PubMed Health⌕ Search

Biomedical subjects

Paula M Vertino

Publications and source records attributed to Paula M Vertino.

10 recordsLinked to original sources
PubMed2006

Infrequent mutation of ATBF1 in human breast cancer.

Deletion at chromosome 16q is frequent in prostate and breast cancers, suggesting the existence of one or more tumor suppressor genes in 16q. Recently, the transcription factor ATBF1 at 16q22 was identified as a strong candidate tumor suppressor gene in prostate cancer, and loss of ATBF1 expression was associated with poorer prognosis in breast cancer. In the present study, we examined mutation, expression, and promoter methylation of ATBF1 in 32 breast cancer cell lines. Only 2 of the 32 cancer cell lines had mutations, although 18 nucleotide polymorphisms were detected. In addition, 24 of 32 (75%) cancer cell lines had reduced ATBF1 mRNA levels, yet promoter methylation was not involved in gene silencing. These findings suggest that ATBF1 plays a role in breast cancer through transcriptional downregulation rather than mutations.

Breast Neoplasms↗
PubMed2006

LKB1 mutation in large cell carcinoma of the lung.

Germline inactivation of LKB1 is responsible for Peutz-Jeghers syndrome, an autosomal dominant disorder characterized by benign hamartomas of the GI tract and an increased predisposition to certain cancers, including lung. Acquired mutations in LKB1 are rarely observed in most sporadic tumor types except for adenocarcinomas of the lung where up to 50% harbor inactivating mutations. In this study, we focused on LKB1 mutations in lung cancer cell lines originating from large cell carcinomas. We identified a novel 1.5kb interstitial deletion within LKB1 gene in H157 cancer cells. Homozygosity mapping-of-deletion analysis (HOMOD) analysis showed that the deletion is accompanied by LOH of one parental allele, indicating biallelic inactivation of LKB1. This deletion results in an LKB1 transcript lacking exons 2 and 3 and a predicted in-frame deletion of 58 amino acids within the kinase domain of the LKB1 protein. The truncated transcript was expressed at relatively low levels, and the truncated LKB1 protein was virtually undetectable in this cell line. To determine the impact of LKB1 protein truncation on its function, we examined AMPK-alpha, a downstream target of LKB1 kinase activity triggered by low energy stress conditions. Phosphorylation of AMPK-alpha was attenuated in H157 cells treated with 2-deoxyglucose, and could be rescued by expression of an exogenous GFP-LKB1 fusion protein. Therefore, our data suggest that LKB1 function is compromised in H157. Of the four cell lines and six primary tumors of large cell lung carcinoma origin that have been evaluated in this and other studies, LKB1 mutations have been found in three cases. These results suggest that, in addition to adenocarcinomas, acquired loss of function mutations in LKB1 may also be frequently involved in the pathogenesis of large cell lung carcinomas.

AMP-Activated Protein Kinase Kinases↗
PubMed2006

Restoration of tamoxifen sensitivity in estrogen receptor-negative breast cancer cells: tamoxifen-bound reactivated ER recruits distinctive corepressor complexes.

Breast tumors expressing estrogen receptor-alpha (ER) respond well to therapeutic strategies using selective ER modulators, such as tamoxifen. However, approximately 30% of invasive breast cancers are hormone independent because they lack ER expression due to hypermethylation of ER promoter. Treatment of ER-negative breast cancer cells with demethylating agents [5-aza-2'-deoxycytidine (5-aza-dC)] and histone deacetylase (HDAC) inhibitors (trichostatin A) leads to expression of ER mRNA and functional protein. Here, we examined whether epigenetically reactivated ER is a target for tamoxifen therapy. Following treatment with trichostatin A and 5-aza-dC, the formerly unresponsive ER-negative MDA-MB-231 breast cancer cells became responsive to tamoxifen. Tamoxifen-mediated inhibition of cell growth in these cells is mediated at least in part by the tamoxifen-bound ER. Tamoxifen-bound reactivated ER induces transcriptional repression at estrogen-responsive genes by ordered recruitment of multiple distinct chromatin-modifying complexes. Using chromatin immunoprecipitation, we show recruitment of two different corepressor complexes to ER-responsive promoters in a mutually exclusive and sequential manner: the nuclear receptor corepressor-HDAC3 complex followed by nucleosome remodeling and histone deacetylation complex. The mechanistic insight provided by this study might help in designing therapeutic strategies directed toward epigenetic mechanisms in the prevention or treatment of breast cancer.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed2006

DNA motifs associated with aberrant CpG island methylation.

