Unknown,Transcriptomics,Genomics,Proteomics

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Inhibition of MYCN by a PNA anti-gene in alveolar rhabdomyosarcoma

ABSTRACT: The objective was to identify the molecular mechanisms responsible for in vitro and in vivo efficacy of an anti-MYCN peptide nucleic acid on a preclinical model of alveolar rhabdomyosarcoma. Cells treated with a anti-MYCN PNA exhibit growth arrest and apoptosis, and in vivo tumor growth is blocked. Keywords: oncogene inhibition RH30 alveolar rhabdomyosarcoma cell line was treated with a 10uM concentration of anti-MYCN PNA or a mutated PNA devoid of any activity. After 12 hours RNA was extracted from untreated and treated cells and gene expression was analyzed by Affymetrix Gene Chips.

ORGANISM(S): Homo sapiens

SUBMITTER: Andrea Pession

PROVIDER: E-GEOD-7959 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:MYCN is an oncogene amplified in approximately 20% of all neuroblastomas and 50% of high risk neuroblastoma. It is a transcription factor regulating the expression of genes involved in proliferation and apoptosis.We would like to identify genes potentially regulated by MYCN in a conditional MYCN expression system. The SHEP Tet21N system is a conditional, tetracycline-regulated MYCN expression system established in the MYCN non-amplified SHEP neuroblastoma cell line (Lutz et al., 1996). Expression of MYCN is switched off by the addition of tetracycline to the growth medium. Levels of MYCN protein and RNA in the absence of tetracycline are comparable with those present in MYCN amplified cell lines (Bell et al., 2006). By performing microarray analyses on the Tet21n cell lines in the presence and absence of MYCN we hope to identify genes whose expression had been altered by MYCN either upregulated or downregulated and may be potential MYCN targets. The altered expression of some of these genes will then be validated using quantitative RTPCR and a selection will be further investigated to determine if they are MYCN transcriptional targets and may be potential candidates for anti-MYCN therapies for neuroblastoma Specific objectives 1) To investigate genes which are altered by 2 fold or more in the presence of or absence of MYCN in Tet21N cells. Refs: Bell, E., Premkumar, R., Carr, J., Lu, X., Lovat, P.E., Kees, U.R., Lunec, J. & Tweddle, D.A. (2006). The role of MYCN in the failure of MYCN amplified neuroblastoma cell lines to G1 arrest after DNA damage. Cell Cycle, 5, 2639-47. Lutz, W., Stohr, M., Schurmann, J., Wenzel, A., Lohr, A. & Schwab, M. (1996). Conditional expression of N-myc in human neuroblastoma cells increases expression of alpha-prothymosin and ornithine decarboxylase and accelerates progression into S-phase early after mitogenic stimulation of quiescent cells. Oncogene, 13, 803-12.

Project description:Background: Alveolar rhabdomyosarcoma (ARMS) has a high propensity to metastasize, leading to its aggressiveness and a poor survival rate among those with the disease. More than 80% of aggressive ARMSs harbor a PAX3-FKHR fusion transcription factor, which regulates cell migration and promotes metastasis, most likely by regulating the fusion protein's transcriptional targets. Therefore, identifying druggable transcription targets of PAX3-FKHR that are also downstream effectors of PAX3-FKHR-mediated cell migration and metastasis may lead to novel therapeutic approaches for treating ARMS. Methods: To identify genes whose expression is directly affected by the level of PAX3-FKHR in an ARMS cellular-context, we first developed an ARMS cell line in which PAX3-FKHR is stably down-regulated, and showed that stably downregulating PAX3-FKHR in ARMS cells significantly decreased the cells' motility. We used microarrays analysis to identify genes whose expression level decreased when PAX3-FKHR was downregulated. We used mutational analysis, promoter reporter assays, and electrophoretic mobility shift assays to determine whether PAX3-FKHR binds directly and specifically to the promoter region of the target gene. We used siRNA and pharmacologic inhibitor to downregulate the target gene of PAX3-FKHR and investigated the effect of such downregulation on cell motility, Results: We found that When PAX3-FKHR was downregulated, the expression of carnitine palmitoyltransferase 1A (CPT1A) decreased. We showed that PAX3-FKHR binds directly and specifically to a paired-domain binding-site in the CPT1A promoter region, indicating that CPT1A is a novel direct transcriptional target of PAX3-FKHR. Furthermore, downregulating CPT1Adecreased cell motility in ARMS cells, indicating that CPT1A is a downstream effector of PAX3-FKHR-mediated cell migration and metastasis. Conclusions: Taken together, we have identified CPT1A as a novel direct transcriptional target of PAX3-FKHR and revealed the novel function of CPT1A in promoting cell motility. CPT1A may represent a novel therapeutic target for the treatment of ARMS. Identification of transcription targets of PAX3-FKHR in human alveolar rhabdomyosarcoma: By stably knocking down PAX3-FKHR in human alveolar rhabdomyosarcoma cell line Rh30 and comparing the gene expression profile of the knockdown clone (KD) to the parental Rh30, transcription targets of PAX3-FKHR have been identified. Gene expression in parental Rh30 cells was compared to that in either Rh30 cells stably expressing shRNA targeting PAX3-FKHR (KD) or control non-targeting shRNA (CON), in duplicate.

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Inhibition of MYCN by a PNA anti-gene in alveolar rhabdomyosarcoma

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