Thymidylate synthase gene expression in solid tumors predicts for response to pemetrexed in vitro

2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 13058-13058 ◽  
Author(s):  
U. Eismann ◽  
O. Oberschmidt ◽  
M. Ehnert ◽  
J. Fleeth ◽  
F. Lüdtke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Statistical Tests ◽  
Human Tumor ◽  
Soft Agar ◽  
Expression Data ◽  
Glycinamide Ribonucleotide Formyltransferase ◽  
Cloning Assay ◽  
Thymidilate Synthase ◽  
Soft Agar Cloning

13058 Background: Pemetrexed (P) is a novel antifolate which targets thymidilate synthase (TS), dihydrofolate reductase (DHFR), and glycinamide ribonucleotide formyltransferase (GARFT). The aim of the present study was to identify gene expression thresholds for these enzymes in human tumor specimens in order to separate P-sensitive from P-resistant patients. Methods: Soft-agar cloning assays were performed on freshly biopsied tumor cells exposed one hour to clinically achievable concentrations of P. In parallel, RNA was isolated, transcribed to cDNA and subsequently used for multiplex real-time PCR. Gene expression data were normalized against beta-actin transcripts followed by correlation against cloning assay results. Iterative calculations (fourfold analysis) were done for each enzyme separately to find the best cutoff for prediction of sensitivity to P. Results: Sensitive and resistant tumor samples were statistically significant different in gene expression of TS, DHFR, and GARFT (p < 0.003). 81% of all tumors with a TS copy number < 144 (related to 104 copies β-actin) were sensitive to P in vitro. (specificity = 0.69; chi2 = 14.14). Statistical tests demonstrated that gene expression of TS, DHFR, and GARFT are dependent variables and that TS transcription is the leading variable. The combination of TS, DHFR, and GARFT expression data was not superior to TS alone. Conclusions: TS expression is the most meaningful predictor for sensitivity (≤ 144 copies) or resistance (> 144 copies) to Pemetrexed in fresh tumor tissue. This observation forms a rationale for clinical trials using TS expression as predictor for clinical response. No significant financial relationships to disclose.

In vitro chemosensitivity against enzastaurin correlates with gene expression of IL8 and GSK3-beta

2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 13046-13046 ◽  
Author(s):  
O. Oberschmidt ◽  
U. Eismann ◽  
M. M. Lahn ◽  
J. Fleeth ◽  
F. Lüdtke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Drug Exposure ◽  
Human Tumor ◽  
Rna Isolation ◽  
Expression Data ◽  
Gene Expressions ◽  
In Vitro Chemosensitivity ◽  
Pkc Β

13046 Background: Enzastaurin (E) is an active antitumoral agent which selectively inhibits the β-isoform of protein kinase C (PKC-β). The compound blocks the enzyme’s ATP-binding site and signal transmission is abrogated resulting in the inhibition of neovascularization. The aim of the present study was to correlate gene expression with in vitro chemosensitivity of freshly explanted human tumor specimens. Such correlations in tumors taken directly from patients will help to rationally design subsequent clinical trials. Methods: Soft-agar colony forming assays were performed on freshly biopsied tumor cells exposed to various concentrations of E. Corresponding pieces of tumor specimens were shock-frozen and prepared for RNA isolation and cDNA generation followed by multiplex real-time PCR experiments. Gene expression data were correlated against cloning assay results. Results: Gene expression data of PKC-β1, PKC-β2, IL8RA, IL8RB, IL8, GSK3-β, and TGF-β were correlated against in vitro chemosensitivity pattern of E from 66 samples. After 1h-drug exposure gene expressions in sensitive versus resistant specimens were statistically significant with p = 0.013 for IL8 [median copy number (mcn): 1881 vs. 694; n = 66] and p = 0.012 for GSK3-beta (mcn: 1.6 vs. 7.0; n = 66). No correlation was detected for PKC-β1, PKC-β2, IL8RA, and IL8RB. Detection of TGF-β failed in most samples. Conclusions: Low expression of GSK3-β and high expression of IL8 correlate statistically significantly with increased in vitro sensitivity to E in freshly explanted human tumors. These findings may help direct further clinical development of this compound. No significant financial relationships to disclose.

