Biomedical subjects

David Cogdell

Publications and source records attributed to David Cogdell.

6 recordsLinked to original sources

PubMed2006

Transcriptional activation of the carboxylesterase 2 gene by the p53 pathway.

The p53 tumor suppressor is an important regulator of cellular response to chemotherapeutic agents by virtue of the protein's ability, upon activation by phosphorylation, to transcriptionally activate a number of genes involved in cell proliferation, apoptosis, and metabolism. Transcriptome analysis following introduction of a constitutively active form of p53 (p53T18D/S20D) into colon carcinoma cell lines identified transcriptional activation of the carboxylesterase 2 (CES-2) gene, which is involved in drug metabolism. We examined whether p53 activated by the DNA-damaging drug 5-fluorouracil (5-FU) also induces CES-2 expression. Our experiments showed that 5-FU induced CES-2 expression in two colon carcinoma cell lines that express wild-type p53 (HCT116 p53(+/+) and RKO) but not in five lines that are p53-null (HCT116 p53(-/- )) or express mutated p53 (HT29, KM12C, KM12SM, and KM12L4A). Sequence analysis revealed a putative p53-binding element in the first intron of CES-2 that differed from consensus by one nucleotide. A reporter gene assay showed that the luciferase construct with the p53-binding element responded to 5-FU treatment, whereas the reporter construct without the binding element did not. Chromatin immunoprecipitation assay confirmed that p53 bound the CES-2 fragment containing the p53-binding element after 5-FU treatment, whereas p21 binding to p53 was present with or without chemotherapy. Knockdown of expression of CES-2 and p53 by small interference RNA in RKO and HCT116 p53(+/+) cells attenuated the anti-proliferation effects of CPT11. These results taken together show that activated p53 directly regulates CES-2 expression via a p53-binding site, representing a novel mechanism through which the p53 pathway modulates drug metabolism. In addition, the degree of homology in the p53-binding element may determine the strength of p53 regulation.

Adenocarcinoma↗

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↗

PubMed2006

Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays.

The progression of gliomas has been extensively studied at the genomic level using cDNA microarrays. However, systematic examinations at the protein translational and post-translational levels are far more limited. We constructed a glioma protein lysate array from 82 different primary glioma tissues, and surveyed the expression and phosphorylation of 46 different proteins involved in signaling pathways of cell proliferation, cell survival, apoptosis, angiogenesis, and cell invasion. An analysis algorithm was employed to robustly estimate the protein expressions in these samples. When ranked by their discriminating power to separate 37 glioblastomas (high-grade gliomas) from 45 lower-grade gliomas, the following 12 proteins were identified as the most powerful discriminators: IBalpha, EGFRpTyr845, AKTpThr308, phosphatidylinositol 3-kinase (PI3K), BadpSer136, insulin-like growth factor binding protein (IGFBP) 2, IGFBP5, matrix metalloproteinase 9 (MMP9), vascular endothelial growth factor (VEGF), phosphorylated retinoblastoma protein (pRB), Bcl-2, and c-Abl. Clustering analysis showed a close link between PI3K and AKTpThr308, IGFBP5 and IGFBP2, and IBalpha and EGFRpTyr845. Another cluster includes MMP9, Bcl-2, VEGF, and pRB. These clustering patterns may suggest functional relationships, which warrant further investigation. The marked association of phosphorylation of AKT at Thr308, but not Ser473, with glioblastoma suggests a specific event of PI3K pathway activation in glioma progression.

Adult↗

PubMed2006

Recombinant human granulocyte-colony-stimulating factor-mobilized and apheresis-collected endothelial progenitor cells: a novel blood cell component for therapeutic vasculogenesis.

