of tumor suppressors. Together, the broad H3K4me3 epigenetic signature we reported here may provide a new direction for the discovery and characterization of novel tumor suppressors.
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Project description:Purpose : In this study we observed that inactivation of the genes encoding for the chromatin associated proteins HP1 lead to a highly increased predisposition of mice to develop tumours within liver. The purpose of this analysis was to identify and characterize genes whose expression was altered early on within livers of the HP1 mutant mice that could explain the tumorigenesis phenotype observed in very old animals. Results : this analysis revealed that only few genes (129 for HP1αKO, 84 for HP1αβliverKO and 87 for HP1αγliverKO) displayed differential expression between control and mutant animals [with a threshold of 1.5 fold difference and an adjusted pvalue≤0.05]. Besides several genes putatively involved in tumorigenesis, we found a significant enrichment in genes encoding several members of the family of transcriptional repressors KRAB-ZFP and presented data arguing that this increased expression resulted from their own loss of repressive activity because of the loss of interaction between their corepressor TRIM28 and HP1. Conclusions: our study represents the first demonstration that HP1 behave as tumour suppressors within liver and provide a comprehensive analysis of the underlying molecular mechanisms suggesting that HP1 main function within liver is to allow an appropriately regulated activity of the KRAB-ZFP/TRIM28/HP1 axis essential for liver homeostasis.
2019-01-02 | GSE84734 | GEO