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Displaying 20 of 639 results for "MDM2"
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  1. Array-based gene expression in neuroblastic tumors OmicsDI

    ID: E-GEOD-18139

    Date Released: 05-02-2014

    Description: ubsequent overexpression of MYCN, MEIS1, CDK4 and MDM2 oncogenes, the aCGH analysis revealed numerous other genetic alterations, including microamplifications at 2p and 12q24.11. Most interestingly, we identified and investigated the clinical relevance of a previously poorly characterized amplicon at 12q24.31. FISH analysis showed low-level gain of 12q24.31 in 14 of 33 (42%) neuroblastomas. Patients with the low-level gain had an intermediate prognosis in comparison to patients with MYCN amplification (poor prognosis) and to those with no MYCN amplification or 12q24.31 gain (good prognosis) (P = 0.001). Using the in silico data mining approach, we identified elevated expression of five genes located at the 12q24.31 amplicon in neuroblastoma (DIABLO, ZCCHC8, RSRC2, KNTC1 and MPHOSPH9). Among these, DIABLO showed the strongest activation suggesting a putative role in neuroblastoma progression. Conclusions: The presented systematic and rapid framework, which integrates aCGH, gene expression and tissue data to obtain novel targets and biomarkers for cancer, identified a low-level gain of the 12q24.31 as a potential new biomarker for neuroblastoma progression. Furthermore, results of in silico data mining suggest a new neuroblastoma target gene, DIABLO, within this region, whose functional and therapeutic role remains to be elucidated in follow-up studies. High-resolution aCGH was utilized to identify novel genetic alterations in two neuroblastoma cell lines, NGP and IMR-32. Through the integration of g...

  2. Subtype classification, grading, and outcome prediction of urothelial carcinomas by combined mRNA profiling and aCGH OmicsDI

    ID: E-GEOD-19915

    Date Released: 05-02-2014

    Description: rs, and that this trait was not dependent on TP53/MDM2 alterations. By combining molecular and pathological data it was possible to distinguish two molecular subtypes of Ta and T1 tumors, respectively. In addition, we define gene signatures validated in two independent data sets that classify urothelial carcinoma into low (G1/G2) and high grade (G3) tumors as well as non-muscle and muscle-invasive tumors with high precisions and sensitivities, suggesting molecular grading as a relevant complement to standard pathological grading. We also present a gene expression signature with independent prognostic impact on metastasis and disease specific survival. We conclude that the combination of molecular and histopathological classification systems may provide a strong improvement for bladder cancer classification and produce new insights into the development of this tumor type. 144 bladder cancer tumor samples and 12 normal samples were analyzed on 2-color cDNA or oligo microarrays using the Stratagene Universal Human Reference RNA as the common reference sample. 24 samples are hybridized to both the cDNA and oligo platform and these were used for merging of dat...

  3. The gene expression response of spontaneous canine sarcomas to thermoradiotherapy – response heterogeneity and combination therapeutics OmicsDI

    ID: E-GEOD-23380

    Date Released: 08-16-2011

    Description: induction of well known cycle regulators p21 and mdm2 and reduced cellular proliferation in most treated tumors. We also identified two tumor subtypes with dramatic differences in the gene expression response and treatment response at the end of therapy. In the subtype with strong expression and increase in DWI, the mRNA level of hsp70, POT1 and centrosomal proteins was significantly higher. In the other subtype with modest response to hyperthermia, levels of CD31, vWF and transferrin was noted to be significantly higher. It is also possible to build a predictive model based on the pre-treatment gene expression to predict the likely treatment response of the tumors. The differential expression between the two tumor subtypes was used to interrogate connectivity map and identify linkages to an HDAC inhibitor and geldanamycin, an HSP90 inhibitor. Both HDAC inhibitors and hsp90 inhibitor geldanamycin are shown to synergerize with thermoradiotherapy in reducing ce...

  4. Expression data of Ell3 overexpressing MCF7 cell line OmicsDI

    ID: E-GEOD-63612

    Date Released: 11-27-2015

    Description: oneoxidoreductase 1 (NQO1), which is linked to an ubiquitin-independent degradation pathway, as well as by suppressing a MDM2 mediated ubiquitin-dependent degradation pathway. Furthermore, Ell3 enhanced interleukin-20 (IL-20) expression leading to the activation of the ERK1/2 signaling pathway. By analyzing the suppressive effects of IL-20 and ERK signaling in the Ell3 expressing MCF7 cells, we confirmed that the IL-20 mediated ERK1/2 signaling pathway is the main cause of p53 stabilization after CDDP exposure in MCF7 cells. Ell3-overexpressing breast cancer cell lines were established using the chromosomal integration of an Ell3 expression plasmid, which was constructed by cloning PCR-amplified Ell3 cDNA into pcDNA3.1 vectors (Invitrogen, Carlsbad, CA; https://www.lifetechnologies.com). Three independent Ell3 overexpressing cell lines were generated. The gene expression profiles of wild type MCF7 and Ell3 overexpressing cell line were compared using Affymetrix PrimeView arrays....

