Biomedical subjects

Loris De Cecco

Publications and source records attributed to Loris De Cecco.

5 recordsLinked to original sources

PubMed2006

Regulation of lipocalin-2 gene by the cancer chemopreventive retinoid 4-HPR.

N-(4-Hydroxyphenyl)retinamide (4-HPR) is a nonclassical retinoid with cancer preventive effects in vivo and antiproliferative and apoptotic activities in vitro. Examining the transcriptional profile of human breast cancer cell lines, MCF7 and T47D, treated with 4-HPR, we identified the lipocalin member LCN2 (NGAL or 24p3) as a gene, markedly induced by the retinoid. Because of its presumed function in apoptosis, LCN2 was examined more thoroughly in response to 4-HPR. Like mRNA, the expression of LCN2 protein in MCF7 and T47D cells was highly induced in a time-dependent manner by 4-HPR, but not by its inactive metabolite 4-MPR and, to some extent, this event was linked to the free radicals normally generated by 4-HPR. All-trans retinoic acid also induced LCN2 protein, particularly in T47D cells. Ectopic LCN2 compromised cell viability, and the few MCF7 clones that survived LCN2 overexpression were less sensitive than do mock cells to 4HPR, indicating that selective pressure for survival to LCN2 confers cross-resistance to 4-HPR. Significantly, ablation of LCN2 induction by siRNA did not modify the response to 4-HPR, implying that LCN2 is not critical for apoptosis by 4-HPR. Our results indicate that 4-HPR markedly induces LCN2 expression, but this event may not represent an apoptotic response.

Acute-Phase Proteins↗

PubMed2005

Limits of predictive models using microarray data for breast cancer clinical treatment outcome.

Data from microarray studies have been used to develop predictive models for treatment outcome in breast cancer, such as a recently proposed predictive model for antiestrogen response after tamoxifen treatment that was based on the expression ratio of two genes. We attempted to validate this model on an independent cohort of 58 patients with resectable estrogen receptor-positive breast cancer. We measured expression of the genes HOXB13 and IL17BR with real time-quantitative polymerase chain reaction and assessed the association between their expression and outcome by use of univariate logistic regression, area under the receiver-operating-characteristic curve (AUC), a two-sample t test, and a Mann-Whitney test. We also applied standard supervised methods to the original microarray dataset and to another independent dataset from similar patients to estimate the classification accuracy obtainable by using more than two genes in a microarray-based predictive model. We could not validate the performance of the two-gene predictor on our cohort of samples (relation between outcome and the following genes estimated by logistic regression: for HOXB13, odds ratio [OR] = 1.04, 95% confidence interval [CI] = 0.92 to 1.16, P = .54; for IL17BR, OR = 0.69, 95% CI = 0.40 to 1.20, P = .18; and for HOXB13/IL17BR, OR = 1.30, 95% CI = 0.88 to 1.93, P = .18). Similar results were obtained with the AUC, a two-sample two-sided t test, and a Mann-Whitney test. In addition, estimates of classification accuracies applied to two independent microarray datasets highlighted the poor performance of treatment-response predictive models that can be achieved with the sample sizes of patients and informative genes to date.

Adult↗

PubMed2004

Gene expression profiling of advanced ovarian cancer: characterization of a molecular signature involving fibroblast growth factor 2.

Epithelial ovarian cancer (EOC) is the gynecological disease with the highest death rate. We applied an automatic class discovery procedure based on gene expression profiling to stages III-IV tumors to search for molecular signatures associated with the biological properties and progression of EOC. