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PubMed2006

The p53 tumor suppressor participates in multiple cell cycle checkpoints.

The process of cell division is highly ordered and regulated. Checkpoints exist to delay progression into the next cell cycle phase only when the previous step is fully completed. The ultimate goal is to guarantee that the two daughter cells inherit a complete and faithful copy of the genome. Checkpoints can become activated due to DNA damage, exogenous stress signals, defects during the replication of DNA, or failure of chromosomes to attach to the mitotic spindle. Abrogation of cell cycle checkpoints can result in death for a unicellular organism or uncontrolled proliferation and tumorigenesis in metazoans (Nyberg et al., 2002). The tumor suppressor p53 plays a critical role in each of these cell cycle checkpoints and is reviewed here.

Animals↗
PubMed2006

Therapeutic biology: checkpoint pathway activation therapy, HIV Tat, and transkingdom RNA interference.

Therapeutic biology is an exciting new frontier in the post-genomic era with the mission to better human health. The explosive increase in the understanding of molecular and regulatory biology has enabled the identification of a plethora of potential targets and pathways for the discovery of new medicines. Conversely, molecularly based therapeutic intervention of biological aberrations in human diseases offers a test of the depth of our understanding of biology. This article discusses three examples of therapeutic biology research. The first concerns the treatment of cancer by activating genome surveillance circuitry, namely checkpoint-pathway activation therapy. The second example is the identification of the HIV Tat protein as both a cause of immune cell activation and apoptosis, and as a vaccine candidate against HIV infection. The third example describes transkingdom RNA interference and its application in the investigational and therapeutic silencing of disease genes.

AIDS Vaccines↗
PubMed2007

Establishment of histone gene regulation and cell cycle checkpoint control in human embryonic stem cells.

Rapid self-renewal of human embryonic stem (ES) cells (NIH designation WA01 and WA09) is accommodated by an abbreviated cell cycle due to a reduction in the G1 phase. Thus, molecular mechanisms operative in ES cells may expedite the cellular commitment to progress into S phase to initiate replication of DNA and biosynthesis of histone proteins to form new chromatin. Here we show that the selective cell cycle regulated expression of individual histone H4 gene copies, which is typical for somatic cell types, is already firmly established in human ES cells. This early establishment of H4 gene regulation, which is E2F independent, is consistent with co-expression of the cognate transcriptional regulators HiNF-P and p220(NPAT). Human ES cells differ from somatic cells in the expression of members of the E2F family and RB-related pocket proteins (p105(RB1), p107(RBL1), and p130(RBL2/RB2)) that control expression of genes encoding enzymes for nucleotide metabolism and DNA synthesis. Human ES cells rapidly and robustly (>200-fold) induce the cyclin dependent kinase (CDK) inhibitor p21(WAF1/CIP1) upon gamma-irradiation. This DNA damage response promptly reduces histone gene expression as well as mRNA levels for HiNF-P and p220(NPAT) and causes accumulation of unprocessed histone H4 precursor RNAs. Furthermore, while E2F4, E2F5 and p130(RBL2/RB2) are the major E2F and pocket protein mRNAs in actively proliferating ES cells, expression levels of E2F5, E2F6, and p105(RB1) are most strongly elevated during cell cycle arrest in cells responding to DNA damage. Our data suggest that the brief G1 phase of ES cells is supported by a potent p21(WAF1/CIP1) related DNA damage response that functions through several mechanisms to rapidly inhibit cell cycle progression. This response may alter the E2F/pocket protein combinations that control E2F dependent genes and block H4 gene expression by inhibiting histone-specific transcription factors and processing of histone gene transcripts, as well as by destabilizing histone mRNAs.

Cell Cycle Proteins↗
PubMed2004

In vivo analysis reveals different apoptotic pathways in pre- and postmigratory cerebellar granule cells of rabbit.

