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At least 199 records · Page 11Linked to original sources

PubMed2000

Dynamic architecture of the yeast cell cycle uncovered by wavelet decomposition of expression microarray data.

Wavelet analysis has been applied to yeast cell cycle expression microchip data to reveal large-scale temporal structures and ubiquitous oscillations in mRNA levels. Discrete intervals in time within the cell cycle when expression levels changed were visualized as contour maps in which points of transition in gene expression among all 6178 genes were plotted as a function of cell cycle time. Time-frequency analysis using wavelet transforms supported the direct visualization and led to the conclusion that the predominant period is not the cell cycle but a higher frequency, 40 min, submultiple of the cycle. Each of the 6178 gene expression profiles was dissected by wavelet decomposition into all permitted frequencies from the Nyquist limit to roughly twice the cell cycle length. Transitions associated with maximum up- or down-regulation of mRNA levels appear as bands at circa 40-min intervals, half the length of the cycle, through two cell cycles. More than two thirds of the genes, including many of the cyclins, showed this half-cycle periodicity. Gene expression and events within the yeast cell cycle may be regulated by an attractor whose fundamental period is an emergent property of dynamic interactions within the yeast transcriptome.

Cell Cycle↗

PubMed2001

Dynamic models of gene expression and classification.

Powerful new methods, like expression profiles using cDNA arrays, have been used to monitor changes in gene expression levels as a result of a variety of metabolic, xenobiotic or pathogenic challenges. This potentially vast quantity of data enables, in principle, the dissection of the complex genetic networks that control the patterns and rhythms of gene expression in the cell. Here we present a general approach to developing dynamic models for analyzing time series of whole genome expression. In this approach, a self-consistent calculation is performed that involves both linear and non-linear response terms for interrelating gene expression levels. This calculation uses singular value decomposition (SVD) not as a statistical tool but as a means of inverting noisy and near-singular matrices. The linear transition matrix that is determined from this calculation can be used to calculate the underlying network reflected in the data. This suggests a direct method of classifying genes according to their place in the resulting network. In addition to providing a means to model such a large multivariate system this approach can be used to reduce the dimensionality of the problem in a rational and consistent way, and suppress the strong noise amplification effects often encountered with expression profile data. Non-linear and higher-order Markov behavior of the network are also determined in this self-consistent method. In data sets from yeast, we calculate the Markov matrix and the gene classes based on the linear-Markov network. These results compare favorably with previously used methods like cluster analysis. Our dynamic method appears to give a broad and general framework for data analysis and modeling of gene expression arrays.

Animals↗

PubMedDate not supplied

Yeast and cancer.

The discovery of genes that control cell division in yeast, and their relation to cancer, is reviewed.

Cell Cycle Proteins↗

PubMed2006

Nutrient sensing in plant meristems.

Plants need nutrient to grow and plant cells need nutrient to divide. The meristems are the factories and cells that are left behind will expand and differentiate. However, meristems are not simple homogenous entities; cells in different parts of the meristem do different things. Positional cues operate that can fate cells into different tissue domains. However, founder/stem cells persist in specific locations within the meristem e.g. the quiescent centre of root apical meristem (RAM) and the lower half of the central zone of the shoot apical meristem (SAM). Given the complexity of meristems, do their cells simply respond to a diffusing gradient of photosynthate? This in turn begs the question, why do stem cell populations tend to have longer cell cycles than their immediate descendants given that like all other cells they are directly in the path of diffusing nutrient? In this review, we have examined the extent to which nutrient sensing might be operating in meristems. The scene is set for sugar sensing, the plant cell cycle, SAMs and RAMs. Special emphasis is given to the metabolic regulator, SnRK1 (SNF1-related protein kinase 1), hexokinase and the trehalose pathway in relation to sugar sensing. The unique plant cell cycle gene, cyclin-dependent kinase B1;1 may have evolved to be particularly responsive to sugar signalling pathways. Also, the homeobox gene, STIMPY, emerges strongly as a link between sugar sensing, plant cell proliferation and development. Flowering can be influenced by sucrose and glucose levels and both meristem identity and organ identity genes could well be differentially sensitive to sucrose and glucose signals. We also describe how meristems deal with extra photosynthate as a result of exposure to elevated CO2. What we review are numerous instances of how developmental processes can be affected by sugars/nutrients. However, given the scarcity of knowledge we are unable to provide uncontested links between nutrient sensing and specific activities in meristems.

