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A Genomic Map of p53 Binding Sites Identifies Novel p53 Targets Involved in an Apoptotic Network

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Abstract

The transcriptional activity of the p53 protein is central to its role in tumor suppression. Identification of the complete repertoire of p53-regulated genes is critical for dissecting the complexity of the p53 network. Although several different approaches have been used to characterize the p53 genetic program, we still lack a comprehensive molecular understanding of how p53 prevents cancer. Using a computational approach, we generated a genome-wide map of p53 binding sites (p53BS) to identify novel p53 target genes. We show that the presence of nearby p53BS can identify new proapoptotic members of the Bcl2 family. We show that p53 binds to p53BS identified in the BCL-G/BCL2L14 gene and that induction of this gene contributes to p53-mediated apoptosis. We found that p53 activates the COL18A1 gene encoding the precursor for the antiangiogenic factor endostatin. We also show that p53 up-regulates the MAP4K4 gene and activates the c-Jun NH2-terminal kinase (JNK) pathway to drive apoptosis. Thus, unbiased mapping of the genomic landscape of p53BS provides a systematic and complementary approach to identify novel factors and connections in the p53 genetic network. Our study illustrates how systematic genomic approaches can identify binding sites that are functionally relevant for a p53 transcriptional program. The genetic link among p53, antiangiogenic factors, and the JNK signaling pathway adds new dimensions to understanding p53 function in highly connected genetic networks.
LAPP-EXP 2002-11
December 2002
Measurement of charged triple gauge-boson
couplings (cTGC) at LEP2
S. Jézéquel
LAPP-IN2P3-CNRS
BP. 110 F-74941 Annecy-le-Vieux Cedex
Talk given at the 31th International Conference on High Energy Physics
Amsterdam (Netherlands), July 24-31, 2002
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... Large-scale sequencing efforts have consistently demonstrated that a vast majority of 15 osteosarcomas have loss-of-function mutations in the TP53 gene 3,4 . In addition to inactivating single nucleotide variants, at least 50% of pediatric osteosarcomas show structural variations in this gene 3,4,6 . ...
... The majority of samples analyzed in this cohort were chemotherapy-treated resection specimens. We found structural 15 rearrangement of TP53 in 13/36 cases ( Figure 1A, Supplementary Tables 1 and 2). We then analyzed an independent validation cohort of treatment-naïve diagnostic biopsies from conventional osteosarcomas, again including both pediatric (age <18 y, n=20) and adult (age range 18-59 y, n=16) patients. ...
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Preprint
The malignant bone tumor osteosarcoma harbors an extreme number of chromosome rearrangements. How such massive DNA errors confer a competitive advantage to a cancer cell has remained an enigma. Osteosarcoma typically presents mutations disrupting normal TP53 gene function, frequently in the form of structural rearrangements that separate the promoter region from the coding parts of the gene. To unravel the consequences of a TP53 promoter relocated in this manner, we performed in-depth genetic analyses of osteosarcoma biopsies (n=148) and cell models. We show that TP53 structural variations not only facilitate further chromosomal alterations, but also allow the constitutively active TP53 promoter to upregulate putative oncogenes erroneously placed under its control. Paradoxically, many of the induced genes are part of the TP53-associated transcriptome, suggesting a need to counterbalance the initial loss of function. Our findings demonstrate how the promoter region of a tumor suppressor gene can functionally turn into an oncogenic driver.
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Article
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... Additionally, immune-related pathways, especially Table 2. Baseline characteristics of the patients in different risk groups. 36,37 , the relationships among these genes and their correlation with BRCA remain largely unknown. To our surprise, more than half of the ferroptosis-related genes (32/63) were differentially expressed between 140 adjacent normal breast tissues and 1139 luminal subtype BRCA tissues, and in the univariate Cox regression analysis, 12 of them were associated with OS. ...
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Ferroptosis is a new form of regulated cell death (RCD), and its emergence has provided a new approach to the progression and drug resistance of breast cancer (BRCA). However, there is still a great gap in the study of ferroptosis-related genes in BRCA, especially luminal-type BRCA patients. We downloaded the mRNA expression profiles and corresponding clinical data of BRCA patients from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and The Cancer Genome Atlas (TCGA) databases. Then, we built a prognostic multigene signature with ferroptosis-related differentially expressed genes (DEGs) in the METABRIC cohort and validated it in the TCGA cohort. The predictive value of this signature was investigated in terms of the immune microenvironment and the probability of a response to immunotherapy and chemotherapy. The patients were divided into a high-risk group and a low-risk group according to the ferroptosis-associated gene signature, and the high-risk group had a worse overall survival (OS). The risk score based on the 10 ferroptosis-related gene-based signature was determined to be an independent prognostic predictor in both the METABRIC and TCGA cohorts (HR, 1.41, 95% CI, 1.14–1.76, P = 0.002; HR, 2.19, 95% CI, 1.13–4.26, P = 0.02). Gene set enrichment analysis indicated that the term “cytokine-cytokine receptor interaction” was enriched in the high-risk score subgroup. Moreover, the immune infiltration scores of most immune cells were significantly different between the two groups, the low-risk group was much more sensitive to immunotherapy, and six drugs might have potential therapeutic implications in the high-risk group. Finally, a nomogram incorporating a classifier based on the 10 ferroptosis-related genes, tumor stage, age and histologic grade was established. This nomogram showed favorable discriminative ability and could help guide clinical decision-making for luminal-type breast carcinoma.
... For example, BCL2 L14 (BCL2-like 14) is a well-reported gene associated with apoptosis. Among its related pathways are TP53, which regulates the transcription of cell death genes (39). GBP2 is also associated with apoptosis, and the upregulation of GBP2 is associated with neuronal apoptosis in the rat brain cortex following traumatic brain injury (40). ...
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Breast cancer patients show significant heterogeneity in overall survival. Current assessment models are insufficient to accurately predict patient prognosis, and models for predicting treatment response are lacking. We evaluated the relationship between various immune cells and breast cancer and confirmed the association between immune infiltration and breast cancer progression. Different bioinformatics and statistical approaches were combined to construct a robust immune infiltration-related gene signature for predicting patient prognosis and responses to immunotherapy and chemotherapy. Our research found that a higher immune infiltration-related risk score (IRS) indicates that the patient has a worse prognosis and is not very sensitive to immunotherapy. In addition, a new nomogram was constructed based on the gene signature and clinicopathological features to improve the risk stratification and quantify the risk assessment of individual patients. Our study might contribute to the optimization of the risk stratification for survival and the personalized management of breast cancer.
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... MAP4K4 is one of the genes involved in the apoptosis signaling pathway, and its over-expression is a prognostic factor for lung adenocarcinoma [41]. MAP4K4 expression is up-regulated upon binding to p53, resulting in the activation of the apoptotic JNK signaling pathway [42]. In the NSCLC dataset, when the expression of MAP4K4-TP53 interaction ("EXP_MAP4K4_X_EXP_TP53") increases, the average IC 50 is slightly decreased (Pearson correlation = − 0.10). ...
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