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Identification of genes regulated by MYCN in retinoblastoma (RB) cell line, Y79.

ABSTRACT: Identification of genes regulated by MYCN in retinoblastoma (RB) cell line, Y79.

PROVIDER: PRJNA714536 | ENA |

REPOSITORIES: ENA

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Identification of genes regulated by MYCN in retinoblastoma (RB) cell line, Y79.

Project description:To determine the downstream genes regulated by MYCN in RB, MYCN was silenced in Y79 cell line, which expressed hign levels of MYCN, using two lentiviral shRNA constructs targetting MYCN.

2021-10-14 | GSE168903 | GEO

Differential expression of miRNAs in Retinoblastoma cells (Y79) in response to anti-HMGA2 siRNA treatment

Project description:The main objective of the study is to identify the de-regulated miRNAs in association with HMGA2 (oncogene) in the Retinoblastoma tumorus. The present experiment was carried out using Y79 (Retinoblastoma cell line), as the invitro model of Retinoblastoma tumor. The HMGA2 transcripts were silenced using siRNA and the post-silenced RB cells (at the end of 48 hours) were subjected to miRNA profiling using agilent platform.The key miRNAs de-regulated in this experiment has been validated using qRT-PCR and further their role has been evaluated by addition of specific antagomirs in RB cell lines (Y79 and Weri Rb 1). Agilent one-color experiment,Organism: Homo sapiens ,Agilent Human miRNA 8x15k Arrays AMADID: 021827 [Agilent miRNA labeling reagent and Hybridization Kit Cat # 5190-0408] RB cells (Y79) treated with anti-HMGA2 siRNA or with control

2013-10-26 | E-GEOD-51696 | biostudies-arrayexpress

Differential expression of miRNAs in Retinoblastoma cells (Y79) in response to anti-HMGA2 siRNA treatment

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Effect of CDK7 inhibitor on MYCN-amplified retinoblastoma

Project description:Retinoblastoma (RB) is a common malignancy that primarily affects pediatric populations. Although a well-known cause of RB is RB1 mutation, MYCN amplification can also lead to the disease, which is a poor prognosis factor. Studies conducted in various tumor types have shown that MYCN inhibition is an effective approach to impede tumor growth. Various indirect approaches have been developed to overcome the difficulty of directly targeting MYCN, such as modulating the super enhancer (SE) upstream of MYCN. The drug used in this study to treat MYCN-amplified RB was THZ1, a CDK7 inhibitor that can effectively suppress transcription by interfering with the activity of SEs. The study findings confirmed the anticancer activity of THZ1 against RB in both in vitro and in vivo experiments. Therapy with THZ1 was found to affect numerous genes in RB according to the RNA-seq analysis. Moreover, the gene expression changes induced by THZ1 treatment were enriched in ribosome, endocytosis, cell cycle, apoptosis, etc. Furthermore, the combined analysis of ChIP-Seq and RNA-seq data suggested a potential role of SEs in regulating the expression of critical transcription factors, such as MYCN, OTX2, and SOX4. Moreover, ChIP‒qPCR experiments were conducted to confirm the interaction between MYCN and SEs. In conclusion, THZ1 caused substantial changes in gene transcription in RB, resulting in inhibited cell proliferation, interference with the cell cycle, and increased apoptosis. The efficacy of THZ1 is positively correlated with the degree of MYCN amplification and is likely exerted by interfering with MYCN upstream SEs.

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Y79 retinoblastoma cell line secretome

Project description:The proteins secreted from Y79 retinoblastoma cell line were analyzed by the GeLC-MS/MS approach.

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Y79 retinoblastoma cell line surface proteome

Project description:The proteins on the surface of Y79 retinoblastoma cell line were analyzed by cell surface biotinylation and streptavidin affinity purification.

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Comparison of Pax6 alpha enhancer Cre-Rblox/lox retinas to Pax6 alpha enhancer Cre-Rblox/lox TET-MYCN retinas at PND12

Project description:The most frequent focal alterations in human retinoblastoma are RB mutation and MYCN amplification. Whether MYCN overexpression drives retinoblastoma has not been assessed in model systems. Here, we show that Rb inactivation collaborates strongly with MYCN overexpression to lead to retinoblastoma in mice. MYCN overexpression in the context of Rb inactivation increased the expression of MYC, E2F and ribosome related gene sets, promoted excessive proliferation and led to retinoblastoma with anaplastic changes. Part of our study compares expression profiles in Rbnull vs Rbnull/MYCN overexpressing retinas collected at 12 days after birth.

2017-01-01 | GSE90961 | GEO

Gene expression profiling of retinoblastoma Y79 cell line post EpCAM silencing using siRNA

Project description:Retinoblastoma Y79 cell line was treated with specific siRNA to silence EpCAM gene expression in vitro and RNA was isolated for microarray experiment to study the changes in the whole gene expression profiling in the Y79 cell line. The study identified 465 up-regulated genes (>1.0 fold) and 205 down-regulated genes (<0.5 fold) in response to knockdown of Ep-CAM.

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Gene expression profiling of retinoblastoma Y79 cell line treated with scopoletin from Morinda citrifolia in vitro

Project description:Retinoblastoma Y79 cell line was treated with scopoletin in vitro and RNA was isolated for microarray experiment to study the changes in the whole gene expression profiling in the Y79 cell line. The study identified 1675 up-regulated genes (>1.0 fold) and 1879 down-regulated genes (<-1 fold) in response to scopoletin treatment

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Gene expression profiling of retinoblastoma Y79 cell line grown with scaffold compared to cells without scaffold

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