Naturally occurring neuronal death (NOND) has been described in the postnatal cerebellum of several species, mainly affecting the cerebellar granule cells (CGCs) by an apoptotic mechanism. However, little is known about the cellular pathway(s) of CGC apoptosis in vivo. By immunocytochemistry, in situ detection of fragmented DNA, electron microscopy, and Western blotting, we demonstrate here the existence of two different molecular mechanisms of apoptosis in the rabbit postnatal cerebellum. These two mechanisms affect CGCs at different stages of their maturation and migration. In the external granular layer, premigratory CGCs undergo apoptosis upon phosphorylation of checkpoint kinase 1 (Chk1), and hyperphosphorylation of retinoblastoma protein. In postmigratory CGCs within the internal granular layer, caspase 3 and to a lesser extent 7 and 9 are activated, eventually leading to poly-ADP-ribose polymerase-1 (PARP-1) cleavage and programmed cell death. We conclude that NOND of premigratory CGCs is linked to activation of DNA checkpoint and alteration of normal cell cycle, whereas in postmigratory CGCs apoptosis is, more classically, dependent upon caspase 3 activation.

Animals↗
PubMed2006

Senescence and serration: a new twist to an old tale.

Interest in the role of oncogene-induced senescence in tumorigenesis is mounting. Raf-associated senescence in cutaneous nevi has been advanced as an example of this process occurring in the context of a human tumour. In this model, conversion from a senescent nevus to a malignant melanoma is accompanied by loss of expression of p16. Serrated polyps of the colorectum may provide a further example of oncogene-induced senescence. BRAF and KRAS mutation may initiate different pathways of senescence-associated serrated neoplasia in the colorectum, the former linked to CpG island methylator phenotype (CIMP)-high (CIMP1) and microsatellite instability (MSI)-high status and the latter with CIMP-low (CIMP2) and MSI-low status. The role of methylation in both Raf- and Ras-associated pathways is to drive tumorigenesis by silencing pro-apoptotic and cell cycle inhibitory genes. Both pathways are associated with mutation of Ras-induced senescence 1 (RIS1), but the biological role of RIS1 requires further elucidation.

Cell Transformation, Neoplastic↗
PubMed2001

Methylation and mutational analysis of p27(kip1) in prostate carcinoma.

BACKGROUND: We have previously identified 12p12-13 as a region of frequent genetic loss in prostate carcinoma. A candidate tumor suppressor gene at this locus is the cyclin dependent kinase inhibitor p27(kip1), which has been implicated as a marker of aggressive prostate carcinoma. Herein, we examine metastatic prostate tumors, xenografts, and cell lines for gene inactivation via mutational inactivation or promoter hypermethylation. METHODS: Mutation analysis was performed on metastatic prostate tumors of 18 patients, eight prostate carcinoma cell lines, and 18 xenografts by PCR amplification of the entire open reading frame of p27(kip1). PCR products were sequenced directly using internal primers. Methylation analysis was performed on four cell lines and nine xenografts using direct sequencing of cloned PCR products of bisulfite treated DNA. Presence of a CpG was consistent with methylation of that cytosine in the original sample. RESULTS: With the exception of the previously reported homozygous deletion, no additional mutations were identified. Methylated CpG residues were identified in three xenografts (LuCAP23, LuCAP35, and PC82) and the methylated residues clustered at six sites; the cytosines 69, 149, 191, 286, 349, and 487 base pairs 5' of the ATG start codon. However, no sample demonstrated promotor methylation in all sequenced clones and the number of methylated base pairs ranged from seven to three, not the level usually associated with gene silencing. CONCLUSIONS: Mutational inactivation of p27(kip1) is a rare event in metastatic prostate carcinoma. While CpG methylation does occur, it is an infrequent event and does not appear to be the mechanism of p27(kip1) down regulation in prostate carcinoma.

Cell Cycle Proteins↗
PubMed2005

New weakly expressed cell cycle-regulated genes in yeast.

We present an approach combining bioinformatics prediction with experimental microarray validation to identify new cell cycle-regulated genes in Saccharomyces cerevisiae. We identify in the order of 100 new cell cycle-regulated genes and show by independent data that these genes in general tend to be more weakly expressed than the genes identified hitherto. Among the genes not previously suggested to be periodically expressed we find genes linked to DNA repair, cell size monitoring and transcriptional control, as well as a number of genes of unknown function. Several of the gene products are believed to be phosphorylated by Cdc28. For many of these new genes, homologues exist in Schizosaccharomyces pombe and Homo sapiens for which the expression also varies with cell cycle progression.

Cell Cycle Proteins↗
PubMed2000

Selective transcriptional regulations in the human liver cell by hepatitis B viral X protein.

