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J Carl Barrett

Publications and source records attributed to J Carl Barrett.

At least 91 records · Page 5Linked to original sources
PubMed2003

Microarrays: the use of oligonucleotides and cDNA for the analysis of gene expression.

Completion of the human genome sequence has made it possible to study the expression of the entire human gene complement (>30,000 estimated genes). Aiding in this remarkable feat, DNA microarrays have become the main technological workhorse for gene expression studies. To date, detection platforms for most microarrays have relied on short (25 base) oligonucleotides synthesized in situ, or longer, highly variable length DNAs from PCR amplification of cDNA libraries. A third choice, long (50-80 base) oligonucleotide arrays, is now available and might eventually eliminate the use of cDNA arrays. The technology has advanced to such a point that researchers now demand microarrays that are cost-effective and have flexibility and quality assurance. Short- and long-oligonucleotide technologies offer such advantages, and could possibly become the major competing platform in the near future.

Animals↗
PubMed2003

Identification of a </= 600-kb region on human chromosome 1q42.3 inducing cellular senescence.

The introduction of a human chromosome 1 via microcell-mediated chromosome transfer (MMCT) induces the cellular senescence in mouse melanoma B16-F10 cells. The senescent cells maintained still the telomerase activity, which is frequently associated with immortal growth of human cells, suggesting that a telomerase-independent mechanism is involved in the senescence observed in this mouse cell line. To map the senescence-inducing gene to a specific chromosomal region, we took two experimental approaches: identification of a minimal region with the senescence-inducing activity via MMCT of a series of subchromosomal transferrable fragments (STFs), each consisting of a different profile of human chromosome 1-derived regions, and identification of a region commonly deleted from the transferred chromosome 1 in the revertant clones that escaped cellular senescence. These approaches identified a 2.7-3.0 Mb of senescence-inducing region shared among the active STFs and a 2.4-3.0 Mb of commonly deleted region in the revertant clones. These two regions overlapped each other to map the responsible gene at the 450 to 600-kb interval between UniSTS93710 and D1S3542 on chromosome 1q42.3. This study provides essential information and materials for cloning and characterization of a novel senescence-inducing gene that functions in a telomerase-independent pathway, which is likely to be conserved between mice and humans.

Animals↗
PubMed2003

Microarray analysis reveals distinct gene expression profiles among different histologic types of endometrial cancer.

Previous studies of oncogene and tumor suppressor gene alterations have suggested that differences exist in the molecular pathogenesis of the various histological types of endometrial cancer. To elucidate further the molecular events involved in endometrial carcinogenesis, we examined global expression patterns of 16 nonendometrioid cancers (13 serous papillary and 3 clear cell), 19 endometrioid cancers, and 7 age-matched normal endometria using cDNA microarrays. Unsupervised analysis of gene expression identified 191 genes that exhibited >2-fold differences (P < 0.001) between the histological groups. Many genes were similarly dysregulated in both nonendometrioid and endometrioid cancers relative to normal endometria. Gene expression differences in only 24 transcripts could distinguish serous from endometrioid cancers, the two most common subgroups. These data provide the basis for investigation of previously unrecognized novel pathways involved in the development of endometrial cancers.

Endometrial Neoplasms↗
PubMed2003

Human chromosome 5 carries a putative telomerase repressor gene.

Telomerase, the ribonucleoprotein enzyme that maintains the telomere, is active in human germ and stem cells and in a majority of tumor tissues and immortalized cell lines. In contrast, telomerase activity is not detected in most somatic cells, suggesting that normal human cells contain a regulatory factor(s) to repress this activity. To identify which human chromosomes carry a gene or genes that function as telomerase repressors, we investigated telomerase activity in hybrids of the B16-F10 cell line, which contain individual human chromosomes transferred previously by microcell fusion and therefore represent a hybrid panel for the entire genome except for the Y chromosome. Microcell hybrids with an introduced normal human chromosome 5 showed inhibition of telomerase activity, but clones at a late passage exhibited reactivation of telomerase activity. Reactivation of telomerase activity was accompanied by deletion and/or rearrangement of the transferred human chromosome 5. The introduction of other human chromosomes did not significantly affect the telomerase activity of B16-F10 cells. The effect of suppression of telomerase activity in microcell hybrids containing chromosome 5 was accompanied by a reduction in the level of mTERT mRNA, which encodes a component of the telomerase complex. The putative telomerase repressor gene was mapped to human chromosome bands 5p11-p13 by a combination of functional analysis using transfer of subchromosomal transferable fragments of chromosome 5 into B16-F10 cells and deletion mapping of revertant clones with reactivated telomerase activity. Thus, these results suggest that loss of a gene(s) on this chromosome was responsible for telomerase reactivation, indicating that human chromosome 5 contains a gene or genes that can regulate the expression of mTERT in B16-F10 cells.