  5. aCGH of neuroblastic tumors OmicsDI

    ID: E-GEOD-18143

    Date Released: 05-02-2014

    Description: ubsequent overexpression of MYCN, MEIS1, CDK4 and MDM2 oncogenes, the aCGH analysis revealed numerous other genetic alterations, including microamplifications at 2p and 12q24.11. Most interestingly, we identified and investigated the clinical relevance of a previously poorly characterized amplicon at 12q24.31. FISH analysis showed low-level gain of 12q24.31 in 14 of 33 (42%) neuroblastomas. Patients with the low-level gain had an intermediate prognosis in comparison to patients with MYCN amplification (poor prognosis) and to those with no MYCN amplification or 12q24.31 gain (good prognosis) (P = 0.001). Using the in silico data mining approach, we identified elevated expression of five genes located at the 12q24.31 amplicon in neuroblastoma (DIABLO, ZCCHC8, RSRC2, KNTC1 and MPHOSPH9). Among these, DIABLO showed the strongest activation suggesting a putative role in neuroblastoma progression. Conclusions: The presented systematic and rapid framework, which integrates aCGH, gene expression and tissue data to obtain novel targets and biomarkers for cancer, identified a low-level gain of the 12q24.31 as a potential new biomarker for neuroblastoma progression. Furthermore, results of in silico data mining suggest a new neuroblastoma target gene, DIABLO, within this region, whose functional and therapeutic role remains to be elucidated in follow-up studies. High-resolution aCGH was utilized to identify novel genetic alterations in two neuroblastoma cell lines, NGP and IMR-32. Through the integration of g...

  6. Subtype classification, grading, and outcome prediction of urothelial carcinomas by combined mRNA profiling and aCGH ArrayExpress

    ID: E-GEOD-19915

    Description: rs, and that this trait was not dependent on TP53/MDM2 alterations. By combining molecular and pathological data it was possible to distinguish two molecular subtypes of Ta and T1 tumors, respectively. In addition, we define gene signatures validated in two independent data sets that classify urothelial carcinoma into low (G1/G2) and high grade (G3) tumors as well as non-muscle and muscle-invasive tumors with high precisions and sensitivities, suggesting molecular grading as a relevant complement to standard pathological grading. We also present a gene expression signature with independent prognostic impact on metastasis and disease specific survival. We conclude that the combination of molecular and histopathological classification systems may provide a strong improvement for bladder cancer classification and produce new insights into the development of this tumor type. 144 bladder cancer tumor samples and 12 normal samples were analyzed on 2-color cDNA or oligo microarrays using the Stratagene Universal Human Reference RNA as the common reference sample. 24 samples are hybridized to both the cDNA and oligo platform and these were used for merging of dat...

  7. Rif1 Prevents Resection of DNA Breaks and Promotes Immunoglobulin Class Switching BioProject

    ID: PRJNA181019

    Keywords: Epigenomics

    Access Type: download

    dataset.description: ion and chromosome rearrangements. The DNA repair protein p53 binding protein 1 (53BP1) protects the genome by limiting nucleolytic processing of DSBs by a mechanism that requires its phosphorylation, but whether it does so directly is not known. Here we identify Rapl-interac...
  8. DNA methylation profiling identifies PTRF/Cavin-1 as a novel tumor suppressor in Ewing sarcoma when co-expressed with Caveolin-1 BioProject

    ID: PRJNA349992

    Keywords: Epigenomics

    Access Type: download

    dataset.description: -1 in Ewing sarcoma cells revealed a role of this protein as a tumor suppressor. Restoration of caveolae in the membrane of Ewing sarcoma cells, by exogenously reintroducing PTRF, disrupts the MDM2/p53 complex, which consequently results in the activation of p53 and the induction of apoptosis. Overall design: 15 primary tumors (Ewing Sarcoma) and 7 Ewing's sarcoma cell lines were interrogated for methylation levels using the Infinium HumanMethylation450k microarray....
  9. Characterization of CT26 colon carcinoma : Extensive characterization of the CT26 colorectal carcinoma genome, transcriptome and immunome BioProject

