Abstract AS31: MEK inhibition reverses antiestrogen resistance in ovarian cancer (OVCA) via alteration of cell cycle pathways and MAPK/estrogen regulated gene expression

Standard Transcriptome-Wide Association Study (TWAS) methods first train gene expression prediction models using reference transcriptomic data, and then test the association between the predicted genetically regulated gene expression and phenotype of interest. Most existing TWAS tools require cumbersome preparation of genotype input files and extra coding to enable parallel computation. To improve the efficiency of TWAS tools, we develop TIGAR-V2, which directly reads VCF files, enables parallel computation, and reduces up to 90% computation cost compared to the original version. TIGAR-V2 can train gene expression imputation models using either nonparametric Bayesian Dirichlet Process Regression (DPR) or Elastic-Net (as used by PrediXcan), perform TWAS using either individual-level or summary-level GWAS data, and implements both burden and variance-component test statistics for inference. We trained gene expression prediction models by DPR for 49 tissues using GTEx V8 by TIGAR-V2 and illustrated the usefulness of these nonparametric Bayesian DPR eQTL weights through TWAS of breast and ovarian cancer utilizing public GWAS summary statistics. We identified 88 and 37 risk genes respectively for breast and ovarian cancer, most of which are either known or near previously identified GWAS (~95%) or TWAS (~40%) risk genes of the corresponding phenotype and three novel independent TWAS risk genes with known functions in carcinogenesis. These findings suggest that TWAS can provide biological insight into the transcriptional regulation of complex diseases. TIGAR-V2 tool, trained Bayesian cis-eQTL weights, and LD information from GTEX V8 are publicly available, providing a useful resource for mapping risk genes of complex diseases.

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Requirement for prolactin during cell cycle regulated gene expression in cloned T-lymphocytes.

Endocrinology ◽

10.1210/endo.130.6.1534539 ◽

1992 ◽

Vol 130 (6) ◽

pp. 3216-3222 ◽

Cited By ~ 31

Author(s):

C V Clevenger ◽

A L Sillman ◽

J Hanley-Hyde ◽

M B Prystowsky

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

T Lymphocytes ◽

Regulated Gene Expression

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Wild-Type Tumor Repressor Protein 53 (TRP53) Promotes Ovarian Cancer Cell Survival

Endocrinology ◽

10.1210/en.2011-2131 ◽

2012 ◽

Vol 153 (4) ◽

pp. 1638-1648 ◽

Cited By ~ 19

Author(s):

Lisa K. Mullany ◽

Zhilin Liu ◽

Erin R. King ◽

Kwong-Kwok Wong ◽

JoAnne S. Richards

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Ovarian Cancer ◽

Dna Repair ◽

Cell Survival ◽

Cancer Cells ◽

Ovarian Cancer Cells ◽

Low Grade ◽

Wild Type ◽

Repressor Protein

Loss of Pten in the KrasG12D;Amhr2-Cre mutant mice leads to the transformation of ovarian surface epithelial (OSE) cells and rapid development of low-grade, invasive serous adenocarcinomas. Tumors occur with 100% penetrance and express elevated levels of wild-type tumor repressor protein 53 (TRP53). To test the functions of TRP53 in the Pten;Kras (Trp53+) mice, we disrupted the Trp53 gene yielding Pten;Kras(Trp53−) mice. By comparing morphology and gene expression profiles in the Trp53+ and Trp53− OSE cells from these mice, we document that wild-type TRP53 acts as a major promoter of OSE cell survival and differentiation: cells lacking Trp53 are transformed yet are less adherent, migratory, and invasive and exhibit a gene expression profile more like normal OSE cells. These results provide a new paradigm: wild-type TRP53 does not preferentially induce apoptotic or senescent related genes in the Pten;Kras(Trp53+) cancer cells but rather increases genes regulating DNA repair, cell cycle progression, and proliferation and decreases putative tumor suppressor genes. However, if TRP53 activity is forced higher by exposure to nutlin-3a (a mouse double minute-2 antagonist), TRP53 suppresses DNA repair genes and induces the expression of genes that control cell cycle arrest and apoptosis. Thus, in the Pten;Kras(Trp53+) mutant mouse OSE cells and likely in human TP53+ low-grade ovarian cancer cells, wild-type TRP53 controls global molecular changes that are dependent on its activation status. These results suggest that activation of TP53 may provide a promising new therapy for managing low-grade ovarian cancer and other cancers in humans in which wild-type TP53 is expressed.

