Meta-Analysis of Microarray Expression Studies on Metformin in Cancer Cell Lines

Several studies have demonstrated that metformin (MTF) acts with variable efficiency as an anticancer agent. The pleiotropic anticancer effects of MTF on cancer cells have not been fully explored yet. By interrogating the Gene Expression Omnibus (GEO) for microarray expression data, we identified eight eligible submissions, representing five different studies, that employed various conditions including different cell lines, MTF concentrations, treatment durations, and cellular components. A compilation of the data sets of 13 different conditions contained 443 repeatedly up- and 387 repeatedly down-regulated genes; the majority of these 830 differentially expressed genes (DEGs) were associated with higher MTF concentrations and longer MTF treatment. The most frequently upregulated genes include DNA damage inducible transcript 4 (DDIT4), chromodomain helicase DNA binding protein 2 (CHD2), endoplasmic reticulum to nucleus signaling 1 (ERN1), and growth differentiation factor 15 (GDF15). The most commonly downregulated genes include arrestin domain containing 4 (ARRDC4), and thioredoxin interacting protein (TXNIP). The most significantly (p-value < 0.05, Fisher’s exact test) overrepresented protein class was entitled, nucleic acid binding. Cholesterol biosynthesis and other metabolic pathways were specifically affected by downregulated pathway molecules. In addition, cell cycle pathways were significantly related to the data set. Generated networks were significantly related to, e.g., carbohydrate and lipid metabolism, cancer, cell cycle, and DNA replication, recombination, and repair. A second compilation comprised genes that were at least under one condition up- and in at least another condition down-regulated. Herein, the most frequently deregulated genes include nuclear paraspeckle assembly transcript 1 (NEAT1) and insulin induced gene 1 (INSIG1). The most significantly overrepresented protein classes in this compilation were entitled, nucleic acid binding, ubiquitin-protein ligase, and mRNA processing factor. In conclusion, this study provides a comprehensive list of deregulated genes and biofunctions related to in vitro MTF application and individual responses to different conditions. Biofunctions affected by MTF include, e.g., cholesterol synthesis and other metabolic pathways, cell cycle, and DNA replication, recombination, and repair. These findings can assist in defining the conditions in which MTF exerts additive or synergistic effects in cancer treatment.

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A Genome-Wide CRISPR Screen Implicates MYC Dysregulation in TCF3-PBX1 B-ALL

Blood ◽

10.1182/blood-2018-99-110015 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 3915-3915

Author(s):

Ruth E Cranston ◽

Paul B Sinclair ◽

Matthew Bashton ◽

Matthew P Selby ◽

Christine J Harrison

Keyword(s):

