Biomedical subjects

Valerie Dunmire

Publications and source records attributed to Valerie Dunmire.

9 recordsLinked to original sources

PubMed2006

The SHREW1 gene, frequently deleted in oligodendrogliomas, functions to inhibit cell adhesion and migration.

Allelic loss of the short arm of chromosome 1 has been observed frequently in oligodendroglioma (60-80%). We evaluated 177 oligodendroglial tumor samples and defined a consensus region of deletion of approximately 630 kb. This region contains a single gene, SHREW1, which encodes a novel transmembrane protein in adherens junctions. Whereas a mutation was not detected in the coding region of the SHREW1 gene in oligodendrogliomas, restoration of SHREW1 expression resulted in suppression of cell adhesion and migration. Thus, SHREW1 inactivation may play a role in the development of oligodendroglial tumors.

Cell Adhesion↗

PubMed2005

Analysis of angiogenesis using in vitro experiments and stochastic growth models.

The global properties of vascular networks grown with an in vitro angiogenesis assay are compared quantitatively, using automated image analysis, with the global properties of networks obtained with discrete, stochastic growth models. The model classes that are investigated are invasion percolation and diffusion limited aggregation. By matching global properties to experimental data, one can infer which model classes and parameters are most reflective of angiogenesis in experimental cells. This sheds light on large-scale emergent properties of angiogenesis from a systems perspective. It is found that invasion percolation is better than diffusion limited aggregation at matching experimental data. We also present evidence that the distribution of the lengths of real tubule complexes follows a power law.

Animals↗

PubMed2005

Attenuated expression of DFFB is a hallmark of oligodendrogliomas with 1p-allelic loss.

Allelic loss of chromosome 1p is frequently observed in oligodendroglioma. We screened 177 oligodendroglial tumors for 1p deletions and found 6 tumors with localized 1p36 deletions. Several apoptosis regulation genes have been mapped to this region, including Tumor Protein 73 (p73), DNA Fragmentation Factor subunits alpha (DFFA) and beta (DFFB), and Tumor Necrosis Factor Receptor Superfamily Members 9 and 25 (TNFRSF9, TNFRSF25). We compared expression levels of these 5 genes in pairs of 1p-loss and 1p-intact tumors using quantitative reverse-transcriptase PCR (QRTPCR) to test if 1p deletions had an effect on expression. Only the DFFB gene demonstrated decreased expression in all tumor pairs tested. Mutational analysis did not reveal DFFB mutations in 12 tested samples. However, it is possible that DFFB haploinsufficiency from 1p allelic loss is a contributing factor in oligodendroglioma development.

Chromosomes, Human, Pair 1↗

PubMed2005

In silico microdissection of microarray data from heterogeneous cell populations.

BACKGROUND: Very few analytical approaches have been reported to resolve the variability in microarray measurements stemming from sample heterogeneity. For example, tissue samples used in cancer studies are usually contaminated with the surrounding or infiltrating cell types. This heterogeneity in the sample preparation hinders further statistical analysis, significantly so if different samples contain different proportions of these cell types. Thus, sample heterogeneity can result in the identification of differentially expressed genes that may be unrelated to the biological question being studied. Similarly, irrelevant gene combinations can be discovered in the case of gene expression based classification. RESULTS: We propose a computational framework for removing the effects of sample heterogeneity by "microdissecting" microarray data in silico. The computational method provides estimates of the expression values of the pure (non-heterogeneous) cell samples. The inversion of the sample heterogeneity can be facilitated by providing accurate estimates of the mixing percentages of different cell types in each measurement. For those cases where no such information is available, we develop an optimization-based method for joint estimation of the mixing percentages and the expression values of the pure cell samples. We also consider the problem of selecting the correct number of cell types. CONCLUSION: The efficiency of the proposed methods is illustrated by applying them to a carefully controlled cDNA microarray data obtained from heterogeneous samples. The results demonstrate that the methods are capable of reconstructing both the sample and cell type specific expression values from heterogeneous mixtures and that the mixing percentages of different cell types can also be estimated. Furthermore, a general purpose model selection method can be used to select the correct number of cell types.

Algorithms↗

PubMed2005

Robust quantification of in vitro angiogenesis through image analysis.

An automated image analysis method for quantification of in vitro angiogenesis is presented. The method is designed for in vitro angiogenesis assays that are based on co-culturing endothelial cells with fibroblasts. Such assays are used in many current studies in which anti-angiogenic agents for the treatment of cancer are being sought. This search requires accurate quantification of the stimulatory and inhibitory effects of the different agents. The quantification method gives lengths and sizes of the tubule complexes as well as the numbers of junctions in each of them. The method is tested with a set of test images obtained with a commercially available in vitro angiogenesis assay. The results correctly indicate the inhibitory effect of suramin and the stimulatory effect of vascular endothelial growth factor. Moreover, the image analysis method is shown to be robust against variations in illumination. We have implemented a software package that utilizes the methods. The software as well as a set of test images are available at http://www.cs.tut.fi/sgn/csb/angioquant/.

Algorithms↗

PubMed2004

Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis.

