scholarly journals Inferring Cell Cycle Phases From a Partially Temporal Network of Protein Interactions

2021 ◽  
Author(s):  
Maxime Lucas ◽  
Arthur Morris ◽  
Alex Townsend-Teague ◽  
Laurent Tichit ◽  
Bianca Habermann ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Protein Interactions ◽  
Temporal Network ◽  
Cell Cycle Phases

scholarly journals Inferring cell cycle phases from a partially temporal network of protein interactions

2021 ◽  
Author(s):  
Maxime Lucas ◽  
Arthur Morris ◽  
Alex Townsend-Teague ◽  
Laurent Tichit ◽  
Bianca H Habermann ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Protein Interactions ◽  
Time Series Data ◽  
A Priori ◽  
Biological Systems ◽  
Series Data ◽  
Biological Knowledge ◽  
Temporal Network ◽  
Protein Protein Interactions ◽  
Temporal Organisation

The temporal organisation of biological systems into phases and subphases is often crucial to their functioning. Identifying this multiscale organisation can yield insight into the underlying biological mechanisms at play. To date, however, this identification requires a priori biological knowledge of the system under study. Here, we recover the temporal organisation of the cell cycle of budding yeast into phases and subphases, in an automated way. To do so, we model the cell cycle as a partially temporal network of protein-protein interactions (PPIs) by combining a traditional static PPI network with protein concentration or RNA expression time series data. Then, we cluster the snapshots of this temporal network to infer phases, which show good agreement with our biological knowledge of the cell cycle. We systematically test the robustness of the approach and investigate the effect of having only partial temporal information. The generality of the method makes it suitable for application to other, less well-known biological systems for which the temporal organisation of processes plays an important role.

Hydrogen peroxide and quercetin induced changes on cell viability, apoptosis and oxidative stress in HepG2 cells

2020 ◽  
Vol 01 ◽  
Author(s):  
Ayşe Mine Yılmaz ◽  
Gökhan Biçim ◽  
Kübra Toprak ◽  
Betül Karademir Yılmaz ◽  
Irina Milisav ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Cell Cycle ◽  
Hydrogen Peroxide ◽  
Cell Viability ◽  
Hepg2 Cells ◽  
Proteasome Activity ◽  
Cell Cycle Phases ◽  
Induced Changes ◽  
And Oxidative Stress ◽  
Quercetin Treatment

Background: Different cellular responses influence the progress of cancer. In this study, we have investigated the effect of hydrogen peroxide and quercetin induced changes on cell viability, apoptosis and oxidative stress in human hepatocellular carcinoma (HepG2) cells. Methods: The effects of hydrogen peroxide and quercetin on cell viability, cell cycle phases and oxidative stress related cellular changes were investigated. Cell viability was assessed by WST-1 assay. Apoptosis rate, cell cycle phase changes and oxidative stress were measured by flow cytometry. Protein expressions of p21, p27, p53, NF-Kβ-p50 and proteasome activity were determined by Western blot and fluorometry, respectively. Results: Hydrogen peroxide and quercetin treatment resulted in decreased cell viability and increased apoptosis in HepG2 cells. Proteasome activity was increased by hydrogen peroxide but decreased by quercetin treatment. Conclusion: Both agents resulted in decreased p53 protein expression and increased cell death by different mechanisms regarding proteostasis and cell cycle phases.

miRNA-mediated Drug Repurposing Unveiled Potential Candidate Drugs for Prolactinoma Treatment

2021 ◽  
Author(s):  
Büşra Aydin ◽  
Sema Arslan ◽  
Fatih Bayraklı ◽  
Betül Karademir ◽  
Kazim Yalcin Arga
Keyword(s):  
Cell Cycle ◽  
Data Integration ◽  
Cell Viability ◽  
Drug Repurposing ◽  
Serum Prolactin ◽  
Drug Candidates ◽  
Mirna Level ◽  
Level Data ◽  
Cell Cycle Phases

Introduction: Prolactinomas, also called lactotroph adenomas, are the most encountered type of hormone-secreting pituitary neuroendocrine tumors (PitNET) in the clinic. The preferred first-line therapy is a medical treatment with dopamine agonists (DA), mainly cabergoline, to reduce serum prolactin levels, tumor volume, and mass effect. However, in some cases, patients have displayed DA-resistance with aggressive tumor behavior or are faced with recurrence after drug withdrawal. Also, currently used therapeutics have notorious side effects and impair the life quality of the patients. Methods: Since the amalgamation of clinical and laboratory data besides tumor histopathogenesis and transcriptional regulatory features of the tumor emerge to exhibit essential roles in the behavior and progression of prolactinomas, in this work, we integrated mRNA and microRNA (miRNA) level transcriptome data that exploit disease-specific signatures in addition to biological and pharmacological data to elucidate a rational prioritization of pathways and drugs in prolactinoma. Results: We identified eight drug candidates through drug repurposing based on mRNA-miRNA level data integration and evaluated their potential through in vitro assays in the MMQ cell line. Seven re-purposed drugs including 5-flourocytosine, nortriptyline, neratinib, puromycin, taxifolin, vorinostat, and zileuton were proposed as potential drug candidates for the treatment of prolactinoma. We further hypothesized possible mechanisms of drug action on MMQ cell viability through analyzing PI3K/Akt signaling pathway and cell cycle arrest via flow cytometry and western blotting. Discussion: We presented the transcriptomic landscape of prolactinoma through miRNA and mRNA level data integration and proposed repurposed drug candidates based on this integration. We validated our findings through testing cell viability, cell cycle phases, and PI3K/Akt protein expressions. Effects of the drugs on cell cycle phases and inhibition of PI3K/Akt pathway by all drugs gave us promising output for further studies using these drugs in the treatment of prolactinoma. This is the first study that reports miRNA-mediated repurposed drugs for prolactinoma treatment via in vitro experiments.

