Mathematical Modeling of p53 Pathways

Cells have evolved balanced systems that ensure an appropriate response to stress. The systems elicit repair responses in temporary or moderate stress but eliminate irreparable cells via apoptosis in detrimental conditions of prolonged or severe stress. The tumor suppressor p53 is a central player in these stress response systems. When activated under DNA damage stress, p53 regulates hundreds of genes that are involved in DNA repair, cell cycle, and apoptosis. Recently, increasing studies have demonstrated additional regulatory roles of p53 in metabolism and mitochondrial physiology. Due to the inherent complexity of feedback loops between p53 and its target genes, the application of mathematical modeling has emerged as a novel approach to better understand the multifaceted functions and dynamics of p53. In this review, we discuss several mathematical modeling approaches in exploring the p53 pathways.

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The Sumoylation Modulated Tumor Suppressor p53 Regulates Cell Cycle Checking Genes to Mediate Lens Differentiation

Current Molecular Medicine ◽

10.2174/1566524019666190111154450 ◽

2019 ◽

Vol 18 (8) ◽

pp. 556-565 ◽

Cited By ~ 1

Author(s):

Xiangcheng Tang ◽

Zhigang Chen ◽

Mi Deng ◽

Ling Wang ◽

Qian Nie ◽

...

Keyword(s):

Cell Cycle ◽

Tumor Suppressor ◽

Tumor Suppressor P53

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Use of Oxidative Stress Responses to Determine the Efficacy of Inactivation Treatments on Cryptosporidium Oocysts

Microorganisms ◽

10.3390/microorganisms9071463 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1463

Author(s):

Tamirat Tefera Temesgen ◽

Kristoffer Relling Tysnes ◽

Lucy Jane Robertson

Keyword(s):

Oxidative Stress ◽

Stress Responses ◽

Target Genes ◽

Cryptosporidium Oocyst ◽

Drinking Water Treatment ◽

Proof Of Concept ◽

Environmental Matrices ◽

Oocyst Wall ◽

Novel Approach ◽

Cryptosporidium Oocysts

Cryptosporidium oocysts are known for being very robust, and their prolonged survival in the environment has resulted in outbreaks of cryptosporidiosis associated with the consumption of contaminated water or food. Although inactivation methods used for drinking water treatment, such as UV irradiation, can inactivate Cryptosporidium oocysts, they are not necessarily suitable for use with other environmental matrices, such as food. In order to identify alternative ways to inactivate Cryptosporidium oocysts, improved methods for viability assessment are needed. Here we describe a proof of concept for a novel approach for determining how effective inactivation treatments are at killing pathogens, such as the parasite Cryptosporidium. RNA sequencing was used to identify potential up-regulated target genes induced by oxidative stress, and a reverse transcription quantitative PCR (RT-qPCR) protocol was developed to assess their up-regulation following exposure to different induction treatments. Accordingly, RT-qPCR protocols targeting thioredoxin and Cryptosporidium oocyst wall protein 7 (COWP7) genes were evaluated on mixtures of viable and inactivated oocysts, and on oocysts subjected to various potential inactivation treatments such as freezing and chlorination. The results from the present proof-of-concept experiments indicate that this could be a useful tool in efforts towards assessing potential technologies for inactivating Cryptosporidium in different environmental matrices. Furthermore, this approach could also be used for similar investigations with other pathogens.

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EGFR-ERK induced activation of GRHL1 promotes cell cycle progression by up-regulating cell cycle related genes in lung cancer

Cell Death and Disease ◽

10.1038/s41419-021-03721-9 ◽

2021 ◽

Vol 12 (5) ◽

Author(s):

Yiming He ◽

Mingxi Gan ◽

Yanan Wang ◽

Tong Huang ◽

Jianbin Wang ◽

...