BACKGROUND: Metastatic disease is a major adverse prognostic factor in breast carcinoma. Lymph node metastases often represent the first step in the metastatic process. METHODS: To gain insight into the molecular events that underlie breast carcinoma metastasis, the authors compared gene expression profiles, obtained by cDNA microarray analysis, of nine matched primary tumors and metastases after screening for enrichment of tumor cells. Statistical analysis identified genes that are expressed at elevated or decreased levels in metastases relative to the corresponding primary tumors. Multidimensional scaling analysis indicated that in terms of expression levels, primary tumors were tightly clustered, whereas metastases exhibited a greater spread; this finding points to the more heterogeneous nature of metastases. Among the differentially expressed entities were the invasion- and tissue modeling-related genes IGFBP5, fibronectin, and MMP2; the cell cycle regulatory gene cyclin D1; other genes, such as enolase 2; and an expressed sequence tag similar to angiopoietin 1. To validate and extend these initial findings, the authors constructed a tissue microarray consisting of 100 primary malignancies paired with their lymph node metastases. Antibodies for the IGFBP-5, fibronectin, MMP-2, cyclin D1, and MDM-2 proteins were used to stain tissue array sections. RESULTS: Consistent with microarray data, statistically significant overexpression of IGFBP-5, down-regulation of cyclin D1, and unchanged MDM-2 levels were observed in metastatic tumor cells. Nonetheless, although fibronectin and MMP2 mRNA expression levels were decreased in many metastasis specimens, expression levels of the corresponding proteins in the extracellular matrix were elevated in most metastases. Decreased expression of fibronectin and MMP2 in lymph node metastases was further confirmed by real-time polymerase chain reaction assays performed on five additional specimen pairs. CONCLUSIONS: The results of the current study suggest that extracellular matrix protein expression and nuclear gene expression are associated via a negative-feedback regulatory mechanism. Therefore, gene expression profiling and tissue array validation should be combined to elucidate molecular events associated with the metastatic process.

Breast Neoplasms↗

PubMed2002

Clonal heterogeneity in mycosis fungoides and its relationship to clinical course.

Mycosis fungoides (MF) is a cutaneous T-cell lymphoma characterized by multifocal disease and protracted clinical course. The few studies that have assessed T-cell receptor (TCR) gene rearrangements (GRs) present at different anatomic sites in MF have generally reported a common clone. We used a previously validated 4-color polymerase chain reaction (PCR) assay to assess the size and V-family usage of TCR-gamma GRs in 102 concurrent and/or sequential morphologically involved biopsy specimens (91 skin and 11 lymph nodes) from 39 MF patients. This assay detected TCR-gamma clonal GRs in 89 samples (87%) from 36 patients (92%). In 24 patients (77%), an identical clonal GR was present in at least 2 skin samples. However, in one third of these patients, additional different clonal GRs were also noted. Four patients (13%) had clonal GRs that were distinct in different skin samples. In 3 patients (10%), no GR was detected in any sample. In a comparison of lymph node and skin samples, 8 patients had the identical clonal GRs at both sites, 2 patients had different clonal GRs, and 1 patient had no GR identified at either site. Independent of clinical stage, patients who had the same GR detected in multiple concurrent biopsy specimens at the time of diagnosis were more likely to have progressive disease than those who had different GRs (P =.04). Four-color TCR-gamma PCR analysis can uncover multiple distinct clonal GRs in different samples consistent with multiclonal or oligoclonal disease in a significant proportion of MF patients. Demonstration of identical clonal GRs in multiple biopsy specimens at the time of diagnosis may provide prognostic information related to disease progression.

Adolescent↗

PubMed2002

Increased yield of total RNA from fine-needle aspirates for use in expression microarray analysis.

Fine-needle aspirate samples hold the potential for gaining valuable insight into the molecular details and prognostic indicators for certain types of cancer in a limited volume of relatively pure tumor cells. Although limited, such clinical samples can be used with high efficiency when analyzed in conjunction with gene-dense expression microarrays. For this reason, it is essential to retrieve as much high-quality genetic material as possible from each fine-needle aspirate sample. We have conducted a study to improve the efficiency of extracting high quality total RNA to use in microarray analysis from single ex vivo fine-needle aspirate samples of 11 breast cancers added to RNAlater RNA Stabilization Reagent immediately upon collection. Approximately half the total RNA from fine-needle aspirate samples of breast cancers was isolated from the supernatant, and that RNA had similar quality and gene expression profile to the RNA that was isolated from the corresponding cell pellet. We recommend that the supernatant not be discarded when extracting RNA from fine-needle aspirate samples stored in RNAlater.

Biopsy, Needle↗

PubMed1999

Genetic suppression analysis of an asgA missense mutation in Myxococcus xanthus.

The asgA gene is required for generation of extracellular A signal, which serves as a cell-density signal for fruiting body development in Myxococcus xanthus. The AsgA protein is a histidine protein kinase and consists of a receiver domain that is conserved among response regulators of two-component signal transduction systems, followed by a histidine protein kinase domain that is conserved among sensor proteins of two-component systems. AsgA is thought to function in a signal transduction pathway that leads to expression of genes required for A-signal generation. A genetic suppression analysis of an asgA missense mutation was undertaken in order to identify genes that may provide information regarding the role of AsgA in A-signal generation and fruiting body formation. Twenty-two independent strains containing mutations that suppress asgA473 were isolated by selecting for production of heat-resistant spores under conditions that promote fruiting body development in wild-type cells. Ten of the 22 suppressor strains contained bypass suppressors. All the suppressor strains had direct spore counts at least three to four times greater than the original asgA473 mutant, and three strains had viable counts that exceeded wild-type by more than one order of magnitude. Surprisingly, none of the suppressor strains produced wild-type levels of extracellular A-signal.

Bacterial Proteins↗