Animals↗
PubMed2003

Neonatal diethylstilbestrol exposure induces persistent elevation of c-fos expression and hypomethylation in its exon-4 in mouse uterus.

Perinatal exposure to diethylstilbestrol (DES) induces reproductive tract cancers later in life in both humans and animals. Because there is no clear evidence that perinatal DES exposure induces gene mutation, we proposed that perinatal DES exposure causes epigenetic methylation changes that result in persistent alterations in gene expression, leading to tumorigenesis. The proto-oncogene c-fos is one of the immediately induced genes in uterine epithelium after estrogen simulation and a key player in uterine carcinogenesis. Here, we investigated c-fos expression in mice neonatally exposed to DES (2 microg/pup/day on postnatal days 1-5). The mRNA levels of c-fos in uteri of neonatal DES-treated mice were persistently 1.4-1.9-fold higher than that in the control mice from day 5 to day 60. Overall, the uterine c-fos expression level in the neonatal DES-exposed group was significantly higher than that in the control group. After examination of the methylation status of the c-fos gene, we found that the CpGs in promoter and intron-1 regions were completely unmethylated. In exon-4, from day 17 to day 60, the percentage of unmethylated CpGs was higher in neonatal DES-exposed mice uteri than that in control (42%, 51%, 47%, and 42% in DES-exposed mice vs 33%, 34%, 33%, and 21% in control mice at day 17, 21, 30, and 60, respectively). These results suggest that perinatal DES exposure may permanently alter gene expression and methylation, and the methylation modification may occur in either the promoter regions or other regulatory sites in the gene.

Animals↗
PubMed2003

DNA hypomethylation and imbalanced expression of DNA methyltransferases (DNMT1, 3A, and 3B) in human uterine leiomyoma.

OBJECTIVE: Despite the high prevalence of uterine leiomyoma in women, little is known about the pathophysiology of this tumor. This study intends to define the epigenetic modulation of this tumor. METHODS: Twenty-three pairs of leiomyomas and their adjacent myometria were collected. Status of DNA global methylation was determined by using DNA methyl acceptance assay and immunohistochemistry staining with 5-methylcytidine antibody. MRNA level of DNA methyltransferases (DNMT1, 3A, and 3B) was assessed by quantitative real time PCR. RESULTS: DNA global hypomethylation was detected in the leiomyoma tissues as compared with the adjacent myometria. DNMT1 expression was increased in 47.5% and was equal in 47.5% in leiomyomas compared to the adjacent myometria. On the other hand, over 74% of cases showed decreased expression of DNMT3A and 3B in leiomyomas compared to the adjacent myometria. CONCLUSION: Global hypomethylation and imbalanced expression of DNMTs in uterine leiomyoma suggested a potential mechanism of epigenetic modulation in the development of this tumor.

DNA (Cytosine-5-)-Methyltransferase 1↗
PubMed2003

Candidate chromosomal regions for genes involved in activation of alternative lengthening of telomeres in human immortal cell lines.

Either telomerase or alternative mechanisms known as alternative lengthening of telomeres (ALT) are activated in human immortal cells to maintain or lengthen their telomeres. To screen candidate chromosomes harboring gene(s) involved in activation of the telomere maintenance mechanisms that are repressed in normal, mortal cells and lost in immortal cells, we examined loss of heterozygosity (LOH) on the 22 autosomes and the X chromosome in 22 in vitro established human immortal cell lines consisting of 9 telomerase-positive cell lines and 13 ALT-positive cell lines. For detecting LOH, PCR analysis was performed with 66 polymorphic microsatellite markers from candidate genomic regions previously implicated for putative human senescence genes, telomerase repressor genes, or tumor suppressor genes. LOH involving chromosome 8 was observed at 25 of 62 (40%) informative loci in 8 of 13 (61%) ALT-positive cell lines. Particularly, when assayed with D8S339 adjacent to the Werner's syndrome gene, LOH was found in 6 of 12 (50%) informative ALT-positive cell lines. In contrast, no LOH on chromosome 8 was detected at 41 informative loci in any of 9 telomerase-positive cell lines. No other chromosomes showed high frequencies of LOH common in either ALT-positive or telomerase-positive cell lines. Although further LOH analysis with additional markers remains to define the specific region on chromosome 8, our results suggest that gene(s) involved in activation of the ALT pathway in human immortal cell lines may localize on chromosome 8.