Cell Line ◽

Cell Lines ◽

Cancer Cell ◽

Pathway Analysis ◽

P Value ◽

Whole Genome ◽

Gene Set Enrichment ◽

Data Set ◽

Genome Wide

Abstract Introduction: Acute lymphoblastic leukaemia (ALL) is the most common paediatric cancer, of which, precursor B-cell ALL (B-ALL) accounts for approximately 80% of diagnoses. B-ALL is a heterogeneous disease, with patients characterised and risk stratified according to their cytogenetic profile. TCF3-PBX1 B-ALL was associated with a poor prognosis, but on current therapies outcome has greatly improved. However, approximately 10% of these patients relapse with their disease and at this stage have a dismal prognosis (Moorman et. al. Lancet Oncology 2010). Thus, this subset of patients pose a clinical challenge, and further understanding of disease mechanisms in relapsed TCF3-PBX1 is required to aid the discovery of novel targets for therapy. Methods: Clustered regularly-interspaced short palindromic repeats (CRISPR) technology was utilised as a whole genome CRISPR knockout (GeCKO) screen (Sanjana et. al. Nature Methods 2014) for genome-wide identification of candidate oncogene and tumour suppressor genes (TSGs) in B-ALL cell lines, including 697 (relapsed TCF3-PBX1), REH (ETV6-RUNX1), NALM16 (hypodiploid) and HAL-01 (TCF3-HLF). The GeCKO screens were performed at 300-fold library coverage, with transduced and selected cells harvested at day 0, weeks 2, 4, 6 and 8. DNA was sequenced across the integrated sgRNA region. The abundance of sgRNA constructs was analysed over time using the model-based analysis of genome-wide CRISPR-Cas9 knockout (MAGeCK) program (Li et. al. Genome Biology 2014) to identify candidate oncogenes and TSGs. Pathway analysis was performed for the identification of significantly dysregulated pathways in TCF3-PBX1 using the 697 data set and the MaGeCK Gene Set Enrichment Analysis pathway program. Results: Whole genome CRISPR screening in the 697 cell line successfully identified 2213 candidate oncogenes (false discovery rate (FDR) <0.05, p value <0.012) and 5 candidate TSGs (FDR <0.3, p value < 6.7x10-5). Amongst the significant candidate oncogenes was MYC (FDR = 3.0x10-6, p value = 2.3x10-8, rank 16) and MaGeCK Gene Set Enrichment pathway analysis using the Molecular Signatures Database (MSigDB) Hallmarks data set, identified HALLMARK_MYC_TARGETS_V1 and HALLMARK_MYC_TARGETS_V2 as the two most significant negatively regulated pathways within the knockout screen (FDR of 1.79x10-55 and 9.876x10-21, respectively). These data indicate a role for MYC dysregulation in TCF3-PBX1 B-ALL. Additionally, the identification of the intriguing TSG candidates CREBBP (FDR = 0.059, p value = 5.5x10-6, rank 2), MLXIP (FDR = 0.24, p value = 3.4x10-5, rank 3), HIF1A (FDR = 0.29, p value = 6.7x10-5, rank 4) and ARNT (FDR = 0.02, p value = 1x10-6, rank 1) further highlighting the importance of MYC signalling in TCF3-PBX1 B-ALL. HIF1A inhibits MYC by direct interaction, induction of the repressor MXI1 and by coordinating the degradation of MYC by the proteasome (Zhang et. al. Cancer Cell 2007, Corn et. al. Cancer Biol. Ther. 2005, Gordan et. al. Cancer Cell 2007). ARNT dimerises with HIF1A and is responsible for the recruitment of transcriptional coactivators for the transcriptional output of HIF1A (Partch et. al. Proc Natl Acad Sci USA 2011), while CREBBP has been reported to have a role in MYC inhibition in G1, preventing the progression from G1 to S phase (Rajabi et. al. J. Biol. Chem. 2005), in addition to interaction with the candidate TSG, HIF1A (Ema et. al. EMBO J. 1999, Bhattacharya et. al. Genes Dev. 1999, Park et. al. Mol. Pharmacol. 2008). Despite the role of MLXIP in glycolysis in B-ALL (Wernicke et. al. Leuk Res. 2012), and MLXIP knockout being synthetic lethal in MYC-overexpressing neuroblastoma cell lines (Carroll et. al. Cancer Cell 2015), CRISPR mediated knockout of MLXIP in the 697 TCF3-PBX1 cell line promoted growth. This may be because knockout of MLXIP reduces the number of MLXIP-MLX heterodimers to compete with MYC-MAX heterodimers at E-box sequences, permitting transcriptional activation of MYC-target genes (Carroll et. al. Cancer Cell 2015). This study has identified a number of potential mechanisms by which MYC deregulation can occur in TCF3-PBX1 B-ALL, highlighting the essential role of MYC in disease maintenance. MYC inhibition offers a potential avenue for targeted therapy in relapsed TCF3-PBX1 B-ALL, which warrants further investigation. Disclosures No relevant conflicts of interest to declare.

