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Biomedical subjects

Jan Oosting

Publications and source records attributed to Jan Oosting.

6 recordsLinked to original sources
PubMed2005

Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed, paraffin-embedded tumors using single nucleotide polymorphism arrays.

Most human cancers show genetic instabilities leading to allelic imbalances, including loss of heterozygosity (LOH). Single nucleotide polymorphism (SNP) arrays can be used to detect LOH. Currently, these arrays require intact genomic DNA as obtained from frozen tissue; however, for most cancer cases, only low-quality DNA from formalin-fixed, paraffin-embedded (FFPE) tissue is available. In this study, we tested Illumina BeadArrays to genotype FFPE tissue and detect LOH/allelic imbalances in matched colorectal tumor and normal tissue. Genotypes were compared between leukocyte and FFPE normal tissue as well as between frozen and FFPE tumor tissue. Identical genotypes and LOH profiles were obtained from normal and tumor isolates. LOH was mainly observed on chromosomes 4, 5q, 12q, 14q, 15q, 17p, 18, and 20p, which are commonly detected regions in colorectal cancer. LOH profiles of the BeadArrays were compared with profiles obtained by Affymetrix GeneChip 10K arrays, showing identical LOH patterns. These data show that genome-wide genotyping of FFPE tissue with the BeadArray gives reliable results and is a powerful technique for LOH analysis.

Colorectal Neoplasms↗
PubMed2005

Differential gene expression in ovarian tumors reveals Dusp 4 and Serpina 5 as key regulators for benign behavior of serous borderline tumors.

PURPOSE: Ovarian serous borderline tumors (SBT) are characterized by arborizing papillae lined by stratified epithelial cells, varying atypia, and absence of stromal invasion. Originally, these tumors have been classified as borderline because they behaved in a remarkably indolent manner, even with widespread tumor deposits called implants and the presence of lymph node involvement. The molecular biology of these lesions has just begun to be explored. High prevalence of B-RAF/K-RAS mutations in SBTs in contrast to serous carcinomas (SCAs) indicates that the mitogenic RAS-RAF-MEK-ERK-MAP kinase pathway is crucial for the pathogenesis of SBTs. The purpose of this study was to further unravel the genetic pathways through which SBTs develop, with a special focus on explaining the generally benign SBT behavior. MATERIALS AND METHODS: We generated RNA expression profiles of 38 ovarian serous neoplasms. Global Test pathway analysis and significance analysis of microarrays (SAM) of the expression profiles was performed. RESULTS: SAM and Global Testing showed that although the mitogenic pathway is activated in SBTs, activation of downstream genes involved in extracellular matrix (ECM) degradation is absent, suggesting an uncoupling of both events. In addition, we show that two genes involved in regulating this uncoupling, ERK-inhibitor Dusp 4 and uPA-inhibitor Serpina 5, are downregulated in SCAs in contrast to SBTs. In SCAs, this was associated with downstream MMP-9 activation at both mRNA and protein level. CONCLUSION: We propose that the putative tumor suppressor genes Dusp 4 and Serpina 5 provide a major clue to the indolent behavior of SBTs.

Dual-Specificity Phosphatases↗
PubMed2005

Substantial changes in gene expression of Wnt, MAPK and TNFalpha pathways induced by TGF-beta1 in cervical cancer cell lines.

Transforming growth factor-beta 1 (TGF-beta1) is a potent inhibitor of epithelial cell proliferation. During the development of cervical carcinoma however, an increase in production of TGF-beta1 is accompanied by decreased sensitivity for the growth-limiting effect of TGF-beta1. TGF-beta1 has an anti-proliferative effect on cells of the immune system and thus can be advantageous for tumor progression. The aim of the present study was to determine the effect of TGF-beta1 on mRNA expression profile of genes in pathways involved in cell growth and cell death, in cervical carcinoma cell lines with different sensitivity to TGF-beta1. For this purpose, we have investigated changes in gene expression in TGF-beta1 stimulated cervical cancer cell lines with high (CC10B), intermediate (SiHa) and low (HeLa) sensitivity to the anti-proliferative effect of TGF-beta1, at timepoints 0, 6, 12 and 24 h. Microarray analysis, using Affymetrics focus arrays, representing 8973 genes, was used to measure gene expression. In our study novel target genes involved in tumor necrosis factor alpha (TNFalpha), mitogen-activated protein kinase (MAPK) and wingless type (Wnt) pathways in response to TGF-beta1 were found. Substantial differences in gene expression between TGF-beta1 sensitive and insensitive cell lines were observed involving genes in TNFalpha, MAPK, Wnt and Smad pathways. Since these pathways are implicated in cell proliferation and cell death, these pathways may play a role in determining the overall sensitivity of a cell to TGF-beta1 induced cell growth inhibition. The results were subsequently validated by quantitative real-time PCR. Increased resistance to TGF-beta1 induced cell growth inhibition was correlated with an elevated production of TGF-beta1 by the cell lines, as measured by enzyme linked immunosorbent assay. TGF-beta1 production did not inhibit cell growth, since blocking TGF-beta1 protein by anti-TGF-beta had no effect on cell proliferation. TGF-beta1 excretion by tumor cells more likely contributes to paracrine stimulation of tumor development.

Base Sequence↗
PubMed2005

Testing association of a pathway with survival using gene expression data.

MOTIVATION: A recent surge of interest in survival as the primary clinical endpoint of microarray studies has called for an extension of the Global Test methodology to survival. RESULTS: We present a score test for association of the expression profile of one or more groups of genes with a (possibly censored) survival time. Groups of genes may be pathways, areas of the genome, clusters from a cluster analysis or all genes on a chip. The test allows one to test hypotheses about the influence of these groups of genes on survival directly, without the intermediary of single gene testing. The test is based on the Cox proportional hazards model and is calculated using martingale residuals. It is possible to adjust the test for the presence of covariates. We also present a diagnostic graph to assist in the interpretation of the test result, visualizing the influence of genes. The test is applied to a tumor dataset, revealing pathways from the gene ontology database that are associated with survival of patients. AVAILABILITY: The Global Test for survival has been incorporated into the R-package globaltest (version 3.0), available at http://www.bioconductor.org

Biomarkers, Tumor↗
PubMed2005

Multiplex ligation-dependent probe amplification for the detection of 1p and 19q chromosomal loss in oligodendroglial tumors.

Multiplex ligation-dependent probe amplification (MLPA) is a new assay for the detection of multiple chromosomal deletions in tumor tissue in a single experiment. Since genotyping of gliomas with oligodendroglial features by the detection of 1p/19q chromosomal deletions became essential for treatment decisions, we developed and validated an MLPA-based assay to determine these losses in formalin fixed and paraffin embedded oligodendroglial tumors (OG). Nineteen OGs, and 10 control samples were analyzed by MLPA and the results were correlated with those obtained by fluorescent in situ hybridization (FISH). The MLPA results were reproducible in all samples in which repeated experiments were performed. In 18 of 19 OGs, MLPA and FISH were concordant for presence or absence of 1p deletion. In 3 OGs, MLPA detected a 19q deletion not shown by FISH. For the other 15 OGs, MLPA and FISH were concordant. In one sample with 50% to 75% of tumor, MLPA failed to detect the 1p/19q deletions revealed by FISH (though with borderline values of significance). We conclude that MLPA is a valid and reproducible method for the detection of 1p/19q chromosomal deletions in OGs stored on formalin fixed, paraffin embedded tissue.

Brain Neoplasms↗