Cell Line, Transformed↗
PubMed2003

Effect of exogenous epidermal-like growth factors on mammary gland development and differentiation in the estrogen receptor-alpha knockout (ERKO) mouse.

The development of the mouse mammary gland requires the interaction between several different ovarian and pituitary hormones such as estrogen, progesterone and prolactin as well as several locally-derived growth factors in the mammary gland such as epidermal growth factor (EGF), transforming growth factor alpha (TGFalpha), amphiregulin (AR) and heregulin (HRG). The focus of this study was to investigate the degree of mammary growth and differentiation in the adult, virgin mammary gland of wild type (wt) and estrogen receptor knockout (ERKO) females that lack estrogen receptor alpha (ERalpha) after reciprocal transplantation into the cleared mammary fat pad of virgin wt or ERKO mice. In addition, we assessed the local response of ERKO mammary tissue to TGFalpha or HRGbeta1 delivered from slow release-Elvax pellets. Our initial results indicated that when we transplanted virgin wt mammary tissue into ERKO mammary fat pads, mammary morphogenesis failed to occur. However, when transplanted virgin ERKO mammary tissue was transplanted into fat pads of virgin or pregnant wt mice, the development and differentiation of lobuloalveoli was readily observed. In addition, treatment of the virgin ERKO mammary gland with TGFalpha or HRGbeta1 stimulated ducts to undergo localized branching and growth and both growth factors induced secretory differentiation as evidenced by the production of milk proteins, caseins and/or whey acidic protein (WAP). The results from this study imply that in ERKO mammary tissue. ERKO ductal epithelium has the capacity to proliferate and differentiate in response to non-estrogenic, morphogenic stimuli.

Animals↗
PubMed2003

Segments missing from the draft human genome sequence can be isolated by transformation-associated recombination cloning in yeast.

The reported draft human genome sequence includes many contigs that are separated by gaps of unknown sequence. These gaps may be due to chromosomal regions that are not present in the Escherichia coli libraries used for DNA sequencing because they cannot be cloned efficiently, if at all, in bacteria. Using a yeast artificial chromosome (YAC)/ bacterial artificial chromosome (BAC) library generated in yeast, we found that approximately 6% of human DNA sequences tested transformed E. coli cells less efficiently than yeast cells, and were less stable in E. coli than in yeast. When the ends of several YAC/BAC isolates cloned in yeast were sequenced and compared with the reported draft sequence, major inconsistencies were found with the sequences of those YAC/BAC isolates that transformed E. coli cells inefficiently. Two human genomic fragments were re-isolated from human DNA by transformation-associated recombination (TAR) cloning. Re-sequencing of these regions showed that the errors in the draft are the results of both missassembly and loss of specific DNA sequences during cloning in E. coli. These results show that TAR cloning might be a valuable method that could be widely used during the final stages of the Human Genome Project.

Cell Adhesion Molecules↗
PubMed2003

Immortal, telomerase-negative cell lines derived from a Li-Fraumeni syndrome patient exhibit telomere length variability and chromosomal and minisatellite instabilities.

Five immortal cell lines derived from a Li-Fraumeni syndrome patient (MDAH 087) with a germline mutant p53 allele were characterized with respect to telomere length and genomic instability. The remaining wild-type p53 allele is lost in the cell lines. Telomerase activity was undetectable in all immortal cell lines. Five subclones of each cell line and five re-subclones of each of the subclones also showed undetectable telomerase activity. All five immortal cell lines exhibited variability in the mean length of terminal restriction fragments (TRFs). Subclones of each cell line, and re-subclones of the subclones also showed TRF variability, indicating that the variability is owing to clonal heterogeneity. Chromosome aberrations were observed at high frequencies in these cell lines including the subclones and re-subclones, and the principal types of aberrations were breaks, double minute chromosomes and dicentric chromosomes. In addition, minisatellite instability detected by DNA fingerprints was observed in the immortal cell lines. However, all of the cell lines were negative for microsatellite instability. As minisatellite sequences are considered recombinogenic in mammalian cells, these results suggest that recombination rates can be increased in these cell lines. Tumor-derived human cell lines, HT1080 cells and HeLa cells that also lack p53 function, exhibited little genomic instability involving chromosomal and minisatellite instabilities, indicating that chromosomal and minisatellite instabilities observed in the immortal cell lines lacking telomerase activity could not result from loss of p53 function.

