scholarly journals Multiparametric Cell-Based Assay for the Evaluation of Transcription Inhibition by High-Content Imaging

2013 ◽  
Vol 18 (5) ◽  
pp. 556-566 ◽  
Author(s):  
Raquel Torres-Guzmán ◽  
Shaoyou Chu ◽  
Juan A. Velasco ◽  
María José Lallena
Keyword(s):  
Cell Cycle ◽  
Cell Proliferation ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Dna Content ◽  
Human Cancer ◽  
Linear Regression Analysis ◽  
Proliferation Index ◽  
Transcription Inhibition ◽  
High Content Imaging

Loss of normal cell cycle regulation is a hallmark of human cancer. Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle and have been actively pursued as promising therapeutic targets. Likewise, members of the CDK family are functionally related to transcriptional modulation, a molecular pathway suitable for therapeutic intervention. We used a set of 2500 compounds in the U2OS cell line to evaluate its effect in the cell division process. Interestingly, out of this analysis, we identified a subpopulation of compounds that are able to inhibit RNA polymerase activity, thus interfering with gene transcription processes. After this finding, we developed, validated, and fully automated a multiparameter high-content imaging (HCI) assay to measure phosphorylation of the RNA polymerase II carboxyl terminal domain (pCTD). Simultaneously, we measured both the DNA content and cell proliferation index in the treated cells. The linear regression analysis comparing the IC50 for pCTD and the 4N EC50 for DNA content or IC50 for cell proliferation showed an excellent agreement ( r2 = 0.84 and r2 = 0.94, respectively). Our results confirm that this method allows discriminating between cell cycle and transcription inhibition and confirms HCI as a powerful technology for the identification of compounds with an effective and selective pathway phenotype.

scholarly journals Cell cycle-dependent regulation of RNA polymerase II basal transcription activity

1995 ◽  
Vol 23 (20) ◽  
pp. 4050-4054 ◽  
Author(s):  
Masatomo Yonaha ◽  
Taku Chibazakura ◽  
Shigetaka Kitajima ◽  
Yukio Yasukochi
Keyword(s):  
Cell Cycle ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Basal Transcription ◽  
Transcription Activity ◽  
Cycle Dependent

scholarly journals Joint changes in RNA, RNA polymerase II, and promoter activity through the cell cycle identify non-coding RNAs involved in proliferation

2021 ◽  
Author(s):  
Siv Anita Hegre ◽  
Helle Samdal ◽  
Antonin Klima ◽  
Endre B. Stovner ◽  
Kristin G. Nørsett ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Promoter Activity ◽  
Cycle Phase ◽  
Specific Expression ◽  
Chip Sequencing ◽  
Non Coding Rnas ◽  
Cycle Dependent ◽  
Rna Levels

AbstractProper regulation of the cell cycle is necessary for normal growth and development of all organisms. Conversely, altered cell cycle regulation often underlies proliferative diseases such as cancer. Long non-coding RNAs (lncRNAs) are recognized as important regulators of gene expression and are often found dysregulated in diseases, including cancers. However, identifying lncRNAs with cell cycle functions is challenging due to their often low and cell-type specific expression. We present a highly effective method that analyses changes in promoter activity, transcription, and RNA levels for identifying genes enriched for cell cycle functions. Specifically, by combining RNA sequencing with ChIP sequencing through the cell cycle of synchronized human keratinocytes, we identified 1009 genes with cell cycle-dependent expression and correlated changes in RNA polymerase II occupancy or promoter activity as measured by histone 3 lysine 4 trimethylation (H3K4me3). These genes were highly enriched for genes with known cell cycle functions and included 59 lncRNAs. We selected four of these lncRNAs – AC005682.5, RP11-132A1.4, ZFAS1, and EPB41L4A-AS1 – for further experimental validation and found that knockdown of each of the four lncRNAs affected cell cycle phase distributions and reduced proliferation in multiple cell lines. These results show that many genes with cell cycle functions have concomitant cell-cycle dependent changes in promoter activity, transcription, and RNA levels and support that our multi-omics method is well suited for identifying lncRNAs involved in the cell cycle.

scholarly journals Fbxl8 suppresses lymphoma growth and hematopoietic transformation through degradation of cyclin D3

Oncogene ◽  
2020 ◽  
Author(s):  
Akihiro Yoshida ◽  
Jaewoo Choi ◽  
Hong Ri Jin ◽  
Yan Li ◽  
Sagar Bajpai ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Proliferation ◽  
Cell Cycle Progression ◽  
Human Cancer ◽  
E3 Ligase ◽  
Protein Stabilization ◽  
Cyclin D3 ◽  
Deficient Mutant ◽  
Cycle Progression ◽  
Functional Investigation

