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Biomedical subjects

Michael Ochs

Publications and source records attributed to Michael Ochs.

9 recordsLinked to original sources
PubMed2006

Pathway-specific differences between tumor cell lines and normal and tumor tissue cells.

BACKGROUND: Cell lines are used in experimental investigation of cancer but their capacity to represent tumor cells has yet to be quantified. The aim of the study was to identify significant alterations in pathway usage in cell lines in comparison with normal and tumor tissue. METHODS: This study utilized a pathway-specific enrichment analysis of publicly accessible microarray data and quantified the gene expression differences between cell lines, tumor, and normal tissue cells for six different tissue types. KEGG pathways that are significantly different between cell lines and tumors, cell lines and normal tissues and tumor and normal tissue were identified through enrichment tests on gene lists obtained using Significance Analysis of Microarrays (SAM). RESULTS: Cellular pathways that were significantly upregulated in cell lines compared to tumor cells and normal cells of the same tissue type included ATP synthesis, cell communication, cell cycle, oxidative phosphorylation, purine, pyrimidine and pyruvate metabolism, and proteasome. Results on metabolic pathways suggested an increase in the velocity nucleotide metabolism and RNA production. Pathways that were downregulated in cell lines compared to tumor and normal tissue included cell communication, cell adhesion molecules (CAMs), and ECM-receptor interaction. Only a fraction of the significantly altered genes in tumor-to-normal comparison had similar expressions in cancer cell lines and tumor cells. These genes were tissue-specific and were distributed sparsely among multiple pathways. CONCLUSION: Significantly altered genes in tumors compared to normal tissue were largely tissue specific. Among these genes downregulation was a major trend. In contrast, cell lines contained large sets of significantly upregulated genes that were common to multiple tissue types. Pathway upregulation in cell lines was most pronounced over metabolic pathways including cell nucleotide metabolism and oxidative phosphorylation. Signaling pathways involved in adhesion and communication of cultured cancer cells were downregulated. The three way pathways comparison presented in this study brings light into the differences in the use of cellular pathways by tumor cells and cancer cell lines.

Biosynthetic Pathways↗
PubMed2003

EXAFS study of Sn(IV) immobilization by hardened cement paste and calcium silicate hydrates.

In this study, the immobilization mechanisms of Sn(IV) onto calcium silicate hydrates (C-S-H) and hardened cement paste (HCP) have been investigated by combining wet chemistry experiments with X-ray absorption spectroscopy (XAS). Evidence is presented which demonstrates the formation of a Sn(IV) inner-sphere surface complex on C-S-H with a CaO/SiO2 weight ratio of 0.7. Two possible structural models, implying a corner sharing between the Sn octahedra and Q1 or Q2b Si tetrahedra, have been developed based on the experimentally determined structural parameters. In HCP, the formation of a different type of Sn(IV) inner-sphere complex has been observed, indicating that C-S-H may not be the uptake-controlling phase for Sn(IV) in the cement matrix. An alternative structural model for Sn(IV) binding in HCP has been developed, assuming that ettringite is the uptake-controlling phase. At high Sn(IV) concentrations, Sn(IV) immobilization in HCP occurs due to the formation of CaSn(OH)6.

Calcium Compounds↗
PubMed2003

Sensitivity analysis of radionuclide migration in compacted bentonite: a mechanistic model approach.

Mechanistic model calculations for the migration of Cs, Ra, Am and Pb in compacted bentonite have been carried out to evaluate sensitivities with respect to different parameter variations. A surface chemical speciation/electric double layer model is used to calculate: (i) porewater composition and radionuclide speciation in solution and at the bentonite surface, yielding the distribution of mobile and sorbed species and (ii) interaction of diffusing species with negatively charged pore walls to obtain diffusion parameters. The basic scenario considers the interaction of compacted bentonite with a fresh-type groundwater; variations include the presence of bentonite impurities and saline groundwater. It is shown that these scenarios result in significant variations of porewater composition that affect migration via three mechanisms that can partly compensate each other: (1) effects on sorption through radionuclide complexation in solution, and competition of major cations for surface sites; (2) changes in radionuclide solution speciation leading to different diffusing species under different conditions; (3) effects on diffusion through changes in the electric double layer properties of the clay pores as a function of ionic strength.

Aluminum Silicates↗
PubMed2003

Response markers and the molecular mechanisms of action of Gleevec in gastrointestinal stromal tumors.

Gastrointestinal stromal tumors (GISTs), defined by the presence of constitutively activated KIT, are the most common gastrointestinal mesenchymal malignancies. This observation has been successfully exploited in clinical trials of Gleevec (also known as imatinib mesylate, STI-571) for patients with unresectable and/or metastatic GISTs. The biological mechanisms of Gleevec as well as its downstream molecular effects are generally unknown. We used a DNA microarray-based approach to identify gene expression patterns and signaling pathways that were altered in response to Gleevec in GIST cells. We identified a total of 148 genes or expressed sequence tags (of 10,367) that were differentially regulated; 7 known genes displayed a durable response after treatment. The significantly down-regulated genes were SPRY4A, FZD8, PDE2A, RTP801, FLJ20898, and ARHGEF2. The only up-regulated gene was MAFbx. On a functional level, we demonstrated that imatinib inhibited phosphorylation of KIT, AKT, and extracellular signal-regulated kinase 1/2 without affecting the total level of these proteins and that differential expression of these response genes involved activation of mitogen-activated protein kinase-dependent and -independent pathways. In an attempt to correlate these in vitro findings to clinical data, we examined GIST needle biopsy specimens taken from patients before and after Gleevec administration according to the CSTI571-B2222 Phase II trial and demonstrated that expression levels of the two gene transcripts evaluated correlated well with clinical response. This study emphasizes the potential value of an in vitro cell model to investigate GIST response to imatinib in vivo, for the purpose of identifying important genetic markers of clinical response, mechanisms of drug action, and possible therapeutic targets.

Antineoplastic Agents↗