Ultrastructural Correlations between Clonal Human Tumor Colonies and in Vivo Neoplasms

1982 ◽  
Vol 40 ◽  
pp. 210-211
Author(s):  
M.J. Murphy ◽  
R.R. Price ◽  
J.C. Sloman
Keyword(s):  
Cultured Cells ◽  
Human Tumor ◽  
Cell Type ◽  
Tumor Mass ◽  
Initial Cell ◽  
Cloning Assay ◽  
Human Tumor Cloning ◽  
The Relationship

The in vitro human tumor cloning assay originally described by Salmon and Hamburger has been applied recently to the investigation of differential anti-tumor drug sensitivities over a broad range of human neoplasms. A major problem in the acceptance of this technique has been the question of the relationship between the cultured cells and the original patient tumor, i.e., whether the colonies that develop derive from the neoplasm or from some other cell type within the initial cell population. A study of the ultrastructural morphology of the cultured cells vs. patient tumor has therefore been undertaken to resolve this question. Direct correlation was assured by division of a common tumor mass at surgical resection, one biopsy being fixed for TEM studies, the second being rapidly transported to the laboratory for culture.

scholarly journals Predicting Host Immune Cell Dynamics and Key Disease-Associated Genes Using Tissue Transcriptional Profiles

Processes ◽  
2019 ◽  
Vol 7 (5) ◽  
pp. 301
Author(s):  
Muying Wang ◽  
Satoshi Fukuyama ◽  
Yoshihiro Kawaoka ◽  
Jason E. Shoemaker
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Immune Cell ◽  
Mean Squared Error ◽  
Expression Profiles ◽  
Statistical Tests ◽  
Critical Factor ◽  
Expression Data ◽  
Cell Dynamics ◽  
Cell Counts

Motivation: Immune cell dynamics is a critical factor of disease-associated pathology (immunopathology) that also impacts the levels of mRNAs in diseased tissue. Deconvolution algorithms attempt to infer cell quantities in a tissue/organ sample based on gene expression profiles and are often evaluated using artificial, non-complex samples. Their accuracy on estimating cell counts given temporal tissue gene expression data remains not well characterized and has never been characterized when using diseased lung. Further, how to remove the effects of cell migration on transcript counts to improve discovery of disease factors is an open question. Results: Four cell count inference (i.e., deconvolution) tools are evaluated using microarray data from influenza-infected lung sampled at several time points post-infection. The analysis finds that inferred cell quantities are accurate only for select cell types and there is a tendency for algorithms to have a good relative fit (R 2 ) but a poor absolute fit (normalized mean squared error; NMSE), which suggests systemic biases exist. Nonetheless, using cell fraction estimates to adjust gene expression data, we show that genes associated with influenza virus replication and increased infection pathology are more likely to be identified as significant than when applying traditional statistical tests.

In vitro gene expression data supporting a DNA non-reactive genotoxic mechanism for ochratoxin A

2007 ◽  
Vol 220 (2) ◽  
pp. 216-224 ◽  
Author(s):  
Leire Arbillaga ◽  
Amaia Azqueta ◽  
Joost H.M. van Delft ◽  
Adela López de Cerain
Keyword(s):  
Gene Expression ◽  
Ochratoxin A ◽  
Gene Expression Data ◽  
Expression Data

In vitro activity of menogaril and N-demethylmenogaril in a human tumor cloning assay

1986 ◽  
Vol 22 (3) ◽  
pp. 245-249 ◽  
Author(s):  
P. Dodion ◽  
C. Sanders ◽  
W. Rombaut ◽  
M. Rozencweig ◽  
M.M. Kitt ◽  
...  
Keyword(s):  
Human Tumor ◽  
Vitro Activity ◽  
In Vitro Activity ◽  
Cloning Assay ◽  
Human Tumor Cloning

scholarly journals Transformation of NIH 3T3 fibroblasts by an activated form of p59hck.

1989 ◽  
Vol 9 (6) ◽  
pp. 2724-2727 ◽  
Author(s):  
S F Ziegler ◽  
S D Levin ◽  
R M Perlmutter
Keyword(s):  
Tyrosine Kinases ◽  
Soft Agar ◽  
Protein Tyrosine Kinases ◽  
3T3 Fibroblasts ◽  
Family Protein ◽  
Cloning Assay ◽  
Transforming Activity ◽  
Nih 3T3 ◽  
Soft Agar Cloning ◽  
Phenylalanine Residue

Phosphorylation of a tyrosine residue near the carboxy terminus of src-family protein tyrosine kinases is believed to regulate the biological activity of these gene products. Conversion of this tyrosine in p59hck (Tyr-501) to a phenylalanine residue by using oligonucleotide-directed mutagenesis yielded a product (p59hckF501) with very potent transforming activity. Quantitative analysis by a soft-agar cloning assay revealed that p59hckF501 was more than 100-fold more effective than a closely related transforming element, p56lckF505, in colony formation. Cells bearing p59hckF501 had increased levels of protein phosphotyrosine. The ability of p59hckF501 to transform NIH 3T3 cells was abolished by a second mutation believed to destroy the ATP-binding domain.

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