Keyword(s):

Lung Cancer ◽

Cell Cycle ◽

Cell Cycle Progression ◽

Potential Role ◽

Target Genes ◽

Nuclear Translocation ◽

Phosphorylation Site ◽

Promoter Regions ◽

Cycle Progression

AbstractGrainyhead-like 1 (GRHL1) is a transcription factor involved in embryonic development. However, little is known about the biological functions of GRHL1 in cancer. In this study, we found that GRHL1 was upregulated in non-small cell lung cancer (NSCLC) and correlated with poor survival of patients. GRHL1 overexpression promoted the proliferation of NSCLC cells and knocking down GRHL1 inhibited the proliferation. RNA sequencing showed that a series of cell cycle-related genes were altered when knocking down GRHL1. We further demonstrated that GRHL1 could regulate the expression of cell cycle-related genes by binding to the promoter regions and increasing the transcription of the target genes. Besides, we also found that EGF stimulation could activate GRHL1 and promoted its nuclear translocation. We identified the key phosphorylation site at Ser76 on GRHL1 that is regulated by the EGFR-ERK axis. Taken together, these findings elucidate a new function of GRHL1 on regulating the cell cycle progression and point out the potential role of GRHL1 as a drug target in NSCLC.

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Target Gene Specificity of E2F and Pocket Protein Family Members in Living Cells

Molecular and Cellular Biology ◽

10.1128/mcb.20.16.5797-5807.2000 ◽

2000 ◽

Vol 20 (16) ◽

pp. 5797-5807 ◽

Cited By ~ 162

Author(s):

Julie Wells ◽

Kathryn E. Boyd ◽

Christopher J. Fry ◽

Stephanie M. Bartley ◽

Peggy J. Farnham

Keyword(s):

Cell Cycle ◽

Target Gene ◽

Target Genes ◽

Protein Complexes ◽

Current Model ◽

Family Members ◽

Living Cells ◽

Gene Promoters ◽

Pocket Protein ◽

Protein Dna Interactions

ABSTRACT E2F-mediated transcription is thought to involve binding of an E2F-pocket protein complex to promoters in the G0 phase of the cell cycle and release of the pocket protein in late G1, followed by release of E2F in S phase. We have tested this model by monitoring protein-DNA interactions in living cells using a formaldehyde cross-linking and immunoprecipitation assay. We find that E2F target genes are bound by distinct E2F-pocket protein complexes which change as cells progress through the cell cycle. We also find that certain E2F target gene promoters are bound by pocket proteins when such promoters are transcriptionally active. Our data indicate that the current model applies only to certain E2F target genes and suggest that Rb family members may regulate transcription in both G0 and S phases. Finally, we find that a given promoter can be bound by one of several different E2F-pocket protein complexes at a given time in the cell cycle, suggesting that cell cycle-regulated transcription is a stochastic, not a predetermined, process.

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Synthesizing artificial devices that redirect cellular information at will

eLife ◽

10.7554/elife.31936 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 5

Author(s):

Yuchen Liu ◽

Jianfa Li ◽

Zhicong Chen ◽

Weiren Huang ◽

Zhiming Cai

Keyword(s):

Cancer Cells ◽

Signaling Pathway ◽

Gene Networks ◽

Target Genes ◽

Logic Gates ◽

Feedback Loops ◽

Oncogenic Signaling ◽

Multiple Signals ◽

Translational Level ◽

At Will

Natural signaling circuits could be rewired to reprogram cells with pre-determined procedures. However, it is difficult to link cellular signals at will. Here, we describe signal-connectors—a series of RNA devices—that connect one signal to another signal at the translational level. We use them to either repress or enhance the translation of target genes in response to signals. Application of these devices allows us to construct various logic gates and to incorporate feedback loops into gene networks. They have also been used to rewire a native signaling pathway and even to create novel pathways. Furthermore, logical AND gates based on these devices and integration of multiple signals have been used successfully for identification and redirection of the state of cancer cells. Eventually, the malignant phenotypes of cancers have been reversed by rewiring the oncogenic signaling from promoting to suppressing tumorigenesis. We provide a novel platform for redirecting cellular information.