Cell Line, Transformed↗
PubMed2003

Environmental exposure, DNA methylation, and gene regulation: lessons from diethylstilbesterol-induced cancers.

DNA methylation is an epigenetic mechanism that regulates chromosomal stability and gene expression. Abnormal DNA methylation patterns have been observed in many types of human tumors, including those of the breast, prostate, colon, thyroid, stomach, uterus, and cervix. We and others have shown that exposure to a wide variety of xenobiotics during critical periods of mammalian development can persistently alter the pattern of DNA methylation, resulting in potentially adverse biological effects such as aberrant gene expression. Thus, this epigenetic mechanism may underlie the observed increased risk in adulthood of several chronic diseases, including cancer, in response to xenobiotic exposures early in life. We present here the lessons learned from studies on the effects of perinatal diethylstilbesterol (DES) exposure on the methylation pattern of the promoters of several estrogen-responsive genes associated with the development of reproductive organs. Perinatal DES exposure, which induces epithelial tumors of the uterus in mice and is associated with several reproductive tract abnormalities and increased vaginal and cervical cancer risk in women, provides a clear example of how estrogenic xenobiotic exposure during a critical period of development can abnormally demethylate DNA sequences during organ development and possibly increase cancer risk later in life. In addition, nutritional factors and stress may also alter DNA methylation during early life and modulate the risk of cancer and other chronic diseases in adulthood. We suggest that DNA methylation status may be influenced by environmental exposures in early life, leading to increased risk of cancer in adulthood.

Animals↗
PubMed2003

Promoter hypermethylation as an epigenetic component in Type I and Type II endometrial cancers.

Epigenetic mechanisms that result in aberrant gene expression are a prominent feature of many cancer types. One main epigenetic mechanism for gene silencing involves promoter hypermethylation. Type I and type II endometrial cancers exhibit differing clinical, histologic, and molecular genetic characteristics. We hypothesize that these differences also extend to epigenetic phenomena. Promoter methylation analysis of 11 genes in a panel of endometrial cancers supports this hypothesis. These initial data indicate that promoter hypermethylation events occur frequently in type 1 cancer and were not detected in type II cancers using this panel of loci. These data tend to support the hypothesis that type I and type II endometrial cancers will exhibit distinct patterns of gene silencing based on promoter hypermethylation events.

Cell Transformation, Neoplastic↗
PubMed2003

Microarray analysis and identification of novel molecules involved in insulin-like growth factor-1 receptor signaling and gene expression.

The insulin receptor (IR) and the insulin-like growth factor-1 receptor (IGF-1R) are members of the same subfamily of receptor tyrosine kinases. The two receptors phosphorylate many of the same substrates and activate the same signaling modules, including the mitogen-activated protein kinase (MAPK) and phosphatidyl inositol 3' kinase (PI3K) signaling pathways. Although the IR and IGF-1R share some redundant functions in metabolism, cell growth, differentiation, and apoptosis, they also exhibit distinct physiological roles. Some of these may be due to differences in tissue distribution, receptor structure, formation of hybrid receptors, or mechanisms of ligand binding. However, the divergent effects of insulin and IGF-1 also may be explained by specificity in the intracellular signals generated by insulin and IGF-1. In particular, the IR and IGF-1R are capable of triggering their own biological responses by using specific or preferential substrates, molecular adapters, or signaling pathways. In a recent study, we used cDNA microarray analysis to identify genes differentially regulated by insulin and IGF-1. Mouse NIH-3T3 fibroblasts expressing either the wild-type human IGF-1R or IR were stimulated with either IGF-1 or insulin, respectively. We identified 39 genes differentially regulated by insulin and IGF-1. Most of these genes had not been reported previously to be responsive to insulin or IGF-1. The genes induced by IGF-1 generally were involved in mitogenesis or differentiation, while the genes found to be induced by insulin did not conform to any particular category. In a separate study, immortalized breast epithelial cells were stimulated with IGF-1 and a cDNA microarray analysis was used to generate a profile of IGF-1-regulated genes. A number of genes known to be involved in angiogenesis were found to be regulated by IGF-1. These results strongly suggest that this technology may be extremely useful in identifying groups of genes that are specifically regulated by different ligands and their activated receptors.

Animals↗
PubMed2003

Phosphatidylinositol 3-kinase and mek1/2 are necessary for insulin-like growth factor-I-induced vascular endothelial growth factor synthesis in prostate epithelial cells: a role for hypoxia-inducible factor-1?