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Influence of AUF1 targeting siRNA on cell cycle-related proteins in thyroid cancer cell lines

Experimental and Clinical Endocrinology & Diabetes ◽

10.1055/s-2006-932951 ◽

2006 ◽

Vol 114 (S 1) ◽

Author(s):

B Trojanowicz ◽

Z Chen ◽

J Bialek ◽

Y Radestock ◽

S Hombach-Klonisch ◽

...

Keyword(s):

Cell Cycle ◽

Thyroid Cancer ◽

Cell Lines ◽

Cancer Cell ◽

Cancer Cell Lines ◽

Thyroid Cancer Cell ◽

Thyroid Cancer Cell Lines ◽

Related Proteins

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In Vitro Antitumor Evaluation of Some Hybrid Molecules Containing Coumarin and Quinolinone Moieties

Anti-Cancer Agents in Medicinal Chemistry ◽

10.2174/1871520619666190930143856 ◽

2020 ◽

Vol 19 (16) ◽

pp. 2010-2018

Author(s):

Youstina W. Rizzk ◽

Ibrahim M. El-Deen ◽

Faten Z. Mohammed ◽

Moustafa S. Abdelhamid ◽

Amgad I.M. Khedr

Keyword(s):

Cell Cycle ◽

Cell Lines ◽

Cancer Cell ◽

Anticancer Agents ◽

Topoisomerase Ii ◽

Cancer Cell Lines ◽

Bax Protein ◽

Hybrid Molecules ◽

Mcf 7

Background: Hybrid molecules furnished by merging two or more pharmacophores is an emerging concept in the field of medicinal chemistry and drug discovery. Currently, coumarin hybrids have attracted the keen attention of researchers to discover their therapeutic capability against cancer. Objective: The present study aimed to evaluate the in vitro antitumor activity of a new series of hybrid molecules containing coumarin and quinolinone moieties 4 and 5 against four cancer cell lines. Materials and Methods: A new series of hybrid molecules containing coumarin and quinolinone moieties, 4a-c and 5a-c, were synthesized and screened for their cytotoxicity against prostate PC-3, breast MCF-7, colon HCT- 116 and liver HepG2 cancer cell lines as well as normal breast Hs-371 T. Results: All the synthesized compounds were assessed for their in vitro antiproliferative activity against four cancer cell lines and several compounds were found to be active. Further in vitro cell cycle study of compounds 4a and 5a revealed MCF-7 cells arrest at G2 /M phase of the cell cycle profile and induction apoptosis at pre-G1 phase. The apoptosis-inducing activity was evidenced by up-regulation of Bax protein together with the downregulation of the expression of Bcl-2 protein. The mechanism of cytotoxic activity of compounds 4a and 5a correlated to its topoisomerase II inhibitory activity. Conclusion: Hybrid molecules containing coumarin and quinolinone moieties represents a scaffold for further optimization to obtain promising anticancer agents.

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Resistance of Hypoxic Cells to Ionizing Radiation Is Mediated in Part via Hypoxia-Induced Quiescence

Cells ◽

10.3390/cells10030610 ◽

2021 ◽

Vol 10 (3) ◽

pp. 610

Author(s):

Apostolos Menegakis ◽

Rob Klompmaker ◽

Claire Vennin ◽

Aina Arbusà ◽

Maartje Damen ◽

...

Keyword(s):