Carbohydrate Metabolism↗

PubMed2006

Expression of cell cycle genes in shoot apical meristems.

This article reviews cell proliferation in the shoot apical meristem. The morphology and function of the meristem depends on the positional control of cell growth and division. The review describes the historical framework of research in this area and then discusses the regulatory pathways that might link developmental controls to the core cell cycle machinery.

Botany↗

PubMed2000

Gene therapy for restenosis.

This review provides an overview of candidate genes that are currently being evaluated for genetic strategies in vascular gene therapy. We discuss treatment strategies that have proven efficacious in limiting postinterventional restenosis through evaluation with in vivo model systems. The candidate strategies utilize genes that are either cytotoxic, regulate vascular smooth muscle cell differentiation or proliferation. In addition, we review oligonuclotide and ribozyme strategies that function by suppressing the expression of cell cycle regulators.

Animals↗

PubMed2006

Therapeutic opportunities to control tumor cell cycles.

Tumor cell proliferation is frequently associated to genetic or epigenetic alterations in key cell cycle regulators. Most human tumors deregulate this pathway to sustain proliferation with independence of external mitogenic factors. In addition, the alteration of cell cycle proteins may confer genomic instability that results in additional mutations in these tumor cells. The frequent alteration of the cell cycle in tumor cells has launched the identification for critical cell cycle regulators as anticancer targets. The inhibition of some cell cycle kinases such as cyclin-dependent kinases (CDKs) or the Aurora and Polo mitotic kinases is currently under study in several preclinical and clinical trials. Similarly, the clinical success of microtubule poisons such as taxol has promoted new applied research in mitosis regulation. Recent investigations have suggested new targets of interest including additional kinases, phosphatases and other mitotic regulators such as microtubule motor proteins (kinesins). Current research in this area will undoubtedly result in new and improved targeted therapies for cancer treatment.

Animals↗

PubMed1995

p25rum1 orders S phase and mitosis by acting as an inhibitor of the p34cdc2 mitotic kinase.

p25rum1 from the fission yeast S. pombe is shown to act as a specific in vitro inhibitor of the p34cdc2/p56cdc13 mitotic kinase. It is also shown that early G1 cells contain p25rum1, which associates with and inhibits the mitotic kinase, and maintains p56cdc13 mitotic B cyclin at a low level, ensuring that these cells do not undergo a premature lethal entry into mitosis. A high level of p25rum1 in G2 cells inhibits the p34cdc2/p56cdc13 kinase that removes the block preventing a further S phase and leads to repeated rounds of DNA replication. Thus, the cyclin-dependent kinase inhibitor p25rum1, acting on the p34cdc2 mitotic kinase, plays an important role in ensuring the correct sequence of S phase and mitosis during the cell cycle.

CDC2 Protein Kinase↗

PubMed1994

The effect of radiation on G2 blocks, cyclin B expression and cdc2 expression in human squamous carcinoma cell lines with different radiosensitivities.