The hepatitis B viral X protein (HBx) is known as a transcription factor and potential oncogene. To gain a better view of the effect of HBx on the transcriptional regulation in the human liver cell, we constructed a HepG2 cell line stably expressing HBx (HepG2-HBx), and performed cDNA microarray analysis on 588 cellular cDNAs comparing with untransformed control cells. Two genes (IGFR-2, RhoA) of oncogenes, one gene (p55CDC) of cell cycle regulators, three genes (thrombin receptor, MLK-3, MacMARCKS) of intracellular transducers, one gene (HSP27) of stress response proteins, two genes (FAST kinase, Bak) of apoptosis response proteins, one gene (p21(WAF)) of transcription factors were highly up-regulated; one gene (transcription elongation factor SII) of transcription factors and two genes (monocyte chemotactic protein 1, T-lymphocyte-secreted protein I-309) of growth factors were highly down-regulated. These results showed selective transcriptional regulation by HBx in the human liver cell.

Apoptosis↗
PubMed2002

Overexpression of cyclin D1 is associated with the decondensation of chromatin during den-induced sequential hepatocarcinogenesis.

D-type cyclins regulate distinct cellular processes such as mitotic cell cycle control, differentiation and transcription. Deregulation of cyclin D1, a component of G1 checkpoint control, can result in enhanced genomic instability, cell transformation, and malignant neoplasia. However, a precise understanding of the molecular and cellular events underlying the regulation of the cyclin D1 gene remains to be elucidated. In this study, we examined the regulation of the cyclin D1 gene during n-nitrosodiethylamine (DEN)-induced sequential liver carcinogenesis. Northern blot studies showed an increase in the level of cyclin D1 mRNA. Southern blot analysis of the DNA restriction fragment showed no alterations and/or amplification in the coding region of the cyclin D1 gene. Bulk chromatin from DEN-treated rat liver is much more sensitive to nuclease digestion than that from normal liver. Increased expression of the cyclin D1 gene is correlated to the upregulation of its transcription, mediated through chromatin decondensation during sequential hepatocarcinogenesis. Thus, the functional inter-relationship between chromatin organization and gene expression appears to be of critical importance for liver tumour development.

Animals↗
PubMed2002

Reappraisal of G1-phase arrest and synchronization by lovastatin.

It has been proposed that lovastatin arrests cells in the G1-phase of the division cycle, and that release from lovastatin inhibition produces a synchronized culture. A new method of methocel time-lapse-videography has been used to analyse cell division patterns following lovastatin treatment. Release of L1210 cells from lovastatin inhibition failed to produce synchronized divisions. Moreover, contrary to earlier proposals, lovastatin did not arrest cells with a G1-phase amount of DNA. Analysis of previous reports of 'synchronization' and growth-arrest support these findings. It is concluded that lovastatin neither synchronizes cells, nor arrests cells in the G1-phase of the division cycle.

Animals↗
PubMed1998

Growth inhibition of cultured human Tenon's fibroblastic cells by targeting the E2F transcription factor.

The transcription factor E2F regulates the expression of several genes concerned with cell growth. The ability to inhibit transcription by blocking E2F expression has great potential in the treatment of proliferative disorders. The effect of double-stranded phosphorothioate oligonucleotides containing E2F transcription factor cis element, a so called 'decoy' has examined on the growth of cultured human Tenon's fibroblastic cells. Human Tenon's fibroblastic cells were cultured and challenged by E2F decoy coated with the Hemagglutinating virus of Japan (HVJ) cationic liposomes (HVJ-CL). The outcome was evaluated using fluorescence microscopy, RT-PCR and growth assays. HVJ-CL facilitated the transfer of external oligonucleotides to cultured human Tenon's fibroblastic cells. The E2F decoy, transferred by HVJ-CL, inhibited simultaneously the expression of the mRNAs of several cell cycle related genes such as c-myc, cdc2, proliferative cell nuclear antigen, and dehydrofolate reductase. Entry into S phase was also reduced to 42.7% of the positive control by the E2F decoy. The total increase of DNA at four days was reduced to 59.7% of the positive control by 5 microM and 29.9% by 15 microM of E2F decoy. It is concluded that gene therapy using the E2F transcription factor offers a potential therapeutic modality for the treatment of proliferative disorders such as proliferative vitreoretinopathy and fibrosis following filtering surgery.