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Live-cell monitoring of periodic gene expression in synchronous human cells identifies Forkhead genes involved in cell cycle control

Molecular Biology of the Cell ◽

10.1091/mbc.e11-02-0170 ◽

2012 ◽

Vol 23 (16) ◽

pp. 3079-3093 ◽

Cited By ~ 21

Author(s):

Gavin D. Grant ◽

Joshua Gamsby ◽

Viktor Martyanov ◽

Lionel Brooks ◽

Lacy K. George ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Dna Binding ◽

Luciferase Activity ◽

Binding Motif ◽

Sequencing Analysis ◽

Peak Expression ◽

Periodic Gene ◽

Regulated Gene Expression ◽

Periodic Gene Expression

We developed a system to monitor periodic luciferase activity from cell cycle–regulated promoters in synchronous cells. Reporters were driven by a minimal human E2F1 promoter with peak expression in G1/S or a basal promoter with six Forkhead DNA-binding sites with peak expression at G2/M. After cell cycle synchronization, luciferase activity was measured in live cells at 10-min intervals across three to four synchronous cell cycles, allowing unprecedented resolution of cell cycle–regulated gene expression. We used this assay to screen Forkhead transcription factors for control of periodic gene expression. We confirmed a role for FOXM1 and identified two novel cell cycle regulators, FOXJ3 and FOXK1. Knockdown of FOXJ3 and FOXK1 eliminated cell cycle–dependent oscillations and resulted in decreased cell proliferation rates. Analysis of genes regulated by FOXJ3 and FOXK1 showed that FOXJ3 may regulate a network of zinc finger proteins and that FOXK1 binds to the promoter and regulates DHFR, TYMS, GSDMD, and the E2F binding partner TFDP1. Chromatin immunoprecipitation followed by high-throughput sequencing analysis identified 4329 genomic loci bound by FOXK1, 83% of which contained a FOXK1-binding motif. We verified that a subset of these loci are activated by wild-type FOXK1 but not by a FOXK1 (H355A) DNA-binding mutant.

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Dual Knockdown of Musashi RNA-Binding Proteins MSI-1 and MSI-2 Attenuates Putative Cancer Stem Cell Characteristics and Therapy Resistance in Ovarian Cancer Cells

International Journal of Molecular Sciences ◽

10.3390/ijms222111502 ◽

2021 ◽

Vol 22 (21) ◽

pp. 11502

Author(s):

Maria T. Löblein ◽

Isabel Falke ◽

Hans Theodor Eich ◽

Burkhard Greve ◽

Martin Götte ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Ovarian Cancer ◽

Stem Cell ◽

Cancer Stem Cell ◽

Cancer Cells ◽

Rna Binding ◽

Rna Binding Proteins ◽

Therapy Resistance ◽

Ovarian Cancer Cells

In ovarian cancer, therapy resistance mechanisms complicate cancer cell eradication. Targeting Musashi RNA-binding proteins (MSI) may increase therapeutic efficacy. Database analyses were performed to identify gene expression associations between MSI proteins and key therapy resistance and cancer stem cell (CSC) genes. Then, ovarian cancer cells were subjected to siRNA-based dual knockdown of MSI-1 and MSI-2. CSC and cell cycle gene expression was investigated using quantitative polymerase chain reaction (qPCR), western blots, and flow cytometry. Metabolic activity and chemoresistance were assessed by MTT assay. Clonogenic assays were used to quantify cell survival post-irradiation. Database analyses demonstrated positive associations between MSI proteins and putative CSC markers NOTCH, MYC, and ALDH4A1 and negative associations with NOTCH inhibitor NUMB. MSI-2 expression was negatively associated with the apoptosis regulator p21. MSI-1 and MSI-2 were positively correlated, informing subsequent dual knockdown experiments. After MSI silencing, CSC genes were downregulated, while cell cycle progression was reduced. Metabolic activity was decreased in some cancer cells. Both chemo- and radioresistance were reduced after dual knockdown, suggesting therapeutic potential. Dual knockdown of MSI proteins is a promising venue to impede tumor growth and sensitize ovarian cancer cells to irradiation and chemotherapy.

