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RNA sequencing analysis of the CAL-27 cell response to over-expressed ZNF750 gene

ABSTRACT: RNA sequencing analysis of the CAL-27 cell response to over-expressed ZNF750 gene

PROVIDER: PRJNA556597 | ENA |

REPOSITORIES: ENA

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RNA sequencing analysis of the CAL-27 cell response to over-expressed ZNF750 gene

Project description:Background: Zinc-finger protein 750 (ZNF750) is a potential tumor suppressor in oral squamous cell carcinoma (OSCC). However, the molecular mechanisms underlying its anti-tumor effect remain elusive in OSCC. We report the application of RNA sequencing to identify differentially expressed genes (DEGs) between vector groups and ZNF750 groups (over-expressed ZNF750 in CAL-27 cell), and to elucidate the genes and pathways involved in tumor suppression following the ZNF750 over-expression in OSCC cell line CAL-27 cell. Methods: The RNA sequence libraries were constructed, and the data were analyzed to identify DEGs between vector groups and ZNF750 groups. QPCR and western-blot was used to validate differential expression of candidate genes with cell cycle regulation. The cell cycle distribution was analyzed by BrdU staining. Results: By RNA sequencing profiling, 7,131 genes were differentially expressed in ZNF750 groups. Among the DEGs, 3,285 genes were upregulated, 3,846 genes were downregulated and 4,507 genes were identified in three main categories (cellular_component, biological process and molecular function) based on the gene ontology (GO) classification. The Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis defined the DEGs could be categorized into 280 pathways and identified the top two most significant pathways involved in spliceosome and cell cycle. Functional categorization and enrichment analysis revealed that most of DEGs involved in binding and catalytic activity, and the cell cycle associated genes was significantly enriched in response to ZNF750 over-expression. ZNF750 induced cell cycle arrest in G0/G1 phase of the cell cycle. Conclusion: Data from this study revealed that the cell cycle pathway was a key factor involved in the anti-tumor effect of ZNF750 in CAL-27 cells.

2020-12-01 | GSE134835 | GEO

Expression data from AKR1C1 over-expression in Cal-27 cells or knockdown in HSC-2 cells, respectively

Project description:To exmaine the AKR1C1 controls transcriptome in HNSCC cells, we preformed the Affymetrix Human Genome U133 Plus 2.0 Array with empty vector or AKR1C1 expression vector in Cal-27 cells and shLuc control or shAKR1C1 in HSC-2 cells

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RNA-Seq analysis LEF1 or KDM4A knockdown effect on CAL-27 cells

Project description:To investigate the carcinogenesis function LEF1 or KDM4A in the regulation of oral squamous cell carcinoma, we used siRNA knockdown of LEF1 or KDM4A in CAL-27 cells.

2023-08-21 | GSE230372 | GEO

Expression data from Empty control, PMM1 wildtype and R150H mutation clones in Cal-27 cells

Project description:To exmaine the PMM1-relative tumor suppression transcriptome in OSCC cells, we preformed the Affymetrix Human Genome U133 Plus 2.0 Array with empty vector, PMM1-wildtype and R150H mutation in Cal-27 cells

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Development of gene expression signatures of CAL-27 cells for treatment of shXBP-1s.

Project description:We have employed mRNA microarray expression profiling as a discovery platform to identify genes with the potential to explain how knockdown of XBP-1s upregulated the cell membrane expression of HLA of CAL-27 cells. Both knockdown group and control group were comfirmed to be stable transfected.

2019-08-06 | GSE135380 | GEO

Pathway-focused PCR array profiling of CAL-27 cell with over-expressed ZNF750.

Project description: Not available

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Expression data from AKR1C1 over-expression in Cal-27 cells or knockdown in HSC-2 cells, respectively

Project description:Expression data from AKR1C1 over-expression in Cal-27 cells or knockdown in HSC-2 cells, respectively

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Transcription profiling of human CAL 27 cells overexpressing Nm23-H1 to identify downstream targets of Nm23-H1

Project description:The human nm23-H1 was discovered as a tumor metastasis suppressor based on its reduced expression in melanoma cell lines with low versus high metastatic potential. It encodes for one of two subunits of the nucleoside-diphosphate kinase. Besides its role in the maintenance of the cells NTP pool, nm23 plays a key role in different cellular processes. The role of nm23-H1 in these processes still has to be elucidated. Our goal was to identify Nm23-H1 downstream targets by subjecting Nm23-H1 overexpressing CAL 27 cells oral squamous cell carcinoma (OSSC) to microarray analysis. The genes with changed expression patterns could be clustered into several groups: transforming growth factor (TGF) signaling pathway, cell adhesion, invasion and motility, proteasome machinery, cell-cycle, epithelial structural and related molecules and others. Based on the expression patterns observed we presume that nm23-H1 might have a role in OSSCs, which should be confirmed by future experiments. Experiment Overall Design: The experiments were conducted on human cell line CAL 27 (poorly differentiated, G3, squamous cell carcinoma of the tongue), obtained by courtesy of Dr. Jeannine Gioanni, Centre Antoine Lacassagne, Nice France). The cells were transfected with pEGFPC1 and pEGFPC1-nm23-H1 constructs, and total cellular RNA was extracted from clones expressing EGFP-Nm23-H1 and the empty vector-carrying clone for microarray analysis.

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Differential Expression of LncRNAs of cisplatin-resistant versus parental CAL-27 cells

Project description:Differential Expression of LncRNAs of cisplatin-resistant versus parental CAL-27 cells

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Analysis of miRNA sublocalization in cisplatin-resistant versus parental CAL-27 cells

Project description:Analysis of miRNA sublocalization in cisplatin-resistant versus parental CAL-27 cells

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