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Transcriptome profiling of drug resistant cell lines (NGP-127).

ABSTRACT: The aim of this research was to uncover transcriptome changes in NGP-127 cells during the acquisition of resistance to anticancer drugs Sorafenib, Sunitinib, Pazopanib, Everolimus, Temsirolimus.

ORGANISM(S): Homo sapiens

PROVIDER: GSE97750 | GEO | 2017/04/14

SECONDARY ACCESSION(S): PRJNA382813

REPOSITORIES: GEO

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Transcriptome profiling of drug resistant cell lines (SKOV3).

Project description:The aim of this research was to uncover transcriptome changes in SKOV3 cells during the acquisition of resistance to anticancer drugs Sorafenib, Sunitinib, Pazopanib, Everolimus, Temsirolimus.

2017-04-14 | GSE97751 | GEO

Global gene expression analysis in NGP CRISPR control cells and NGP ALK(LF655del) cells.

Project description:We performed gene expression profiling by Affymetrix primeview array in both NGP CRISPR control cells and NGP ALK(LF655del) cells.

2021-08-11 | GSE140025 | GEO

Chemical proteomics reveals that the anticancer drug everolimus affects ubiquitin-proteasome system

Project description:Rapamycin is a natural antifungal, immunosuppressive, and antiproliferative compound allosterically inhibiting mTOR complex 1. The ubiquitin-proteasome system (UPS) responsible for protein turnover is usually not listed among the pathways affected by mTOR signaling; however, a number of reports indicated the interplay between UPS and mTOR. It is also reported that rapamycin and analogs can allosterically inhibit the proteasome itself. We studied the molecular effect of rapamycin and its analogs (rapalogs), everolimus, and temsirolimus by expression chemical proteomics on A549 cell line. The analysis revealed that the cellular response to everolimus differs dramatically from that of rapamycin and temsirolimus. In cluster analysis the effect of everolimus was similar to that of bortezomib, a well-established proteasome inhibitor. UPS-related pathways were enriched in the cluster of proteins specifically up-regulated upon everolimus and bortezomib treatments, suggesting that both compounds have similar proteasome inhibition effects. In particular, the total amount of ubiquitin was significantly elevated in the samples treated with everolimus and bortezomib, and the analysis of the polyubiquitination patterns revealed elevated intensities of the ubiquitin peptide with a GG modification at K48 residue, consistent with a bottleneck in the proteasomal protein degradation. Moreover, everolimus treatment resulted in both ubiquitin phosphorylation and a significant amount of semi-tryptic peptides illustrating the induction of protease activity. These observations suggest that everolimus affects the ubiquitin-proteasome system in a unique way and its mechanism of action is strikingly different from that of its close chemical analogs, rapamycin and temsirolimus.

2024-02-09 | PXD045774 | Pride

Differential activity of treatment with protein kinase inhibitors on tumor phosphotyrosine profiles in patients with advanced cancer

Project description:Mass spectrometry-based phosphoproteomics of tumor tissue lysates provides a potential personalized medicine approach based on its ability to identify activated signaling pathways and novel drug targets. We performed a pilot study (NCT01636908) to determine the effect of protein kinase inhibitors (PKIs) on tyrosine-(pTyr)-phosphoproteomic profiles of serial tumor biopsies in patients with advanced cancer. Tumor needle biopsies were analyzed from 31 patients with advanced cancer before and after 2 weeks treatment with sorafenib (SOR), erlotinib (ERL), dasatinib (DAS), vemurafenib (VEM), sunitinib (SUN) or everolimus (EVE). pTyr-Phosphoproteomics of pre- and on-treatment biopsies was performed by phosphotyrosine immunoprecipitation followed by LC-MS/MS.

2019-04-18 | PXD008032 | Pride

microRNAs as predictive biomarkers of response to sunitinib or pazopanib in patients with metastatic renal cell carcinoma

Project description:The aim of the experiment was to discover differentially expressed miRNAs correlating with prolonged response to targeted therapy in patients with metastatic renal cell carcinoma treated with sunitinib or pazopanib

2018-02-08 | E-MTAB-6296 | biostudies-arrayexpress

SMARTer single cell total RNA sequencing [NGP]

Project description:single cell polyA+ and total RNA-seq data was generated for NGP, SK-N-BE-2C and SHSY5Y-MYCN-TR cells

2019-01-01 | GSE119936 | GEO

Chlamydia psittaci strain:Ful-127 | isolate:Ful-127

Project description:Chlamydia psittaci strain:Ful-127 | isolate:Ful-127 Genome sequencing

| PRJNA490061 | ENA

Expression data of CFC1 overexpressed neuroblastoma cell line, NGP

Project description:We performed a microarray analysis on CFC1-expressing NGP cells. Expression data in CFC1- and mock-NGP cells were generated and compared. Differentially expressed genes (DEGs) were functionally annotated by a pathway analysis and Gene Set Enrichment Analysis (GSEA). Both analyses showed that genes involved in “differentiation”, “oncogene-induced senescence”, “stem cell proliferation” and “Activin signaling” pathways were significantly enriched in DEGs. “TGFbeta pathway” and “Nodal pathway” were also enriched in the GeneSpring GX pathway analysis, but were not significant in the GSEA analysis. This result suggests that the pathways involved in cell stemness and Activin signaling were enhanced by the expression of CFC1 in NB cells accompanied by transcriptional changes in their related gene members.

2017-12-01 | GSE90790 | GEO

Genes regulated by miR-127-3p in glioblastoma cell line

Project description:Overexpression of miR-127-3p in LN229 glioblastoma cells promotes their migration and invasion in vitro and in vivo in xenograft models. We used microarrays to detail the global programme of gene expression in miR-127-3p overexpression LN229 cells compared with mock overexpression LN229 cells MiR-127-3p overexpression LN229 cells and and mock overexpression LN229 cells were cultured in DMEM cell culture media for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the genes regulated by miR-127-3p in glioblastoma cell lines.

2014-09-01 | E-GEOD-50173 | biostudies-arrayexpress

ERK inhibitor, ulixertinib induces transcriptomic changes in NGP cells

Project description:To investigate the effect of ERK inhibitor, ulixertinib, on NB cell proliferation and delineate the mechanisms of ulixertinib-mediated ERK pathway inhibition in NB. We treated human neuroblastoma cell line, NGP with ulixertinib and performed gene expression profiling analysis using data obtained from RNA-seq.

2023-03-01 | GSE213153 | GEO

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