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A toxin-antitoxin system associated transcription factor of Caulobacter crescentus can influence cell cycle-regulated gene expression during the SOS response

10.1101/2020.07.22.216945 ◽

2020 ◽

Author(s):

Koyel Ghosh ◽

Kamilla Ankær Brejndal ◽

Clare L. Kirkpatrick

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Dna Damage ◽

Transcription Factor ◽

Caulobacter Crescentus ◽

Sos Response ◽

Cell Cycle Gene ◽

Regulated Gene Expression ◽

Cell Cycle Gene Expression

AbstractToxin-antitoxin (TA) systems are widespread in bacterial chromosomes but their functions remain enigmatic. Although many are transcriptionally upregulated by stress conditions, it is unclear what role they play in cellular responses to stress and to what extent the role of a given TA system homologue varies between different bacterial species. In this work we investigate the role of the DNA damage-inducible TA system HigBA of Caulobacter crescentus in the SOS response and discover that in addition to the toxin HigB affecting cell cycle gene expression through inhibition of the master regulator CtrA, HigBA possesses a transcription factor third component, HigC, which both auto-regulates the TA system and acts independently of it. Through HigC, the system exerts downstream effects on antibiotic (ciprofloxacin) resistance and cell cycle gene expression. HigB and HigC had inverse effects on cell cycle gene regulation, with HigB reducing and HigC increasing the expression of CtrA-dependent promoters. Neither HigBA nor HigC had any effect on formation of persister cells in response to ciprofloxacin. Rather, their role in the SOS response appears to be as transcriptional and post-transcriptional regulators of cell cycle-dependent gene expression, transmitting the status of the SOS response as a regulatory input into the cell cycle control network via CtrA.ImportanceAlmost all bacteria respond to DNA damage by upregulating a set of genes that helps them to repair and recover from the damage, known as the SOS response. The set of genes induced during the SOS response varies between species, but frequently includes toxin-antitoxin systems. However, it is unknown what the consequence of inducing these systems is, and whether they provide any benefit to the cells. We show here that the DNA damage-induced TA system HigBA of the asymmetrically dividing bacterium Caulobacter crescentus affects the cell cycle regulation of this bacterium. HigBA also has a transcription factor encoded immediately downstream of it, named here HigC, which controls expression of the TA system and potentially other genes as well. Therefore, this work identifies a new role for TA systems in the DNA damage response, distinct from non-specific stress tolerance mechanisms which had been proposed previously.

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High-Resolution Cell Cycle Analysis of Cell Cycle-Regulated Gene Expression

Flow Cytometry Applications in Cell Culture ◽

10.4324/9781003067467-4 ◽

2020 ◽

pp. 63-83

Author(s):

Manfred Kubbies ◽

Bernhard Goller ◽

Guenter Giese

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

High Resolution ◽

Cell Cycle Analysis ◽

Regulated Gene Expression ◽

Resolution Cell

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High-resolution timing of cell cycle-regulated gene expression

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0706022104 ◽

2007 ◽

Vol 104 (43) ◽

pp. 16892-16897 ◽

Cited By ~ 61

Author(s):

M. Rowicka ◽

A. Kudlicki ◽

B. P. Tu ◽

Z. Otwinowski

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

High Resolution ◽

Regulated Gene Expression

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Δ9–Tetrahydrocannabinol (THC)-Rich Compositions from Cannabis Have Cytotoxic Activity Against Ovarian Cancer Cells and Act Synergistically With Niraparib in vitro

10.20944/preprints202109.0179.v1 ◽

2021 ◽

Author(s):

Nurit Shalev ◽

Michelle Kendall ◽

Seegehalli M Anil ◽

Ajjampura C Vinayaka ◽

Hinanit Koltai

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Ovarian Cancer ◽

Cytotoxic Activity ◽

Cannabis Sativa ◽

Mitogen Activated Protein Kinase ◽

Ovarian Cancer Cells ◽

Xtt Assay ◽

Mitogen Activated Protein

Ovarian cancer (OC) is the most lethal gynecologic malignancy. Cannabis sativa is being used to treat different medical conditions. We sought to examine the effectiveness of combinations of cannabis compounds against OC. Cytotoxic activity was determined by XTT assay on HTB75 and HTB161 cell lines. Apoptosis and cell cycle were determined by fluorescence-activated cell sorting (FACS). Gene expression was determined by quantitative PCR. The two most active fractions, F5 and F7, from a high Δ9–tetrahydrocannabinol (THC) cannabis strain extract and their standard mix (SM) showed cytotoxic activity against OC cells. The most effective phytocannabinoid combination was THC+cannabichromene (CBC)+cannabigerol (CBG). F5, F7 and SM affected cell cycle, led to cell apoptosis and to a marked reduction in cell migration. Moreover, these fractions act in synergy with niraparib, and were ~50 fold more cytotoxic to OC cells than to normal keratenocytes. Niraparib+F7 treatment was effective on OC patient's cells. F7 and the niraparin+fraction (F5 and F7) treatments reduced Mitogen-Activated Protein Kinase 4 (MAPK4) gene expression; this reduction may act in synergy with the niraparib inhibition of Poly (ADP-ribose) polymerase 1 (PARP1) activity. Combinations of cannabis compounds and niraparib should be examined for efficacy in pre-clinical studies and clinical trials.

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