Cell Cycle ◽

Cell Lines ◽

Cancer Cell ◽

Radiation Treatment ◽

Large Fraction ◽

Radiation Sensitivity ◽

Cancer Cell Lines ◽

Cycle Phase ◽

Multicellular Spheroids ◽

Phase Duration

Double strand breaks (DSBs) are highly toxic to a cell, a property that is exploited in radiation therapy. A critical component for the damage induction is cellular oxygen, making hypoxic tumor areas refractory to the efficacy of radiation treatment. During a fractionated radiation regimen, these hypoxic areas can be re-oxygenated. Nonetheless, hypoxia still constitutes a negative prognostic factor for the patient’s outcome. We hypothesized that this might be attributed to specific hypoxia-induced cellular traits that are maintained upon reoxygenation. Here, we show that reoxygenation of hypoxic non-transformed RPE-1 cells fully restored induction of DSBs but the cells remain radioresistant as a consequence of hypoxia-induced quiescence. With the use of the cell cycle indicators (FUCCI), cell cycle-specific radiation sensitivity, the cell cycle phase duration with live cell imaging, and single cell tracing were assessed. We observed that RPE-1 cells experience a longer G1 phase under hypoxia and retain a large fraction of cells that are non-cycling. Expression of HPV oncoprotein E7 prevents hypoxia-induced quiescence and abolishes the radioprotective effect. In line with this, HPV-negative cancer cell lines retain radioresistance, while HPV-positive cancer cell lines are radiosensitized upon reoxygenation. Quiescence induction in hypoxia and its HPV-driven prevention was observed in 3D multicellular spheroids. Collectively, we identify a new hypoxia-dependent radioprotective phenotype due to hypoxia-induced quiescence that accounts for a global decrease in radiosensitivity that can be retained upon reoxygenation and is absent in cells expressing oncoprotein E7.

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Broader utilization of origins of DNA replication in cancer cell lines along a 78 kb region of human chromosome 2q34

Journal of Cellular Biochemistry ◽

10.1002/jcb.23336 ◽

2011 ◽

Vol 113 (1) ◽

pp. 132-140 ◽

Cited By ~ 9

Author(s):

Manuel S. Valenzuela ◽

Lan Hu ◽

John Lueders ◽

Robert Walker ◽

Paul S. Meltzer

Keyword(s):

Dna Replication ◽

Human Chromosome ◽

Cell Lines ◽

Cancer Cell ◽

Cancer Cell Lines

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A chemical screen in diverse breast cancer cell lines reveals genetic enhancers and suppressors of sensitivity to PI3K isoform-selective inhibition

Biochemical Journal ◽

10.1042/bj20080639 ◽

2008 ◽

Vol 415 (1) ◽

pp. 97-110 ◽

Cited By ~ 98

Author(s):

Neil E. Torbett ◽

Antonio Luna-Moran ◽

Zachary A. Knight ◽

Andrew Houk ◽

Mark Moasser ◽

...

Keyword(s):

Breast Cancer ◽

Cell Cycle ◽

Cell Lines ◽

Cancer Cell ◽

Breast Cancer Cell ◽

Cancer Therapeutics ◽

Cancer Cell Lines ◽

Genetic Alterations ◽

Breast Cancer Cell Lines ◽

Selective Inhibitors

The PI3K (phosphoinositide 3-kinase) pathway regulates cell proliferation, survival and migration and is consequently of great interest for targeted cancer therapy. Using a panel of small-molecule PI3K isoform-selective inhibitors in a diverse set of breast cancer cell lines, we have demonstrated that the biochemical and biological responses were highly variable and dependent on the genetic alterations present. p110α inhibitors were generally effective in inhibiting the phosphorylation of PKB (protein kinase B)/Akt and S6, two downstream components of PI3K signalling, in most cell lines examined. In contrast, p110β-selective inhibitors only reduced PKB/Akt phosphorylation in PTEN (phosphatase and tensin homologue deleted on chromosome 10) mutant cell lines, and was associated with a lesser decrease in S6 phosphorylation. PI3K inhibitors reduced cell viability by causing cell-cycle arrest in the G1 phase, with multi-targeted inhibitors causing the most potent effects. Cells expressing mutant Ras were resistant to the cell-cycle effects of PI3K inhibition, which could be reversed using inhibitors of Ras signalling pathways. Taken together, our data indicate that these compounds, alone or in suitable combinations, may be useful as breast cancer therapeutics, when used in appropriate genetic contexts.

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