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Gene expression analysis of JVM-2 and Granta-519 after CCDC50 gene modulation

ABSTRACT: Microarray-based gene expression analysis identified genes differentially expressed in JVM-2 and Granta-519 after CCDC50 gene modulation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE16435 | GEO | 2010/06/03

SECONDARY ACCESSION(S): PRJNA122879

REPOSITORIES: GEO

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Homo sapiens

Project description:Gene expression analysis of JVM-2 and Granta-519 after CCDC50 gene modulation

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CCDC50 promotes tumor growth through regulation of lysosome homeostasis

Project description:Cutaneous melanoma is characterized by lineage-specific lysosome-associated vesicular trafficking. Specifically, we report a melanoma enrichened lysophagy receptor, CCDC50, controlling lysosomal homeostasis and autolysosomal activity. We reveal that targeting CCDC50 in melanoma may be a promising therapeutic strategy, as nearly 70% of human melanomas highly express CCDC50. Moreover, targeting CCDC50 together with BRAFV600E inhibition induces synergistic function in regression of melanoma tumors, representing an alternative strategy for melanoma therapy. We performed transcriptome profiling (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT–PCR) in shCtrl and shCCDC50 cells to evaluate the melanoma growth and metastasis controlled by CCDC50. The deep sequencing results showed that CCDC50 defciency caused increased lysosome and vacuolar memebrane and blocked autophagy flux.

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The genes regulated by SOX11 in mantle cell lymphoma

Project description:The genes regulated by SOX11 in MCL was investigated in MCL cell line Granta 519 by siRNA knock down system. Cells were transfected using the LONZA electroporation system. Results represent cells harvested after 20 hours. Details of the experiment is published in PMID 21124928. Gene expression profiles (Human Gene 1.0 ST) of mantle cell lymphoma (MCL) cell line Granta 519 treated with SOX11 siRNA. Data analyses were performed using the Affymetrix Expression Console (v. 1.1)

2010-11-29 | E-GEOD-25621 | biostudies-arrayexpress

CCDC50 promotes glioblastoma progression through regulating EGFR cell-surface recycle

Project description:Glioblastomas (GBM) are a kind of malignant tumor with high mortality. However, the mechanism of tumor progression remains poorly understood. Specifically, we find that the expression of autolysosome-associated protein CCDC50, is positively correlated with tumor malignancy, and poor survival of GBM patients. CCDC50 functions as a specific cargo adaptor to assist EGFR recycling back to the plasma membrane, leading to prolonged activation of the downstream signaling pathways. We reveal that targeting CCDC50 in GBM may be a promising therapeutic strategy, as CCDC50 deficiency significantly inhibited the proliferation and migration of tumor cells in vitro and in vivo. Moreover, targeting CCDC50 together with alkylating agent temozolomide (TMZ) induces synergistic function in regression of GBM tumors, representing an alternative strategy for malignant tumor therapy. We performed transcriptome profiling (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT–PCR) in shCtrl and shCCDC50 cells to evaluate the GBM tumor growth and metastasis controlled by CCDC50.

2023-08-21 | GSE240516 | GEO

Transcription profiling by array of human B cell lymphoma cell lines in response to rituximab treatment

Project description:HF-1, Granta-519, SUDHL4,Oci-Ly10 and Oci-Ly3 cell lines, representing different B cell lymphoma subtypes, were induced with rituximab (R) for three hours and analyzed for differentially expressed genes compared to untreated control.

2010-06-22 | E-MEXP-2317 | biostudies-arrayexpress

Cyclical quasispecies re-equilibration of dual-tropic measles virus

Project description:RNAseq analysis of purified measles virus ribonucleocapsids after adaptation to lymphocytes (Granta-519) or epithelial cells (H358)

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Next Generation Sequencing of Mantle cell lymphoma Granta-519 Transcriptomes

Project description:Purpose: The goal of this study is to get a deeper insight of whole transcriptome changes and of signaling pathways involved in eliciting the DPN-mediated effects on Granta-519 tumor progression in vivo. Methods: Mantle cell lymphoma cell line Granta-519 cells were grafted to male NSG mice, followed by treated with ESR2 selective agonist DPN or vehicle. When tumor size reached around 1300 mm3, RNA was extracted with RNeasy Plus Mini Kit (Qiagen) for sequencing. Results: ESR2 selective agonist DPN could inhibit cell adhesion, EMT and angiogenesis in vivo which likely involves regulation of VEGFA, FOS, FOSB, CXCR4, MALAT1 and NEAT1. Conclusions: Our study represents the detailed analysis of Granta-519 transcriptomes in vivo experiment after DPN treatment, with biologic replicates, generated by RNA-seq technology.

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CCDC50 suppresses NLRP3 inflammasome activity by mediating the autophagic degradation of NLRP3

Project description:Autophagy and autophagy-associated genes are closely linked to NLRP3-mediated inflammation in inflammatory disorders. This study determined that the functions of CCDC50, the novel autophagy receptor, in regulating the activation of NLRP3 inflammasome and associated inflammatory diseases. We performed transcriptome profiling (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT–PCR) in shCtrl and shCCDC50 cells to evaluate the inflammatory responses regulated by CCDC50. The deep sequencing results showed that CCDC50 defciency caused increased NLRP3 inflammasome assembly and upregulation of associated disease pathways.

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Gene expression analysis of HEK293T cells after CHMP5 gene modulation

Project description:Microarray-based gene expression analysis identified genes differentially expressed in HEK293T cells after CHMP5 gene modulation.

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Gene knock down studies revealed CCDC50 as candidate gene in mantle cell lymphoma and chronic lymphocytic leukemia

Project description:The two B-cell non-Hodgkin lymphoma (NHL) entities chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) show recurrent chromosomal gains of 3q25 q29, 12q13 q14 and 18q21-q22. The pathomechanisms affected by these aberrations are not understood. The aim of this study was to identify genes, located within these gained regions, which control cell death and cell survival of MCL and CLL cancer cells. Blood samples from 24 CLL and 6 MCL patients as well as 6 cell lines representing both malignancies were analyzed by gene expression profiling. By comparison of genomic DNA and gene expression, 72 candidate genes were identified. We performed a limited RNAi screen with these candidates in order to identify genes affecting cell survival. CCDC50, SERPINI2 and SMARCC2 mediated a reduction of cell viability in primary CLL cells as well as in cell lines. Gene knock down and a NFkB reporter gene assay revealed that CCDC50 is required for survival in MCL and CLL cells and controls NFkB signaling. This SuperSeries is composed of the SubSeries listed below.

2010-06-03 | GSE16413 | GEO

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