The purpose of the present study was to investigate the role of cyclin B and cdc2 in the G2 delay and to test whether the magnitude of the G2 delay correlated with sensitivity to ionizing radiation in two human cell lines. Cell cycle delays were measured by flow cytometry after pulse labeling with bromodeoxyuridine, and expression of cell cycle control genes were measured in Western blots in radiosensitive SCC61 and radioresistant SQ20B cell lines. Flow cytometry data demonstrated that the duration of the G2 arrest was dose dependent in both cell lines, amounting to approximately 1.1 h/Gy. No difference was found between the cell lines in the length of the G2 block. Radiation exposure did not result in a decrease of cyclin B. Cyclin B protein levels in both asynchronous and synchronized populations in fact showed a dose dependent increase, concomitant with the rise in the fraction of cells in G2/M. Similarly, the cdc2 protein levels did not decrease after irradiation. However, it was found that the levels of hyperphosphorylated, and therefore inactive, kinase were significantly higher in irradiated cells than in unirradiated cells. The accumulation of this hyperphosphorylated form correlated with the arrest of cells in the G2 phase. Finally, immunocytochemical staining of cyclin B revealed an increase of this protein in the cytoplasm after irradiation and a decrease in nuclear staining. This differential localization could possibly account for the reduced nuclear phosphorylation of cdc2 kinase leading to the G2 arrest.

Blotting, Western↗

PubMed1996

How viral oncogenes make the cell cycle.

Oncogenic viruses provide their host cells with additional growth stimuli, thereby extending their proliferative capacity. This implies that viral oncogenes can override growth-suppressive signals, which control cell-cycle progression in untransformed cells. Viral oncoproteins deregulate cell-cycle control by interfering with receptor-mediated signal transduction pathways and the function of nuclear cell-cycle regulatory proteins. As a consequence of these regulatory interactions, many viral oncogenes induce the expression of cellular genes required for cell-cycle progression, including genes encoding G1 cyclins. Apparently, different oncogenic viruses target different subsets of these cell-cycle regulatory pathways to transform cells.

Cell Cycle↗

PubMed2006

Inhibition of retinoblastoma tumor suppressor activity by RNA interference in lung cancer lines.

BACKGROUND: Inactivation of retinoblastoma (RB) tumor suppressor function occurs frequently in lung cancer. Short-hairpin RNA can be constructed to target specific sequences and efficiently knock down protein expression. We developed a short-hairpin RNA approach to specifically target Rb in lung cancer cells to determine the influence of RB knockdown on proliferation. METHODS: NCI-H520 human lung cancer cells (wild-type Rb) were transfected with pMSCVpuro-Rb3C, a plasmid containing a short-hairpin sequence targeted to human Rb. Transfectants harboring the construct were selected with puromycin. Loss of RB expression in selected cell populations was determined by immunoblotting. Proliferating cells were counted to establish growth rates. Retinoblastoma-proficient and RB-deficient tumor growth was monitored in nude mice. RESULTS: Transfection with pMSCVpuro-Rb3C dramatically diminished RB expression and led to aberrant expression of RB-regulated genes. Cells harboring pMSCVpuro-Rb3C grew at an increased rate compared with control cells: 480.6 +/- 37.7 versus 159.4 +/- 36.2 (relative cell count at 12 days). Tumor growth in nude mice also increased with RB knockdown compared with control mice: 135.2 +/- 73.6 mm3 versus 40.0 +/- 17.0 mm3 (tumor volume at 10 days). CONCLUSIONS: Inhibition of RB expression is efficiently achieved in lung cancer cells with short-hairpin RNA. Genetic targets of RB are deregulated with RB knockdown. Retinoblastoma depletion increases growth in vitro and in murine xenografts. These studies indicate that even in the context of an established tumor cell line, RB limits tumorigenic proliferation. Additionally, this model will serve as an ideal system to evaluate the role of RB activity on therapeutic response.

Animals↗

PubMed2004

Cdk inhibitor ste9p/srw1p is involved in response to protein synthesis inhibition in fission yeast.

It remains unknown whether the cell cycle system responds properly to protein synthesis inhibition. In this paper I report finding in Schizosaccharomyces pombe that partially deleted elongation factor 3 genes rescue various mitotic catastrophe mutants depending on deltaste9 in a dominant-negative manner. In response to protein synthesis inhibitors, deltaste9 and some other mutants delay halting the cell cycle at G2-M and the combined cdc2-M26 deltaste9 mutant greatly loses viability. It is suggested that cell cycle be positively controlled in an ste9-dependent manner before essential factors for viability and other important functions are exhausted when protein synthesis is inhibited.