Carrier Proteins↗
PubMed2002

The DNA damage response in filamentous fungi.

The mechanisms used by fungal cells to repair DNA damage have been subjects of intensive investigation for almost 50 years. As a result, the model yeasts Schizosaccharomyces pombe and Saccharomyces cerevisiae have led the way in yielding critical insights into the nature of the DNA damage response. At the same time, largely through the efforts of Etta Kafer, Hirokazu Inoue, and colleagues, a substantial collection of Aspergillus nidulans and Neurospora crassa DNA repair mutants has been identified and characterized in detail. As the analysis of these mutants continues and increasing amounts of annotated genome sequence become available, it is becoming readily apparent that the DNA damage response of filamentous fungi possesses several features that distinguish it from the model yeasts. These features are emphasized in this review, which describes the genes, regulatory networks, and processes that compose the fungal DNA damage response. Further characterization of this response will likely yield general insights that are applicable to animals and plants. Moreover, it may also become evident that the DNA damage response can be manipulated to control fungal growth.

Apoptosis↗
PubMed2002

Identification and characterization of a paralog of human cell cycle checkpoint gene HUS1.

A paralog of the human cell cycle checkpoint gene HUS1 has been identified and designated HUS1B. It encodes a 278-amino-acid protein, 48% identical and 69% similar to HUS1. Mouse and rat orthologs of HUS1B have also been detected by a BLAST search. HUS1B is expressed variably in many human tissues, and the tissue-specific levels observed parallel those for HUS1. A HUS1-RAD1-RAD9 protein complex is thought to form a proliferating cell nuclear antigen (PCNA)-like structure, important for cell cycle checkpoint function. However, HUS1B directly interacts with RAD1, but not RAD9 or HUS1, whereas HUS1 can bind RAD1, RAD9, and another molecule of HUS1, suggesting that HUS1B cannot simply substitute for HUS1 in the complex. HUS1B is less conserved evolutionarily than HUS1. Furthermore, overexpression of HUS1B but not HUS1 in human cells induces clonogenic cell death. We suggest that HUS1B and HUS1 have distinct but related roles in regulating cell cycle checkpoints and genomic integrity.

Amino Acid Sequence↗
PubMed2000

Periodic accumulation of cdc15 mRNA is not necessary for septation in Schizosaccharomyces pombe.

Analysis of Schizosaccharomyces pombe mutants that are defective in septum formation and cytokinesis has identified the product of the cdc15 gene as a key element in formation of a division septum. S. pombe cells lacking cdc15p function cannot assemble a functional medial ring, and do not make a division septum. cdc15 mRNA accumulates periodically during the cell cycle, peaking after entry into mitosis, and increased expression of the gene in G2-arrested cells can promote F-actin ring formation. Here, we have investigated the effects of mutations that block cell division upon the expression of cdc15 in synchronised cell populations, and analysed the expression of cdc15 when septum formation is induced by ectopic activation of the septation signalling network. We concluded the following: (i) the septation signalling network genes are not required for periodic accumulation of cdc15 mRNA; (ii) induction of septum formation in G2-arrested cells by activation of the septation signalling network does not result in accumulation of cdc15 mRNA, which is therefore not a prerequisite for septum formation; (iii) failure to turn off septum formation at the end of mitosis results in continued expression of cdc15; and (iv) periodic accumulation of cdc15 mRNA is mediated by a 97 bp region 5' to the mRNA start site.

Cell Cycle↗
PubMed2001

Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors.