Abstract Overexpression of D-type cyclins in human cancer frequently occurs as a result of protein stabilization, emphasizing the importance of identification of the machinery that regulates their ubiqutin-dependent degradation. Cyclin D3 is overexpressed in ~50% of Burkitt’s lymphoma correlating with a mutation of Thr-283. However, the E3 ligase that regulates phosphorylated cyclin D3 and whether a stabilized, phosphorylation deficient mutant of cyclin D3, has oncogenic activity are undefined. We describe the identification of SCF-Fbxl8 as the E3 ligase for Thr-283 phosphorylated cyclin D3. SCF-Fbxl8 poly-ubiquitylates p-Thr-283 cyclin D3 targeting it to the proteasome. Functional investigation demonstrates that Fbxl8 antagonizes cell cycle progression, hematopoietic cell proliferation, and oncogene-induced transformation through degradation of cyclin D3, which is abolished by expression of cyclin D3T283A, a non-phosphorylatable mutant. Clinically, the expression of cyclin D3 is inversely correlated with the expression of Fbxl8 in lymphomas from human patients implicating Fbxl8 functions as a tumor suppressor.

Iron Chelator ICL670 Inhibits HIV-1 Transcription.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 3863-3863
Author(s):  
Zufan Debebe ◽  
Tatyana Ammosova ◽  
Hanspeter Nick ◽  
Xiaomei Niu ◽  
Marina Jerebtsova ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Protein Level ◽  
Iron Chelator ◽  
Iron Chelators ◽  
Cyclin T1 ◽  
Terminal Domain ◽  
Cycle Dependent ◽  
Hiv 1

Abstract HIV-1 replication is induced by the excess of iron and iron chelation by desferrioxamine (DFO) inhibits viral replication in HIV-1 infected CEM T cells [1]. Treatment of cells with DFO or 2-hydroxy-1-naphthylaldehyde isonicotinoyl hydrazone inhibits expression of proteins that regulate cell-cycle progression, including cycle-dependent kinase 2 (CDK2) [2]. HIV-1 transcription is activated by Tat protein, which recruits transcriptional co-activators to the HIV-1 promoter. Elongation of HIV-1 transcription is mediated by the interaction of HIV Tat with host cell cycle-dependent kinase 9 (CDK9)/cyclin T1, which phosphorylates the C-terminal domain of RNA polymerase II. Our recent studies showed that CDK2 participates in HIV-1 transcription by phosphorylating Tat [3]. Thus inhibition of CDK2 by iron chelators might present a new approach to inhibit HIV-1 transcription. We evaluated the effect of a clinically approved orally effective iron chelator, 4-[3,5-bis-(hydroxyphenyl) -1,2,4-triazol-1-yl]-benzoic acid (ICL670 or deferasirox) on HIV-1 transcription. ICL670 inhibited Tat-induced HIV-1 transcription in CEM, 293T and HeLa cells at concentrations that did not induce cytotoxicity. The chelator decreased cellular activity of CDK2 but not its protein level and reduced HIV-1 Tat phosphorylation by CDK2. ICL670 did not decrease CDK9 protein level but significantly reduced association of CDK9 with cyclin T1 and reduced phosphorylation of Ser-2 residues of RNA polymerase II C-terminal domain. In conclusion, our findings add to the evidence that iron chelators may inhibit HIV-1 transcription by deregulating CDK2 and Cdk9. Further consideration should be given to the evaluation of ICL670 for future anti-retroviral therapeutics and to the development of iron chelators specifically as anti-retroviral agents.

Flavopiridol Down-Regulates Genes Involved in Cell Cycle Regulation and Tumor Progression in Adults with Refractory or Poor-Risk Acute Leukemia.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 953-953 ◽  
Author(s):  
Linda Resar ◽  
Joelle Hillion ◽  
Katrina Alino ◽  
Michelle Rudek ◽  
Judith Karp
Keyword(s):  
Cell Cycle ◽  
Acute Leukemia ◽  
Rna Polymerase ◽  
Cyclin D1 ◽  
Rna Polymerase Ii ◽  
Target Genes ◽  
Mrna Levels ◽  
Cyclin Dependent Kinase ◽  
Poor Risk ◽  
Before And After