Epigenetic silencing involving the aberrant methylation of promoter region CpG islands is widely recognized as a tumor suppressor silencing mechanism in cancer. However, the molecular pathways underlying aberrant DNA methylation remain elusive. Recently we showed that, on a genome-wide level, CpG island loci differ in their intrinsic susceptibility to aberrant methylation and that this susceptibility can be predicted based on underlying sequence context. These data suggest that there are sequence/structural features that contribute to the protection from or susceptibility to aberrant methylation. Here we use motif elicitation coupled with classification techniques to identify DNA sequence motifs that selectively define methylation-prone or methylation-resistant CpG islands. Motifs common to 28 methylation-prone or 47 methylation-resistant CpG island-containing genomic fragments were determined using the MEME and MAST algorithms (). The five most discriminatory motifs derived from methylation-prone sequences were found to be associated with CpG islands in general and were nonrandomly distributed throughout the genome. In contrast, the eight most discriminatory motifs derived from the methylation-resistant CpG islands were randomly distributed throughout the genome. Interestingly, this latter group tended to associate with Alu and other repetitive sequences. Used together, the frequency of occurrence of these motifs successfully discriminated methylation-prone and methylation-resistant CpG island groups with an accuracy of 87% after 10-fold cross-validation. The motifs identified here are candidate methylation-targeting or methylation-protection DNA sequences.

Algorithms↗
PubMed2004

Aberrant methylation and down-regulation of TMS1/ASC in human glioblastoma.

TMS1/ASC is an intracellular signaling molecule with proposed roles in the regulation of apoptosis, nuclear factor-kappaB activation, and cytokine maturation. Previous studies have shown that TMS1/ASC is silenced by epigenetic means in human breast tumors. In this study, we examined methylation and expression of TMS1/ASC in glioblastoma multiforme (GBM). Whereas normal brain tissue was unmethylated at the TMS1 locus and expressed TMS1 message, 11 of 23 human GBM cell lines exhibited reduced or absent expression of TMS1 that was associated with aberrant methylation of a CpG island in the promoter of the TMS1 gene. Quantitative analysis showed that there was an inverse correlation between the degree of methylation and level of TMS1 expression. Treatment of GBM cell lines lacking TMS1 expression with the methyltransferase inhibitor 5-aza-2'deoxycytidine resulted in partial demethylation and re-expression of TMS1. Analysis of primary tissues indicated that the TMS1 gene is unmethylated and expressed in normal brain, where its expression is restricted to astrocytes. In contrast, TMS1 was aberrantly methylated in 43% (10 of 23) primary GBM specimens. Tumors that exhibited aberrant methylation of TMS1 generally expressed reduced or absent expression of TMS1 as compared to unmethylated cases. Methylation of TMS1 was not associated with patient age, gender, or treatment status. Although the relationship did not reach statistical significance, there was a trend toward increased overall survival for patients with unmethylated tumors. For one patient, disease progression from astrocytic astrocytoma (World Health Organization grade III) to GBM (World Health Organization grade IV) was associated with selective expansion of TMS1-negative cells. The data suggest a role for the epigenetic silencing of TMS1 in the pathogenesis of human GBM. Methylation of TMS1 may prove to be a useful prognostic marker and/or predictor of patient survival and tumor malignancy.

Biomarkers, Tumor↗
PubMed2003

Effects of methylation on expression of TMS1/ASC in human breast cancer cells.