Cell Cycle↗

PubMed2004

Peroxisome proliferator-activated receptor gamma ligands, 15-deoxy-Delta12,14-prostaglandin J2, and ciglitazone, induce growth inhibition and cell cycle arrest in hepatic oval cells.

There is growing evidence to show that hepatic oval cells contribute to liver regeneration, dysplastic nodule formation, and hepato-carcinogenesis. Peroxisome proliferator-activated receptors (PPARs) and their ligands play an important role in cell growth, inflammatory responses, and liver pathogenesis including fibrosis and cancer. However, little is known about the role of PPARgamma/its ligands in the growth and differentiation of hepatic oval cells. In this study, we found that OC15-5, a rat hepatic oval cell line, expressed PPARgamma at mRNA and protein levels, and a natural ligand for PPARgamma, 15-deoxy-Delta12,14-prostaglandin J2 (15d-PGJ2), and a synthetic ligand, ciglitazone, inhibited growth of OC15-5 cells by arresting at G1-S in a dose-dependent manner. Apoptosis was also induced in OC15-5 cells by 15d-PGJ2 treatment. In OC15-5 cells treated with 15d-PGJ2, the expression of CDK inhibitor, p27(Kip1), was up-regulated, while that of p21(WAF1/Cip1), p18(INK4C) CDK2, CDK4, and cyclin E was unchanged. In addition, delayed up-regulation of AFP expression was observed in OC15-5 cells after 15d-PGJ2 or ciglitazone treatment. This is the first report to show that the PPARgamma ligand was involved in the growth, cell cycle, and differentiation of hepatic oval cells, raising the possibility that the PPARgamma ligands may regulate liver regeneration and hepato-carcinogenesis.

Animals↗

PubMed2006

Checkpoint deficient rad53-11 yeast cannot accumulate dNTPs in response to DNA damage.

Deoxyribonucleotide pools are maintained at levels that support efficient and yet accurate DNA replication and repair. Rad53 is part of a protein kinase regulatory cascade that, conceptually, promotes dNTP accumulation in four ways: (1) it activates the transcription of ribonucleotide reductase subunits by inhibiting the Crt1 repressor; (2) it plays a role in relocalization of ribonucleotide reductase subunits RNR2 and RNR4 from nucleus to cytoplasm; (3) it antagonizes the action of Sml1, a protein that binds and inhibits ribonucleotide reductase; and (4) it blocks cell-cycle progression in response to DNA damage, thus preventing dNTP consumption through replication forks. Although several lines of evidence support the above modes of Rad53 action, an effect of a rad53 mutation on dNTP levels has not been directly demonstrated. In fact, in a previous study, a rad53-11 mutation did not result in lower dNTP levels in asynchronous cells or in synchronized cells that entered the S-phase in the presence of the RNR inhibitor hydroxyurea. These anomalies prompted us to investigate whether the rad53-11 mutation affected dNTP levels in cells exposed to a DNA-damaging dose of ethylmethyl sulfonate (EMS). Although dNTP levels increased by 2- to 3-fold in EMS treated wild-type cells, rad53-11 cells showed no such change. Thus, the results indicate that Rad53 checkpoint function is not required for dNTP pool maintenance in normally growing cells, but is required for dNTP pool expansion in cells exposed to DNA-damaging agents.

Cell Cycle↗

PubMed2003

The Fanconi anemia pathway and the DNA interstrand cross-links repair.

Fanconi anemia (FA) is a genetic cancer-predisposition syndrome characterized by bone marrow failure and cellular and chromosomal hypersensitivity to DNA cross-linking agents. Seven FA genes have been isolated and their products associate to form a pathway that interacts functionally or physically with several DNA-damage response proteins involved in cell cycle checkpoints and/or DNA repair. These proteins include BLM, ATM, BRCA1, XPF and the MRE11/RAD50/NBS1 complex. In spite of several recent striking progresses in the biochemistry and the molecular biology of the disorder, the precise function(s) of the FA proteins remain(s) poorly determined. However, several recent data indicate that the FA pathway could be involved in the coordination of both cell cycle checkpoints and DNA repair.