Abstract Acute leukemia in adults continues to be a formidable clinical challenge that demands further investigation to identify more rational therapies. To optimize anti-leukemia therapy, we are investigating the prototypical cyclin dependent kinase (cdk) inhibitor, flavopiridol, in refractory or poor-risk disease. Flavopiridol is a cytotoxic molecule that is thought to induce cell cycle arrest by blocking cyclin-dependent kinase (cdk) function, thereby interfering with RNA Polymerase II activity and globally down-regulating gene expression. In the setting of pan-cdk inhibition, E2F1 is released and appears to drive apoptosis in transformed cells. Consistent with these proposed mechanisms of action, a previous study from our group showed that flavopiridol induces apoptosis in vitro in leukemic blasts from patients with refractory leukemia. Administration of flavopiridol was associated with a decrease in one or more of the following proteins in the leukemic blasts: RNA Polymerase II, STAT3, cyclin D1, Bcl-2, and Mcl-1. Serum VEGF levels also decreased in most patients. We are now investigating mRNA levels of the genes encoding these proteins by quantitative, RT-PCR in leukemic blasts from adult patients with refractory or poor-risk leukemia before and after flavopiridol therapy. We have treated 26 patients with flavopiridol at an escalating, hybrid dose followed by ara-c and mitxantrone. Adequate RNA from leukemic blasts before and after flavopiridol administration was available from 8 of 11 patients studied thus far. All cases (8/8) exhibit a marked decrease in mRNA for VEGF following flavopiridol. mRNA levels for other putative flavopiridol target genes is also decreased in a subset of leukemic blast samples after therapy, as follows: E2F1 (6/8), STAT3 (6/8), Mcl-1 (6/8), RNA Polymerase subunit 2a (3/3), and cyclin D1 (2/3). In contrast, bcl-2 mRNA levels increased after flavopiridol in most cases (7/8), which could represent a compensatory mechanism of leukemic blasts to avoid apoptotic cell death. Our preliminary studies indicate that flavopiridol is cytotoxic in poor-risk and refractory acute leukemia. Studies are underway to determine if down-regulation of any putative target genes correlates with pharmacologic data or clinical responses.

Comparative DNA cytometry of primary and recurrent soft tissue sarcomas.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e22516-e22516
Author(s):  
Irina Dashkova ◽  
Larisa N. Vashchenko ◽  
Oleg Ivanovich Kit ◽  
Inna A. Novikova ◽  
Ekaterina Komarova ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Soft Tissue ◽  
Dna Content ◽  
Soft Tissue Sarcomas ◽  
Literary Analysis ◽  
Proliferation Index ◽  
Cell Distribution ◽  
Dna Cytometry ◽  
Flow Cytofluorometry ◽  
M Phase

e22516 Background: Soft tissue sarcomas (STS) are aggressive tumors with a high degree of recurrence. Radical resection within healthy tissues allows to reduce the recurrence percentage to 25-30% without subsequent therapy. The literary analysis has shown that the study of various biological properties of primary and recurrentsoft tissue tumorsis being conducted. However, currently there is a lack of information to understand the reasons for STS recurrence. The goal of investigation was to reveal the distinctive features of the DNA content and cell distribution in the phases of the cell cycle of recurrent STS. Methods: DNA cytometry in the tumor tissue of 30 primary soft tissue sarcomas and 30 STS recurrences was carried out using the method of flow cytofluorometry. The tumor ploidy and cell distribution in the cell cycle phases were analyzed. Results: A number of differences in the DNA cytometric parameters of primary and recurrent STS have been revealed, they include: an increase in the proportion of aneuploid tumors in case of recurrence, the number of tumors with DNA index within the mitotic cycle, an increase in the proportion of cells in G2+M- phase of diploid and aneuploid tumors and a decrease in S- phase of aneuploid ones. It has been shown that with a G2 differentiation degree, the proportion of cells in G2+M, S- and proliferation index of recurrent STS is significantly lower than the primary parameters. An increase in the proportion of cells in G2+M- phase and a decrease in the rate of proliferation of recurrent STS, depending on the stage, are shown only in case of stage III. Conclusions: The revealed features of DNA content and cell cycle of tumor cells of soft tissue sarcomas will allow to approach to understanding of biological bases of recurrence of this malignant disease.

Changes in RNA polymerase II in a cell cycle-specific temperature-sensitive mutant of hamster cells

1980 ◽  
Vol 103 (1) ◽  
pp. 97-103 ◽  
Author(s):  
Mara Rossini ◽  
Susan Baserga ◽  
C. H. Huang ◽  
C. James Ingles ◽  
Renato Baserga
Keyword(s):  
Cell Cycle ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Temperature Sensitive ◽  
Sensitive Mutant ◽  
Temperature Sensitive Mutant ◽  
A Cell ◽  
Specific Temperature
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