scholarly journals Identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gergely Attila Rácz ◽  
Nikolett Nagy ◽  
József Tóvári ◽  
Ágota Apáti ◽  
Beáta G. Vértessy
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Reference Genes ◽  
Normal Cell ◽  
Human Cancer ◽  
Expression Patterns ◽  
Biological Research ◽  
Serum Starvation ◽  
Stable Gene ◽  
Human Cancer Cell Lines

AbstractReverse transcription—quantitative real-time PCR (RT-qPCR) is a ubiquitously used method in biological research, however, finding appropriate reference genes for normalization is challenging. We aimed to identify genes characterized with low expression variability among human cancer and normal cell lines. For this purpose, we investigated the expression of 12 candidate reference genes in 13 widely used human cancer cell lines (HeLa, MCF-7, A-549, K-562, HL-60(TB), HT-29, MDA-MB-231, HCT 116, U-937, SH-SY5Y, U-251MG, MOLT-4 and RPMI-8226) and, in addition, 7 normal cell lines (HEK293, MRC-5, HUVEC/TERT2, HMEC, HFF-1, HUES 9, XCL-1). In our set of genes, we included SNW1 and CNOT4 as novel candidate reference genes based on the RNA HPA cell line gene data from The Human Protein Atlas. HNRNPL and PCBP1 were also included along with the „classical” reference genes ACTB, GAPDH, IPO8, PPIA, PUM1, RPL30, TBP and UBC. Results were evaluated using GeNorm, NormFiner, BestKeeper and the Comparative ΔCt methods. In conclusion, we propose IPO8, PUM1, HNRNPL, SNW1 and CNOT4 as stable reference genes for comparing gene expression between different cell lines. CNOT4 was also the most stable gene upon serum starvation.

scholarly journals Systematic variation in gene expression patterns in human cancer cell lines

10.1038/73432 ◽  
2000 ◽  
Vol 24 (3) ◽  
pp. 227-235 ◽  
Author(s):  
Douglas T. Ross ◽  
Uwe Scherf ◽  
Michael B. Eisen ◽  
Charles M. Perou ◽  
Christian Rees ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Cancer Cell ◽  
Human Cancer ◽  
Expression Patterns ◽  
Cancer Cell Lines ◽  
Systematic Variation ◽  
Gene Expression Patterns ◽  
Human Cancer Cell ◽  
Human Cancer Cell Lines

Regulation of DNA repair gene expression in human cancer cell lines

2006 ◽  
Vol 97 (5) ◽  
pp. 1121-1136 ◽  
Author(s):  
Claire J. McGurk ◽  
Michele Cummings ◽  
Beate Köberle ◽  
John A. Hartley ◽  
R. Timothy Oliver ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Cell Lines ◽  
Cancer Cell ◽  
Human Cancer ◽  
Cancer Cell Lines ◽  
Human Cancer Cell ◽  
Repair Gene ◽  
Human Cancer Cell Lines ◽  
Dna Repair Gene

Do wine polyphenols modulate p53 gene expression in human cancer cell lines?

2001 ◽  
Vol 34 (5) ◽  
pp. 415-420 ◽  
Author(s):  
George J Soleas ◽  
David M Goldberg ◽  
Linda Grass ◽  
Michael Levesque ◽  
Eleftherios P Diamandis
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Cancer Cell ◽  
Human Cancer ◽  
P53 Gene ◽  
Cancer Cell Lines ◽  
Human Cancer Cell ◽  
Human Cancer Cell Lines ◽  
Wine Polyphenols

scholarly journals Galectin-3 Stimulates Tyro3 Receptor Tyrosine Kinase and Erk Signalling, Cell Survival and Migration in Human Cancer Cells

Biomolecules ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1035
Author(s):  
Nour Al Kafri ◽  
Sassan Hafizi
Keyword(s):  
Cell Migration ◽  
Cell Survival ◽  
Cancer Cells ◽  
Cell Lines ◽  
Cancer Cell ◽  
Tyrosine Kinases ◽  
Human Cancer ◽  
Serum Starvation ◽  
Human Cancer Cell Lines ◽  
Galectin 3