    ID: PRJEB5321

    Keywords: Other

    Access Type: download

    dataset.description: 8a (MS4A8B) and Epcam are not. Myc, Trp53 (tp53), Mdm2, Hif1a, and Nras are highly expressed while Egfr and Flt1 are not. MHC class I but not MHC class II is expressed. Several known cancer-testis antigens are expressed, including Atad2, Cep55, and Pbk. The highest expressed gene is a mutated form of the mouse tumor antigen gp70. Of the 1,688 non-synonymous point variations, 154 are both in expressed genes and in peptides predicted to bind MHC and thus potential targets for immunotherapy development. Based on its molecular signature, we predicted that CT26 is refractory to anti-EGFR mAbs and sensitive to MEK and MET inhibitors, as have been previously reported. CONCLUSIONS: CT26 cells share molecular features with aggress...
  10. Gene Expression Analysis of ARC (NSC 188491) Treated MCF7 cells BioProject

    ID: PRJNA110155

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: ents showed that ARC also repressed expression of hdm2 and survivin, leading to its classification as a global inhibitor of transcription 1. The following Hu U133 plus 2.0 arrays represent single time point (24 hour) gene expression analysis of transcripts altered by ARC treatment. Arrays for the other compounds (sangivamycin and doxorubicin) are included as comparators. Overall design: MCF7 cells treated with ARC, Sangivamycin or Doxorubicin for 24 hours....
  11. PSD95_MDM2 KOs_Phospho and Ubi YPED

    Description: clear. PSD-95 is a major postsynaptic scaffolding protein of glutamatergic synapses that regulates synaptic strength and plasticity. PSD-95 is ubiquitinated by the ubiquitin E3 ligase Mdm2, and rapid and transient PSD-95 ubiquitination has been implicated in NMDA receptor-induced AMPA receptor endocytosis. Here we demonstrate that genetic or pharmacological reduction of Cdk5 activity increases t...

  12. Role of SMAR1 in global gene regulation through interaction with tumor suppressor p53 BioProject

    ID: PRJNA287548

    Keywords: Epigenomics

    Access Type: download

    dataset.description: Scaffold Matrix Attachment Region binding protein 1, SMAR1 has vital role to play as a general repressor of transcription. SMAR1 is known to retard cell cycle progression an...
  13. The gene expression response of spontaneous canine sarcomas to thermoradiotherapy – response heterogeneity and combination therapeutics BioProject

    ID: PRJNA131265

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: induction of well known cycle regulators p21 and mdm2 and reduced cellular proliferation in most treated tumors. We also identified two tumor subtypes with dramatic differences in the gene expression response and treatment response at the end of therapy. In the subtype with strong expression and increase in DWI, the mRNA level of hsp70, POT1 and centrosomal proteins was significantly higher. In the other subtype with modest response to hyperthermia, levels of CD31, vWF and transferrin was noted to be significantly higher. It is also possible to build a predictive model based on the pre-treatment gene expression to predict the likely treatment response of the tumors. The differential expression between the two tumor subtypes was used to interrogate connectivity map and identify linkages to an HDAC inhibitor and geldanamycin, an HSP90 inhibitor. Both HDAC inhibitors and hsp90 inhibitor geldanamycin are shown to synergerize with thermoradiotherapy in reducing ce...
  14. Subtype classification, grading, and outcome prediction of urothelial carcinomas by combined mRNA profiling and aCGH BioProject

    ID: PRJNA122099

    Keywords: Other

    Access Type: download

    dataset.description: rs, and that this trait was not dependent on TP53/MDM2 alterations. By combining molecular and pathological data it was possible to distinguish two molecular subtypes of Ta and T1 tumors, respectively. In addition, we define gene signatures validated in two independent data sets that classify urothelial carcinoma into low (G1/G2) and high grade (G3) tumors as well as non-muscle and muscle-invasive tumors with high precisions and sensitivities, suggesting molecular grading as a relevant complement to standard pathological grading. We also present a gene expression signature with independent prognostic impact on metastasis and disease specific survival. We conclude that the combination of molecular and histopathological classification systems may provide a strong improvement for bladder cancer classification and produce new insights into the development of this tumor type. Overall design: 144 bladder cancer tumor samples and 12 normal samples were analyzed on 2-color cDNA or oligo microarrays using the Stratagene Universal Human Reference RNA as the common reference sample. 24 samples are hybridized to both the cDNA and oligo platform and these were used f...
  15. Gene expression changes induced by the human aristolochic acid I in renal and hepatic tissue of mice BioProject