The processes that take place during development and differentiation are directed through coordinated regulation of expression of a large number of genes. One such gene regulatory network provides cell cycle control in eukaryotic organisms. In this work, we have studied the structural features of the 5' regulatory regions of cell cycle-related genes. We developed a new method for identifying composite substructures (modules) in regulatory regions of genes consisting of a binding site for a key transcription factor and additional contextual motifs: potential targets for other transcription factors that may synergistically regulate gene transcription. Applying this method to cell cycle-related promoters, we created a program for context-specific identification of binding sites for transcription factors of the E2F family which are key regulators of the cell cycle. We found that E2F composite modules are found at a high frequency and in close proximity to the start of transcription in cell cycle-related promoters in comparison with other promoters. Using this information, we then searched for E2F sites in genomic sequences with the goal of identifying new genes which play important roles in controlling cell proliferation, differentiation and apoptosis. Using a chromatin immunoprecipitation assay, we then experimentally verified the binding of E2F in vivo to the promoters predicted by the computer-assisted methods. Our identification of new E2F target genes provides new insight into gene regulatory networks and provides a framework for continued analysis of the role of contextual promoter features in transcriptional regulation. The tools described are available at http://compel.bionet.nsc.ru/FunSite/SiteScan.html.

Animals↗
PubMed2002

The cyclin-dependent kinase inhibitors p19(Ink4d) and p27(Kip1) are coexpressed in select retinal cells and act cooperatively to control cell cycle exit.

Cyclin-dependent kinase inhibitors (cdki's), including p19(Ink4d) and p27(Kip1), mediate exit from the cell cycle. To determine the function of these cdki's in regulating neurogenesis, we examined retina from wild-type, Ink4d-null, and Ink4d/Kip1-double null animals. Ink4d was expressed in progenitors and select neurons in the mature retina. Ink4d-null retina showed an extended period of proliferation, followed by apoptosis. Colabeling for p19(Ink4d) and p27(Kip1) revealed that a subpopulation of cells expressed both inhibitors. Deletion of Ink4d and Kip1 resulted in continued proliferation that was synergistic. This hyperproliferation led to an increase in number of horizontal cells and differentiated neurons reentering the cell cycle. Deletion of Ink4d and Kip1 also exacerbated the retinal dysplasia observed in Kip1-null mice, which was shown to be partly dependent on p53. These data indicate that select retinal cells express both p19(Ink4d) and p27(Kip1) and that they act cooperatively to ensure cell cycle exit.

Amacrine Cells↗
PubMed1998

Genomic organization, 5' flanking enhancer region, and chromosomal assignment of the cell cycle gene, p55Cdc.

p55Cdc is a mammalian homologue of a family of cell cycle proteins from widely divergent species, which contains WD repeats and has been implicated in cell cycle-regulated ubiquitin-mediated proteolysis. p55Cdc is highly expressed in proliferating but not in differentiated or growth-arrested cells. The expression, phosphorylation, and degradation of this protein have been shown to be cell cycle-regulated. We analyzed a 5.3-kb genomic region that contains the entire rat p55Cdc gene. The gene contains 10 exons ranging in size from 97 to 373 bp. The promoter region has a TAT box, four E-box consensus sequences, and potential binding sites for cell cycle-specific transcription factors. In transient transfection assays, a construct containing a 1000-nucleotide p55Cdc promoter region upstream of the chloramphenicol acetyltransferase reporter gene demonstrated a 12-fold increase in transcriptional activity. Finally, using radiation hybrid mapping techniques, we localized this gene to the human chromosome, 9q13-21.

Animals↗
PubMed1995

Fission yeast sta mutations that stabilize an unstable minichromosome are novel cdc2-interacting suppressors and are involved in regulation of spindle dynamics.

Cytological observations have shown that the presence of unstable minichromosomes can delay progression through the early stages of mitosis in fission yeast (Schizosaccharomyces pombe), suggesting that such minichromosomes may provide a useful tool for examining the system that regulates the coordinated segregation of chromosomes. One such unstable minichromosome is a large circular minichromosome. We previously showed that the mitotic instability of this minichromosome is probably due to the frequent occurrence of catenated forms of DNA after replication. To identify genes involved in the regulation of chromosome behavior in mitosis, we isolated mutants which stabilized this minichromosome. Three loci (sta1, sta2, and sta3) were identified. Two of them were found to be suppressors of temperature-sensitive mutations in cdc2, which encodes the catalytic subunit of muturation promoting factor (MPF). They show no linkage to, and are thus different from, suc1, and cdc13, previously identified as genes that interact with cdc2. The other mutation mapped to a gene previously identified as being required for the correct formation of the mitotic spindle. Data provided in this study suggest that the sta genes are involved in the regulation of spindle dynamics to ensure proper chromosome segregation during mitosis.

CDC2 Protein Kinase↗