Animals↗

PubMed2006

Cell cycle deregulation and loss of stem cell phenotype in the subventricular zone of TGF-beta adaptor elf-/- mouse brain.

The mammalian forebrain subependyma contains neural stem cells and other proliferating progenitor cells. Recent studies have shown the importance of TGF-beta family members and their adaptor proteins in the inhibition of proliferation in the nervous system. Previously, we have demonstrated that TGF-beta induces phosphorylation and association of ELF (embryonic liver fodrin) with Smad3 and Smad4 resulting in nuclear translocation. Elf(-/-) mice manifest abnormal neuronal differentiation, with loss of neuroepithelial progenitor cell phenotype in the subventricular zone (SVZ) with dramatic marginal cell hyperplasia and loss of nestin expression. Here, we have analyzed the expression of cell cycle-associated proteins cdk4, mdm2, p21, and pRb family members in the brain of elf(-/-) mice to verify the role of elf in the regulation of neural precursor cells in the mammalian brain. Increased proliferation in SVZ cells of the mutant mice coincided with higher levels of cdk4 and mdm2 expression. A lesser degree of apoptosis was observed in the mutant mice compared to the wild-type control. Elf(-/-) embryos showed elevated levels of hyperphosphorylated forms of pRb, p130 and p107 and decreased level of p21 compared to the wild-type control. These results establish a critical role for elf in the development of a SVZ neuroepithelial stem cell phenotype and regulation of neuroepithelial cell proliferation, suggesting that a mutation in the elf locus renders the cells susceptible to a faster entry into S phase of cell cycle and resistance to senescence and apoptotic stimuli.

Animals↗

PubMed2005

Molecular genetic alterations and gene expression profile of a malignant rhabdoid tumor of the kidney.

Malignant rhabdoid tumor of the kidney (MRTK) is a rare but highly aggressive tumor in children, and knowledge about the molecular signature of this tumor is limited. We report the molecular genetic alterations and gene expression profile of an MRTK tumor that arose in a 4-month-old Japanese girl. Fluorescence in situ hybridization and Southern blot analyses revealed a homozygous deletion of an approximately 0.29-Mb genomic region bordered by the Rgr and DDT genes in these tumor cells. This deleted region encodes SMARCB1, a candidate tumor suppressor gene for MRTK. Using a high-density oligonucleotide DNA array, we found increased expression of 25 genes, including genes involved in the cell cycle (10 genes), DNA replication (3 genes), cell growth (5 genes), and cell proliferation (5 genes), in this MRTK tumor sample, compared with a noncancerous kidney (NK) sample. On the other hand, 64 genes, including 4 genes regulating apoptosis, were found to show decreased expression in this MRTK tumor sample, compared with the NK sample. Among these alterations, we found alterations of expression of some genes, such as IGF2, MDK, TP53, and TNFSF10, in this MRTK tumor, as described previously. The molecular genetic alterations and altered pattern of gene expression found in this case may have contributed to the biological characteristics of the MRTK tumor that arose in our patient.

Apoptosis↗

PubMed2005

Cutaneous melanoma susceptibility and progression genes.

This review aims to provide an up-to-date view on our understanding of the molecular genetics of melanoma development. It gives an overview of genes (and loci) currently known to be substantially involved in melanoma predisposition and progression. Broadly, the review falls into 3 sections: genes/loci involved in melanoma susceptibility through germline mutation, tumor suppressor genes somatically mutated or deleted in melanoma, and oncogenes mutated somatically in melanoma. The main cellular pathways in which these genes are involved are summarized and discussed. From this it is evident that abberations of cell cycle regulation, DNA repair and receptor-mediated signal transduction are important for melanocytic neoplasia.

Animals↗