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Proposed megakaryocytic regulon of p53: the genes engaged to control cell cycle and apoptosis during megakaryocytic differentiation

Physiological Genomics ◽

10.1152/physiolgenomics.00028.2012 ◽

2012 ◽

Vol 44 (12) ◽

pp. 638-650 ◽

Cited By ~ 16

Author(s):

Pani A. Apostolidis ◽

Stephan Lindsey ◽

William M. Miller ◽

Eleftherios T. Papoutsakis

Keyword(s):

Cell Cycle ◽

Dna Synthesis ◽

Cell Line ◽

Target Genes ◽

Control Cell ◽

P53 Expression ◽

Megakaryocytic Differentiation ◽

Knock Down ◽

Cell Cycling ◽

And Control

During endomitosis, megakaryocytes undergo several rounds of DNA synthesis without division leading to polyploidization. In primary megakaryocytes and in the megakaryocytic cell line CHRF, loss or knock-down of p53 enhances cell cycling and inhibits apoptosis, leading to increased polyploidization. To support the hypothesis that p53 suppresses megakaryocytic polyploidization, we show that stable expression of wild-type p53 in K562 cells (a p53-null cell line) attenuates the cells' ability to undergo polyploidization during megakaryocytic differentiation due to diminished DNA synthesis and greater apoptosis. This suggested that p53's effects during megakaryopoiesis are mediated through cell cycle- and apoptosis-related target genes, possibly by arresting DNA synthesis and promoting apoptosis. To identify candidate genes through which p53 mediates these effects, gene expression was compared between p53 knock-down (p53-KD) and control CHRF cells induced to undergo terminal megakaryocytic differentiation using microarray analysis. Among substantially downregulated p53 targets in p53-KD megakaryocytes were cell cycle regulators CDKN1A (p21) and PLK2, proapoptotic FAS, TNFRSF10B, CASP8, NOTCH1, TP53INP1, TP53I3, DRAM1, ZMAT3 and PHLDA3, DNA-damage-related RRM2B and SESN1, and actin component ACTA2, while antiapoptotic CKS1B, BCL2, GTSE1, and p53 family member TP63 were upregulated in p53-KD cells. Additionally, a number of cell cycle-related, proapoptotic, and cytoskeleton-related genes with known functions in megakaryocytes but not known to carry p53-responsive elements were differentially expressed between p53-KD and control CHRF cells. Our data support a model whereby p53 expression during megakaryopoiesis serves to control polyploidization and the transition from endomitosis to apoptosis by impeding cell cycling and promoting apoptosis. Furthermore, we identify a putative p53 regulon that is proposed to orchestrate these effects.

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Regulation of Yeast-to-Hyphae Transition inYarrowia lipolytica

mSphere ◽

10.1128/msphere.00541-18 ◽

2018 ◽

Vol 3 (6) ◽

Cited By ~ 9

Author(s):

Kyle R. Pomraning ◽

Erin L. Bredeweg ◽

Eduard J. Kerkhoven ◽

Kerrie Barry ◽

Sajeet Haridas ◽

...

Keyword(s):