BACKGROUND: Endothelial progenitor cells (EPCs) have been identified among hematopoietic tissue-derived progenitor cells that are mobilized into the peripheral blood (PB) as a result of tissue injury. It therefore seems likely that circulating EPCs have therapeutic potential by aiding in the neovascularization of ischemic tissue. This study provides clinical data on the availability of circulating EPCs at steady state and after recombinant human granulocyte-colony-stimulating factor (rHuG-CSF) mobilization and their collection by leukapheresis. STUDY DESIGN AND METHODS: Eight healthy donors underwent rHuG-CSF treatment over 4 days, followed by leukapheresis. Blood samples taken before rHuG-CSF treatment and before apheresis as well as apheresis-collected samples were analyzed by flow cytometry and by real time reverse transcription-polymerase chain reaction for cells expressing EPC-specific surface markers and tissue markers, respectively, and for EPC colony-forming cells. RESULTS: The median PB concentration of CD34+133+ vascular endothelial growth factor receptor-2 (VEGFR-2)-+ EPCs increased 8-fold from steady state to mobilized, and the concentration of CD34+133-VEGFR-2+ EPCs increased by 10-fold. This mobilization pattern was similar to that of hematopoietic CD34+, CD133+, and CD34+117+ progenitor cells. The increase in the median circulating colony-forming unit EPC concentration was 10-fold over baseline. The median absolute number of CD34+133+VEGFR-2+ cells collected by large-volume leukapheresis was 0.8 x 10(6) per kg of body weight. In addition, a small subset of immature CD133+34- cells coexpressing VEGFR-2 was identified in mobilized PB and in the apheresis collection. EPC-specific cells contained in the apheresis product were also identified as expressing mRNA for the CD31 antigen, Tie-2, and VEGFR-2. CONCLUSION: Circulating EPCs represent a novel blood cell component that can be collected by apheresis in large quantities and can be used clinically, either unmanipulated or EPC-selected, for therapeutic vasculogenesis.

Adult↗

PubMed2005

Robust estimation of protein expression ratios with lysate microarray technology.

MOTIVATION: The protein lysate microarray is a developing proteomic technology for measuring protein expression levels in a large number of biological samples simultaneously. A challenge for accurate quantification is the relatively narrow dynamic range associated with the commonly used chromogenic signal detection system. To facilitate accurate measurement of the relative expression levels, each sample is serially diluted and each diluted version is spotted on a nitrocellulose-coated slide in triplicate. Thus, each sample yields multiple measurements in different dynamic ranges of the detection system. This study aims to develop suitable algorithms that yield accurate representations of the relative expression levels in different samples from multiple data points. RESULTS: We evaluated two algorithms for estimating relative protein expression in different samples on the lysate microarray by means of a cross-validation procedure. For this purpose as well as for quality control we designed a 1440-spot lysate microarray containing 80 identical samples of purified bovine serum albumin, printed in triplicate with six 2-fold dilutions. Our analysis showed that the algorithm based on a robust least squares estimator provided the most accurate quantification of the protein lysate microarray data. We also demonstrated our methods by estimating relative expression levels of p53 and p21 in either p53(+/+) or p53(-/-) HCT116 colon cancer cells after two drug treatments and their combinations on another lysate microarray. AVAILABILITY: http://www.cs.tut.fi/~mirceanc/lysate_array_bioinformatics.htm

Algorithms↗

PubMed2003

Data extraction from composite oligonucleotide microarrays.

Microarray or DNA chip technology is revolutionizing biology by empowering researchers in the collection of broad-scope gene information. It is well known that microarray-based measurements exhibit a substantial amount of variability due to a number of possible sources, ranging from hybridization conditions to image capture and analysis. In order to make reliable inferences and carry out quantitative analysis with microarray data, it is generally advisable to have more than one measurement of each gene. The availability of both between-array and within-array replicate measurements is essential for this purpose. Although statistical considerations call for increasing the number of replicates of both types, the latter is particularly challenging in practice due to a number of limiting factors, especially for in-house spotting facilities. We propose a novel approach to design so-called composite microarrays, which allow more replicates to be obtained without increasing the number of printed spots.

Gene Expression Profiling↗