Due to the importance of vascular endothelial growth factor (VEGF) in the neovascularization of solid tumors, a clear understanding of how VEGF is regulated in normal and tumor cells is warranted. We investigated insulin-like growth factor (IGF)-I-stimulated signaling pathways that increase the rate of VEGF synthesis in primary cultures of normal prostate epithelial cells (PrEC). IGF-I increased the secretion of VEGF(165) into PrEC growth medium and stimulated transcription of a reporter gene driven by a 1.5-kb region of the VEGF promoter. Inhibition of either phosphatidylinositol 3-kinase (PI3-K) or Mek1/2 signaling pathways completely abrogated the IGF-I-induced increase in VEGF secretion and promoter activity, indicating a dependence on coordinate signaling from both pathways to produce this effect. Levels of the transcription factors hypoxia-inducible factor (HIF)-1 and Fos were elevated in response to IGF-I in a PI3-K-dependent and Mek1/2-dependent manner, respectively. The expression of an activator protein (AP)-1 dominant negative in an immortalized prostate epithelial cell line PZ-HPV-7 suppressed the IGF-I-induced increase in VEGF promoter activity. Mutation of the hypoxia response element (HRE), which mediates hypoxic stimulation of VEGF transcription, did not inhibit the effect of IGF-I on the VEGF promoter, despite the fact that this mutation inhibited PI3-K-stimulated VEGF promoter activity in prostate cancer cells. These data indicate that PI3-K signaling does not increase VEGF transcription through transactivation by HIF-1 at the HRE in normal PrEC. This work also suggests that an additional signal, not stimulated by IGF-I in PrEC, is needed for HIF-1 to stimulate transcription from the VEGF HRE.

Cell Line↗
PubMed2003

Linking laboratory and clinical research: the development of molecularly targeted therapeutics inside the national cancer institute center for cancer research.

Understanding the molecular basis of the pathways regulating the cancer cell promises to revolutionize clinical practice. The results of genomic- an proteomic-based studies at the National Cancer Center Institute Center for Cancer Research (NCI CCR) include the indentation of a molecular biomarker for ovarian cancer based on serum proteomic patterns that permits early detection and a new method for the diagnostic and prognostic assessment of subclasses of diffuse large B-cell lymphoma based on molecular criteria. The biological informativeness of molecularly based diagnostic categories confers the additional clinical advantage of identifying molecular pathways that can be selectively targeted for treatment. Molecular profiling of clear cell renal carcinoma, eg, has revealed that it responds to antiangiogenic agents. Moreover, targeted immunomodulatory interventions are proving effective against many cancers. The discovery and development of molecularly based means for detecting, diagnosis, and treating cancer are central priorities of the NCI CCR, which provides an interactive environment encouraging multidisciplinary collaborations, especially among basic and clinical investigators. Its infrastructure supports the iterative flow of information from the bench to the bedside and from the bedside to the bench, expediting the delivery of molecularly based therapeutics to cancer patients.

Antineoplastic Agents↗
PubMed2002

Tumor-specific activation of hTERT-derived promoters by tumor suppressive E1A-mutants involves recruitment of p300/CBP/HAT and suppression of HDAC-1 and defines a combined tumor targeting and suppression system.

Adenovirus (Ad) E1A proteins are transcriptional regulators with antioncogenic but also transforming properties. We have previously shown that transformation-defective Ad5 E1A-derivatives are excellent tumor suppressors. For tumor-specific expression of the E1A-derivatives we intend to use tumor specific human telomerase reverse transcriptase (hTERT) core promoters. Here, we show that Spm2 and other E1A proteins with an intact amino terminus activated all hTERT constructs 10-20-fold in malignant tumor cells but not in primary fibroblasts, without affecting the activity of endogenous telomerase. The transcription rate in tumor cells was in the range of transcription from the SV40 promoter, which qualifies an E1A-hTERT system as a putative tumor targeting/expression system. The activation of the hTERT promoter by E1A was enhanced upon deletion of the Wilms' tumor 1 negative regulatory element and maintained high after deletion of the adjacent c-Myc-responsive E-box, demonstrating an important role of the remaining sequences that contain several Sp1-motifs. E1A-mediated hTERT activation was independent from the presence of the conserved region 3 (CR3) of E1A but dependent on E1A's binding to p300/CBP and recruitment of its histone acetyltransferase activity. Moreover, E1A-Spm2 and histone deacetylase-1 behaved as antagonists with respect to the regulation of transcription from the hTERT promoter. Overall, hTERT promoter/E1A-Spm2 systems may turn out to be excellent tools for transcriptionally targeted anticancer gene therapy.

Adenovirus E1A Proteins↗