Q-FIHC: Quantification of fluorescence immunohistochemistry to analysep63 isoforms and cell cycle phases in human limbal stem cells

2006 ◽  
Vol 69 (12) ◽  
pp. 983-991 ◽  
Author(s):  
Enzo Di Iorio ◽  
Vanessa Barbaro ◽  
Stefano Ferrari ◽  
Claudio Ortolani ◽  
Michele De Luca ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Stem Cells ◽  
Limbal Stem Cells ◽  
Cell Cycle Phases ◽  
Fluorescence Immunohistochemistry

scholarly journals The Prpl  + Gene Required for Pre-mRNA Splicing in Schizosaccharomyces pombe Encodes a Protein That Contains TPR Motifs and Is Similar to Prp6p of Budding Yeast

Genetics ◽  
1997 ◽  
Vol 147 (1) ◽  
pp. 101-115 ◽  
Author(s):  
Seiichi Urushiyama ◽  
Tokio Tani ◽  
Yasumi Ohshima
Keyword(s):  
Cell Cycle ◽  
Amino Acid ◽  
Schizosaccharomyces Pombe ◽  
Protein Interactions ◽  
Nuclear Export ◽  
Cell Cycle Progression ◽  
Synthetic Lethality ◽  
Cell Cycle Control ◽  
Mrna Splicing ◽  
Restrictive Temperature

Abstract The prp (pre-mRNA processing) mutants of the fission yeast Schizosaccharomyces pombe have a defect in pre-mRNA splicing and accumulate mRNA precursors at a restrictive temperature. One of the prp mutants, prp1-4, also has a defect in poly(A)+ RNA transport. The prp1  + gene encodes a protein of 906 amino acid residues that contains 19 repeats of 34 amino acids termed tetratrico peptide repeat (TPR) motifs, which were proposed to mediate protein-protein interactions. The amino acid sequence of Prplp shares 29.6% identity and 50.6% similarity with that of the PRP6 protein of Saccharomyces cerevisiae, which is a component of the U4/U6 snRNP required for spliceosome assembly. No functional complementation was observed between S. pombe prp1  + and S. cerevisiae PRP6. We examined synthetic lethality of prp1-4 with the other known prp mutations in S. pombe. The results suggest that Prp1p interacts either physically or functionally with Prp4p, Prp6p and Prp13p. Interestingly, the prp1  + gene was found to be identical with the zer1  + gene that functions in cell cycle control. These results suggest that Prp1p/Zer1p is either directly or indirectly involved in cell cycle progression and/or poly(A)+ RNA nuclear export, in addition to pre-mRNA splicing.

CEP110 and ninein are located in a specific domain of the centrosome associated with centrosome maturation

2002 ◽  
Vol 115 (9) ◽  
pp. 1825-1835 ◽  
Author(s):  
Young Y. Ou ◽  
Gary J. Mack ◽  
Meifeng Zhang ◽  
Jerome B. Rattner
Keyword(s):  
Cell Cycle ◽  
Protein Interactions ◽  
Protein Function ◽  
Similar Distribution ◽  
Microtubule Organizing Center ◽  
Specific Domain ◽  
The Reformation ◽  
Mother And Daughter ◽  
Organizing Center ◽  
Pericentriolar Material