Cell Cycle ◽

Transcription Factor ◽

Stress Response ◽

Hyphal Growth ◽

Genetic Screen ◽

Morphological Transition ◽

Histidine Kinases ◽

Content Type ◽

Forward Genetic Screen ◽

Response To Stress

ABSTRACTThe yeastYarrowia lipolyticaundergoes a morphological transition from yeast-to-hyphal growth in response to environmental conditions. A forward genetic screen was used to identify mutants that reliably remain in the yeast phase, which were then assessed by whole-genome sequencing. All thesmoothmutants identified, so named because of their colony morphology, exhibit independent loss of DNA at a repetitive locus made up of interspersed ribosomal DNA and short 10- to 40-mer telomere-like repeats. The loss of repetitive DNA is associated with downregulation of genes with stress response elements (5′-CCCCT-3′) and upregulation of genes with cell cycle box (5′-ACGCG-3′) motifs in their promoter region. The stress response element is bound by the transcription factor Msn2p inSaccharomyces cerevisiae. We confirmed that theY. lipolyticamsn2(Ylmsn2) ortholog is required for hyphal growth and found that overexpression of Ylmsn2enables hyphal growth insmoothstrains. The cell cycle box is bound by the Mbp1p/Swi6p complex inS. cerevisiaeto regulate G1-to-S phase progression. We found that overexpression of either the Ylmbp1or Ylswi6homologs decreased hyphal growth and that deletion of either Ylmbp1or Ylswi6promotes hyphal growth insmoothstrains. A second forward genetic screen for reversion to hyphal growth was performed with thesmooth-33mutant to identify additional genetic factors regulating hyphal growth inY. lipolytica. Thirteen of the mutants sequenced from this screen had coding mutations in five kinases, including the histidine kinases Ylchk1and Ylnik1and kinases of the high-osmolarity glycerol response (HOG) mitogen-activated protein (MAP) kinase cascade Ylssk2, Ylpbs2, and Ylhog1. Together, these results demonstrate thatY. lipolyticatransitions to hyphal growth in response to stress through multiple signaling pathways.IMPORTANCEMany yeasts undergo a morphological transition from yeast-to-hyphal growth in response to environmental conditions. We used forward and reverse genetic techniques to identify genes regulating this transition inYarrowia lipolytica. We confirmed that the transcription factor Ylmsn2is required for the transition to hyphal growth and found that signaling by the histidine kinases Ylchk1and Ylnik1as well as the MAP kinases of the HOG pathway (Ylssk2, Ylpbs2, and Ylhog1) regulates the transition to hyphal growth. These results suggest thatY. lipolyticatransitions to hyphal growth in response to stress through multiple kinase pathways. Intriguingly, we found that a repetitive portion of the genome containing telomere-like and rDNA repeats may be involved in the transition to hyphal growth, suggesting a link between this region and the general stress response.

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Influence of High Duty Ratio and Frequency in WECM Employing In Situ Fabricated Wire Electrode

Journal of Micro and Nano-Manufacturing ◽

10.1115/1.4037768 ◽

2017 ◽

Vol 5 (4) ◽

Cited By ~ 2

Author(s):

S. Debnath ◽

J. Kundu ◽

B. Bhattacharyya

Keyword(s):

Mathematical Modeling ◽

Electrochemical Machining ◽

Burr Formation ◽

Duty Ratio ◽

Minimum Width ◽

Applied Frequency ◽

Early Adoption ◽

Novel Approach ◽

Microfabrication Techniques

To adapt with today's rapidly changing world, fabrication of intricate microparts is becoming an urgent need. Manufacturing of these microparts with stringent requirements necessitates the early adoption of different microfabrication techniques. Wire electrochemical machining (WECM) is such a process which removes excess metal by dissolving it electrochemically. This process can easily generate features downscaled to micron ranges and offers several advantages like the requirement of very simple setup, fabrication of accurate complex microfeatures without undergoing any thermal stress, burr formation, and tool wear, which make it superior from other existing micromachining processes. However, this process is new, and little is known about its applicability and feasibility. Hence, the present work is directed towards developing suitable WECM setup to fabricate microfeatures by introducing proper means for enhancing the mass transport phenomenon. The tungsten tool wire for machining has been in situ etched to a diameter of 23.43 μm by a novel approach for retaining its regular cylindrical form and has been implemented during machining. Moreover, the influences of high duty ratio and applied frequency have been investigated on the corresponding width of the fabricated microslits and the experimental results have been represented graphically where the minimum width of the microslit is obtained as 44.85 μm. Furthermore, mathematical modeling has been developed to correlate duty ratio and applied frequency with generated slit width. Additionally, the mathematical modeling has been validated with practical results and complex stepped type microfeatures have been generated to establish process suitability.

