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Downstream targets of Nm23-H1: Gene expression profiling of CAL 27 cells using DNA microarray

ABSTRACT: 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. Keywords: disease state analysis

ORGANISM(S): Homo sapiens

PROVIDER: GSE4069 | GEO | 2006/08/01

SECONDARY ACCESSION(S): PRJNA95183

REPOSITORIES: GEO

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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.

2008-06-12 | E-GEOD-4069 | biostudies-arrayexpress

CAL-51 breast cancer side population cells

Project description:Human solid tumors contain rare cancer side population (SP) cells, which expel the fluorescencent dye H33342 and display cancer stem cell characteristics. Transcriptional profiling of cancer SP cells isolated by H33342 fluorescence analysis is a newly emerging approach to discover cancer stem cell markers and aberrant differentiation pathways. Using Affymetrix expression microarrays this study investigated differential gene expression between SP and non-SP (NSP) cells isolated from the CAL-51 human mammary carcinoma cell line. Keywords: cell type comparison To characterize differential gene expression between CAL-51 breast cancer SP and NSP cells, three consecutive cell culture passages of CAL-51 were independently subjected to H33342 labeling and dual wavelength fluorescence analysis and were then flow cytometrically sorted into SP and NSP cell fractions. Subsequently, each of the six cell preparations was subjected to global transcriptional profiling using Affymetrix HG U133 Plus 2.0 expression microarrays.

2009-12-31 | E-GEOD-18773 | biostudies-arrayexpress

Genome-wide RNA deep sequencing of CAL-101 or AKTi primed human T cells in comparison to traditionally expanded T cells

Project description:Differential expression patterns of total mRNA in traditionally expanded T cells (vehicle) compared to T cells expanded under drugs (AKT inhibitor and CAL-101)

2017-11-09 | GSE101497 | GEO

Calcium-dependent proximal biotinylation via Cal-ID

Project description:Calcium ions serve as key intracellular signals. Local, transient increases in calcium concentrations can activate calcium sensor proteins that in turn trigger downstream effectors. In neurons, such calcium transients trigger pre-synaptic vesicle release and mediate post-synaptic plasticity. It is challenging to capture the molecular events associated with these localized and ephemeral calcium signals, however. Here we report the development of an engineered biotin ligase that combines the power of genetically encoded calcium indicators with protein proximity labeling. The enzyme, Cal-ID, biotinylates nearby proteins in response to elevated local calcium levels. The biotinylated proteins can be visualized by microscopy and identified via mass spectrometry. Cal-ID mass spectrometry applied to HEK293T cells identified cell cycle-dependent calcium signaling microdomains at centrosomes. Our results from mouse primary neurons indicated active calcium signaling near calcium extrusion sites on the plasma membrane. Therefore, we propose Cal-ID as a biochemical recorder of calcium signaling in living cells.

2024-02-04 | PXD033244 | Pride

RNA-seq analysis after GSK595 treatment in CAL-1 cells

Project description:RNA-seq analysis was performed in BPDCN patient-derived cell line CAL-1 (WT and METTL3 KO) to analyze gene expression changes after loss of METTL3 concurrent with GSK595 treatment

2022-09-15 | GSE185506 | GEO

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

CAL-51 breast cancer side population cells

2009-12-31 | GSE18773 | GEO

Transcriptome profiling of the Nitric Oxide reponsive genes in the Col-0 and ap1/cal mutant

Project description:Despite the importance of Nitric oxide (NO) in both plant and animal development, the regulatory and mechanism of NO function remain elusive. To test if response to NO in the ap1/cal mutant is comparable to the Col-o wild type, we then analysed the genome wide transcriptome profiling of NO responsive genes both in the wild type and ap1/cal seedling using RNA-seq. We observed that about 88% of differential expressed genes in wild type were overlapped with ap1/cal mutant.

2023-12-01 | GSE243447 | GEO

Recurrent 8q24 rearrangement in BPDCN: association with immunoblastoid cytomorphology, MYC expression, and drug response (CAL-1, JQ1 treatment)

Project description:Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare skin-tropic hematological malignancy of uncertain pathogenesis and poor prognosis. We examined 118 BPDCN cases for cytomorphology, MYC locus rearrangement, and MYC expression. Sixty-two (53%) and 41 (35%) showed the classic and immunoblastoid cytomorphology, respectively. Forty-one (38%) MYC+BPDCN (positive for rearrangement and expression) and 59 (54%) MYC-BPDCN (both negative) cases were identified. Immunoblastoid cytomorphology was significantly associated with MYC+BPDCN. All examined MYC+BPDCNs were negative for MYB/MYBL1 rearrangement (0/36). Clinically, MYC+BPDCN showed older onset, poorer outcome, and localized skin tumors more commonly than MYC-BPDCN. MYC was demonstrated by expression profiling as one of the clearest discriminators between CAL-1 (MYC+BPDCN) and PMDC05 (MYC-BPDCN) cell lines, and its shRNA knockdown suppressed CAL-1 viability. Inhibitors for bromodomain and extraterminal protein (BETis) and aurora kinases (AKis) inhibited CAL-1 growth more effectively than PMDC05. We further showed that a BCL2 inhibitor was effective in both CAL-1 and PMDC05, indicating that this inhibitor can be used to treat MYC-BPDCN, to which BETis and AKis are probably less effective. Our data will provide a rationale for the development of new treatment strategies for patients with BPDCN in accordance with precision medicine.

2018-05-29 | GSE112210 | GEO

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

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