The TAM (Tyro3, Axl, MerTK) subfamily of receptor tyrosine kinases (RTKs) and their ligands, Gas6 and protein S (ProS1), are implicated in tumorigenesis and chemoresistance in various cancers. The β-galactoside binding protein galectin-3 (Gal-3), which is also implicated in oncogenesis, has previously been shown to be a ligand for MerTK. However, the selectivity of Gal-3 for the other TAM receptors, and its TAM-mediated signalling and functional properties in cancer cells, remain to be explored. The present study was aimed at determining these, including through direct comparison of Gal-3 with the two canonical TAM ligands. Exogenous Gal-3 rapidly stimulated Tyro3 receptor phosphorylation to the same extent as the Tyro3 ligand ProS1, but not Axl, in the cultured human cancer cell lines SCC-25 (express both Tyro3 and Axl) and MGH-U3 (express Tyro3 only). Gal-3 also activated intracellular Erk and Akt kinases in both cell lines and furthermore protected cells from acute apoptosis induced by staurosporine but not from serum-starvation induced apoptosis. In addition, Gal-3 significantly stimulated cancer cell migration rate in the presence of the Axl blocker BGB324. Therefore, these results have shown Gal-3 to be a novel agonist for Tyro3 RTK, activating a Tyro3-Erk signalling axis, as well as Akt signalling, in cancer cells that promotes cell survival, cell cycle progression and cell migration. These data therefore reveal a novel mechanism of Tyro3 RTK activation through the action of Gal-3 that contrasts with those of the known TAM ligands Gas6 and ProS1.

scholarly journals P11.20 Assessing TTFields-response and associated gene expression in various human cancer cell lines

2019 ◽  
Vol 21 (Supplement_3) ◽  
pp. iii46-iii47
Author(s):  
A Kinzel ◽  
G Lavy-Shahaf ◽  
M Giladi ◽  
R Schneiderman ◽  
K Gotlib ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Cancer Cell ◽  
Human Cancer ◽  
Synergistic Effects ◽  
Cancer Cell Lines ◽  
Human Cancer Cell ◽  
Optimal Frequency ◽  
Human Cancer Cell Lines ◽  
Cell Counts

Abstract BACKGROUND Various cancer cell lines were reported to be affected in an inhibitory manner of varying magnitude by tumor treating fields (TTFields). Here, we aimed to detect response markers for TTFields treatment by analyzing specific properties of cell lines according to their response pattern to these alternating electric fields of intermediate frequency and low intensity. MATERIAL AND METHODS We treated 45 cell lines of diverse types of human cancer with TTFields at their specific optimal frequency and equal nominal intensity of 1.7 V/cm for 72 h. In addition to investigating cytotoxicity and clonogenic potential, we used the Cancer Cell Line Encyclopedia (CCLE) database for further analysis: First, to functionally examine patterns of differentially expressed genes or mutations associated with response to TTFields; and second, to compare sensitivity to TTFields using pharmacological profiling (CCLE). RESULTS TTFields had a cytotoxic effect on tested cell lines of 50 % on average (range: 14–86% reduced cell counts), whereas the clonogenic effect varied between no effect and 88 % reduction in the number of colonies. With regard to differential gene expression and mutation analysis, our analysis detected upregulated pathways associated with migration, DNA damage repair response, oxidative stress, and hypoxia. Further, cells identified as having a better response to TTFields were also more sensitive to lapatinib, PHA-665752 and PLX-4720. CONCLUSION In this study, we determined the optimal frequency for maximum response to TTFields in numerous human cancer cell lines. Our results argue strongly for a vast effectiveness of TTFields treatment in cancer cells, and synergistic effects in combination with other therapeutic agents might be revealed in future studies using pharmacological profiling. Beyond that, further research is needed on the role of identified response-associated mutations.

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