The mammalian centrosome consists of a pair of centrioles surrounded by pericentriolar material (PCM). The architecture and composition of the centrosome, especially the PCM, changes during the cell cycle. Recently, a subset of PCM proteins have been shown to be arranged in a tubular conformation with an open and a closed end within the centrosome. The presence of such a specific configuration can be used as a landmark for mapping proteins in both a spatial and a temporal fashion. Such mapping studies can provide information about centrosome organization, protein dynamics,protein-protein interactions as well as protein function. In this study, the centrosomal proteins CEP110 and ninein were mapped in relationship to the tubular configuration. Both proteins were found to exhibit a similar distribution pattern. In the mother centrosome, they were found at both ends of the centrosome tube, including the site of centrosome duplication. However,in the daughter centrosome they were present only at the closed end. At the closed end of the mother and daughter centrosome tube, both CEP110 and ninein co-localized with the centriolar protein CEP250/c-Nap1, which confirms ninein's centriole association and places CEP110 in association with this structure. Importantly, the appearance of CEP110 and ninein at the open end of the daughter centrosome occurred during the telophase-G1 transition of the next cell cycle, concomitant with the maturation of the daughter centrosome into a mother centrosome. Microinjection of antibodies against either CEP110 or ninein into metaphase HeLa cells disrupted the reformation of the tubular conformation of proteins within the centrosome following cell division and consequently led to dispersal of centrosomal material throughout the cytosol. Further, microinjection of antibodies to either CEP110 or ninein into metaphase PtK2 cells not only disrupted the tubular configuration within the centrosome but also affected the centrosome's ability to function as a microtubule organizing center (MTOC). This MTOC function was also disrupted when the antibodies were injected into postmitotic cells. Taken together, our results indicate that: (1) a population of CEP110 and ninein is located in a specific domain within the centrosome, which corresponds to the open end of the centrosome tube and is the site of protein addition associated with maturation of a daughter centrosome into a mother centrosome; and (2) the addition of CEP110 and ninein are essential for the reformation of specific aspects of the interphase centrosome architecture following mitosis as well as being required for the centrosome to function as a MTOC.

scholarly journals Protein interactions withpiALURNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly

2012 ◽  
Vol 2 (1) ◽  
pp. 26-35 ◽  
Author(s):  
Benjamin J. Blackwell ◽  
Mary F. Lopez ◽  
Jianrong Wang ◽  
Bryan Krastins ◽  
David Sarracino ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Repair ◽  
Protein Interactions ◽  
Chromatin Assembly

scholarly journals Continued initiation of DNA synthesis in arginine-deprived Chinese hamster ovary cells.

1977 ◽  
Vol 73 (1) ◽  
pp. 200-205 ◽  
Author(s):  
A S Weissfeld ◽  
H Rouse
Keyword(s):  
Cell Cycle ◽  
Dna Synthesis ◽  
Chinese Hamster Ovary ◽  
Cho Cells ◽  
Chinese Hamster Ovary Cells ◽  
Chinese Hamster ◽  
Cell Multiplication ◽  
Ovary Cells ◽  
Cell Cycle Phases

When exponentially growing CHO cells were deprived of arginine (Arg), cell multiplication ceased after 12 h, but initiation of DNA synthesis continued: after 48 h of starvation with continuous [3H]thymidine exposure, 85% of the population had incorporated label, as detected autoradiographically. Consideration of the distribution of exponential cells in the various cell cycle phases leads to a calculation that most cells in G1 at the time that Arg was removed, as well as those in S, engaged in some DNA synthesis during starvation. In contrast, isoleucine (Ile)-starved cells did not initiate DNA synthesis, as has been reported by others. Experiments with cells synchronized by mitotic selection confirmed this difference in Arg- and Ile- deprived behavior, but also showed that cells which underwent the mitosis leads to G1 transition during Arg starvation remained arrested in G1 (G0?). The results suggest that Arg-deprived cells continue to maintain some proliferative function(s) while Ile-deprived cells do not.

scholarly journals Schistosoma mansoni polo-like kinases and their function in control of mitosis and parasite reproduction

2011 ◽  
Vol 83 (2) ◽  
pp. 627-635 ◽  
Author(s):  
Colette Dissous ◽  
Christoph G Grevelding ◽  
Thavy Long
Keyword(s):  
Cell Cycle ◽  
Schistosoma Mansoni ◽  
Protein Interactions ◽  
Cell Cycle Progression ◽  
Gonad Development ◽  
Cancer Drug ◽  
Protein Protein Interactions ◽  
Centriole Duplication ◽  
Regulation Of Cell Cycle ◽  
Functional Analyses

Polo-like kinases are important regulators of cell cycle progression and mitosis. They constitute a family of conserved serine/threonine kinases which are highly related in their catalytic domains and contain polo boxes involved in protein-protein interactions and subcellular localization. In mammals, five Plks (Plk 1-5) encompass diverse roles in centrosome dynamics, spindle formation, intra S-phase and G2/M checkpoints and DNA damage response. Plk1 is a key positive regulator of mitosis and is overexpressed in various types of cancers. Plk4 is a divergent member of the Plk family, with essential functions in centriole duplication. Homozygous disruption of Plk1 or Plk4 in mice is lethal in embryos. Two Plk members SmPlk1 and SmSak, homologous to Plk1 and Plk4 respectively, are present in the parasitic platyhelminth Schistosoma mansoni. Structural and functional analyses of SmPlk1 have demonstrated its conserved function in the regulation of cell cycle G2/M transition in Xenopus oocytes. The anti-cancer drug BI 2536 (the most potent and selective Plk1 inhibitor) inhibits specifically the catalytic activity of SmPlk1 and induced profound alterations in schistosome gonads, indicating a role of SmPlk1 in parasite gametogenesis and its potential as a novel chemotherapeutic target against schistosomiasis. Functions of SmSak in cell cycle regulation and schistosome gonad development are currently investigated

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