Gene silencing associated with aberrant methylation of promoter region CpG islands is one mechanism in which tumor suppressor genes are inactivated in human cancers. Recently, we identified a novel gene, Target of Methylation-associated Silencing-1 (TMS1) (also called ASC), which is aberrantly methylated and silenced in human breast cancers. To further investigate the mechanism of TMS1 silencing, we defined the transcription initiation site and detailed the DNA methylation pattern of the TMS1 CpG island in normal breast epithelial cells, breast cancer cell lines, and primary tumors. We find that in normal cells, the TMS1 CpG island lies within a 1.2 kb unmethylated domain, the 5' boundary of which is in close proximity to the transcription initiation site. In breast cancer cell lines, this boundary appeared to be unstable in that methylation tended to accumulate in the 5' end of the CpG island relative to normal epithelial cells. In contrast, the 3' methylation boundary remained intact. Gene silencing was not correlated with the methylation of specific CpG sites nor the inability to transactivate the TMS1 promoter, but was correlated with the percentage of alleles in the population exhibiting dense methylation across the entire CpG island. Using 5-aza-deoxycytidine to reactivate TMS1 in methylated and silent cell lines, and a cassette methylation strategy to determine the impact of methylation on different parts of the promoter, we find that demethylation of a small region immediately surrounding the transcription start site is critical to TMS1 expression. Our data support the idea that gene silencing and dense methylation are tightly coupled events that affect individual chromosomal copies of TMS1 in an all-or-none manner. The transition to this stably repressed state may be facilitated by spreading of methylation into the proximal promoter and direct effects of methylation on TMS1 transcription.

Breast Neoplasms↗
PubMed2001

Methylation-mediated silencing of TMS1/ASC is accompanied by histone hypoacetylation and CpG island-localized changes in chromatin architecture.

Aberrant methylation of CpG-dense islands in the promoter regions of genes is an acquired epigenetic alteration associated with the silencing of tumor suppressor genes in human cancers. In a screen for endogenous targets of methylation-mediated gene silencing, we identified a novel CpG island-associated gene, TMS1, which is aberrantly methylated and silenced in response to the ectopic expression of DNA methyltransferase-1. TMS1 functions in the regulation of apoptosis and is frequently methylated and silenced in human breast cancers. In this study, we characterized the methylation pattern and chromatin architecture of the TMS1 locus in normal fibroblasts and determined the changes associated with its progressive methylation. In normal fibroblasts expressing TMS1, the CpG island is defined by an unmethylated domain that is separated from densely methylated flanking DNA by distinct 5' and 3' boundaries. Analysis of the nucleoprotein architecture of the locus in intact nuclei revealed three DNase I-hypersensitive sites that map within the CpG island. Strikingly, two of these sites coincided with the 5'- and 3'-methylation boundaries. Methylation of the TMS1 CpG island was accompanied by loss of hypersensitive site formation, hypoacetylation of histones H3 and H4, and gene silencing. This altered chromatin structure was confined to the CpG island and occurred without significant changes in methylation, histone acetylation, or hypersensitive site formation at a fourth DNase I-hypersensitive site 2 kb downstream of the TMS1 CpG island. The data indicate that there are sites of protein binding and/or structural transitions that define the boundaries of the unmethylated CpG island in normal cells and that aberrant methylation overcomes these boundaries to direct a local change in chromatin structure, resulting in gene silencing.

Acetylation↗
PubMedDate not supplied

DNMT1 is a component of a multiprotein DNA replication complex.

DNA methylation is a major determinant of epigenetic inheritance and plays an important role in genome stability. The accurate propagation of DNA methylation patterns with cell division requires that methylation be closely coupled to DNA replication, however the precise molecular determinants of this interaction have not been defined. In the present study, we show that the predominant DNA methyltransferase species in somatic cells, DNMT1, is a component of a multiprotein DNA replication complex termed the DNA synthesome that fully supports semi-conservative DNA replication in a cell-free system. DNMT1 protein and activity were found to co-purify with the human DNA synthesome through a series of subcellular fractionation and chromatography steps, resulting in an enrichment of methyltransferase specific activity from two human cell lines. DNA methyltransferase activity co-eluted with in vitro replication activity and DNA polymerase alpha activity on sucrose density gradients suggesting that DNMT1 is a tightly bound, core component of the replication complex. The synthesome-associated pool of DNA methyltransferase exhibited both maintenance and de novo methyltransferase activity and the ratio of the two was similar to that observed in whole cell lysates and for recombinant DNMT1. These data indicate that interactions within the synthesome complex do not influence the intrinsic preference of DNMT1 for hemimethylated DNA, but suggest that newly replicated DNA may be subject to low level de novo methylation. The data indicate that DNA methylation is tightly coupled to replication through physical interaction of DNMT1 and core components of the replication machinery. The definition of the molecular interactions between DNMT1 and other proteins in the replication complex in normal and neoplastic cells will provide further insight into the regulation of DNA methylation and the mechanisms underlying the alteration of DNA methylation patterns during carcinogenesis.

Cell Division↗