    ID: PRJNA119637

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: R) and was consistent with the induction of Nfkb1 protein. Myc oncogene, frequently over-expressed in urothelial tumours, was up-regulated by AAI on the microarrays and confirmed by qRT-PCR and protein induction. Collectively we found that microarray gene expression analysis is a useful tool to define tissue-specific responses in AAI-induced toxicity. Several genes identified such as TP53, Rb1, Mdm2, Cdkn2a and Myc are frequently affected in human urothelial cancer, and may be valuable prognostic markers in future clinical studies. Keywords: Carcinogen treatment Overall design: Two-color Agilent array. A reference design was chosen that all samples were hybridised to universal mouse reference RNA (UMRR). 12-condition experiment (2 mouse organs: kidney and liver; 2 treatments: AAI and water; 3 time points: 3, 12 and 21 days). Three biological replicates for each condition. One replicate per array....
  16. Adrenocortical Carcinoma Gene Expression Profiling [Agilent] BioProject

    ID: PRJNA124015

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: esent in low grade tumors. Additionally, p53 and MDM2 were consistently identified as drivers in leading edge analyses of the tumors, implicating the p53 pathway in ACC pathogenesis. Finally, over-expression of PTTG1, which encodes securin, and is involved in sister chromatid adhesion as well as negative regulation of p53, was associated with poor prognosis in our samples. Taken together, these data point toward a tumor type driven in part by dysregulated IGF2 signaling in the context of a lack of a functional p53 response, with potential vulnerabilities in the G2/M transition that may make viable therapeutic targets. Overall design: RNA from fifteen adrenocortical carcinomas and a pool of four normal adrenal glands was extracted, labeled, and hybridized to Agilent Human 1A Oligo Microarray (v2) chips. The resulting data was first background subtracted. Each array then had the median intenisty subtracted from each channel, and finally both M and A values were quantile normalized across arrays. All calculations were done in R using the Bioconductor packages of marray and limma....
  17. Expression data of Ell3 overexpressing MCF7 cell line BioProject

    ID: PRJNA268445

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: oneoxidoreductase 1 (NQO1), which is linked to an ubiquitin-independent degradation pathway, as well as by suppressing a MDM2 mediated ubiquitin-dependent degradation pathway. Furthermore, Ell3 enhanced interleukin-20 (IL-20) expression leading to the activation of the ERK1/2 signaling pathway. By analyzing the suppressive effects of IL-20 and ERK signaling in the Ell3 expressing MCF7 cells, we confirmed that the IL-20 mediated ERK1/2 signaling pathway is the main cause of p53 stabilization after CDDP exposure in MCF7 cells. Overall design: Ell3-overexpressing breast cancer cell lines were established using the chromosomal integration of an Ell3 expression plasmid, which was constructed by cloning PCR-amplified Ell3 cDNA into pcDNA3.1 vectors (Invitrogen, Carlsbad, CA; https://www.lifetechnologies.com). Three independent Ell3 overexpressing cell lines were generated. The gene expression profiles of wild type MCF7 and Ell3 overexpressing cell line were compared using Affymetrix PrimeView arrays....
  18. Wild Type Tumor Repressor Protein 53 (TRP53) Promotes Ovarian Cancer Cell survival BioProject

    ID: PRJNA150207

    Keywords: Transcriptome or Gene expression

    Access Type: download

  19. Molecular effects of 1-naphthyl-methylcarbamate and solar radiation exposures on human melanocytes BioProject

    ID: PRJNA316223

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: in a synergistic manner, for CDKN1A, BRCA1/2 and MDM2 genes. Likewise, flow cytometry assays demonstrated S-phase cell cycle arrest, reduced apoptosis levels and faster induction of cyclobutane pyrimidine dimers (CPD) lesions in carbaryl treated groups. Our data suggests that carbaryl is genotoxic to human melanocytes, especially when associated with solar radiation. Overall design: Twenty-four hours after plating, cells were at 80% confluency and were subjected to the following experimental treatment groups: Group 1: No treatment; Group 2: Irradiation and no treatment; Group 3: Carbaryl treatment; Group 4: Irradiation and carbaryl treatment; Group 5: Vehicle treatment; Group 6: Irradiation and vehicle treatment. Treatment regimen consisted of melanocyte incubation with carbaryl 100 µM (Sigma-Aldrich, St Louis, USA) for 6 hours after single dose exposure to 375mJ/cm2 of solar radiation using a solar simulator (SS2.5kW, Sciencetech Inc., Ontario, Canada) with a global air mass filter (A.M 1.5G, Sciencetech Inc, Ontario, Canada). For the irradiation assays, culture medium was replaced by PBS buffer without Ca2+ or Mg2+ (PBS-A). All experiments were performed in triplicates....

Displaying 20 of 639 results for "MDM2"