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Predicting cell-cycle expressed genes identifies canonical and non-canonical regulators of time-specific expression in Saccharomyces cerevisiae

10.1101/387050 ◽

2018 ◽

Author(s):

Nicholas L Panchy ◽

John P. Lloyd ◽

Shin-Han Shiu

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Cycle ◽

Target Genes ◽

Specific Cell ◽

Data Sets ◽

Cell Cycle Regulators ◽

Specific Expression ◽

Regulatory Data ◽

Time Specific ◽

Cycle Regulation

AbstractThe collection all TFs, target genes and their interactions in an organism form a gene regulatory network (GRN), which underly complex patterns of transcription even in unicellular species. However, identifying which interactions regulate expression in a specific temporal context remains a challenging task. With multiple experimental and computational approaches to characterize GRNs, we predicted general and phase-specific cell-cycle expression in Saccharomyces cerevisiae using four regulatory data sets: chromatin immunoprecipitation (ChIP), TF deletion data (Deletion), protein binding microarrays (PBMs), and position weight matrices (PWMs). Our results indicate that the source of regulatory interaction information significantly impacts our ability to predict cell-cycle expression where the best model was constructed by combining selected TF features from ChIP and Deletion data as well as TF-TF interaction features in the form of feed-forward loops. The TFs that were the best predictors of cell-cycle expression were enriched for known cell-cycle regulators but also include regulators not implicated in cell-cycle regulation previously. In addition, ChIP and Deletion datasets led to the identification different subsets of TFs important for predicting cell-cycle expression. Finally, analysis of important TF-TF interaction features suggests that the GRN regulating cell cycle expression is highly interconnected and clustered around four groups of genes, two of which represent known cell-cycle regulatory complexes, while the other two contain TFs that are not known cell-cycle regulators (Ste12-Tex1 and Rap1-Hap1-Msn4), but are nonetheless important to regulating the timing of expression. Thus, not only do our models accurately reflect what is known about the regulation of the S. cerevisiae cell cycle, they can be used to discover regulatory factors which play a role in controlling expression during the cell cycle as well as other contexts with discrete temporal patterns of expression.

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Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to Oesophageal Adenocarcinoma

10.1101/2020.02.10.941872 ◽

2020 ◽

Author(s):

Connor Rogerson ◽

Samuel Ogden ◽

Edward Britton ◽

Yeng Ang ◽

Andrew D. Sharrocks ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Molecular Mechanisms ◽

Target Genes ◽

Prognostic Significance ◽

Gene Expression Signature ◽

Chromatin Accessibility ◽

Oesophageal Adenocarcinoma ◽

Cell Cycle Gene ◽

A Cell

AbstractOesophageal adenocarcinoma (OAC) is one of the most common causes of cancer deaths and yet compared to other common cancers, we know relatively little about the underlying molecular mechanisms. Barrett’s oesophagus (BO) is the only known precancerous precursor to OAC, but our understanding about the specific events leading to OAC development is limited. Here, we have integrated gene expression and chromatin accessibility profiles of human biopsies of BO and OAC and identified a strong cell cycle gene expression signature in OAC compared to BO. Through analysing associated chromatin accessibility changes, we have implicated the transcription factor KLF5 in the transition from BO to OAC. Importantly, we show that KLF5 expression is unchanged during this transition, but instead, KLF5 is redistributed across chromatin in OAC cells to directly regulate cell cycle genes specifically in OAC. Our findings have potential prognostic significance as the survival of patients with high expression of KLF5 target genes is significantly lower. We have provided new insights into the gene expression networks in OAC and the mechanisms behind progression to OAC, chiefly the repurposing of KLF5 for novel regulatory activity in OAC.

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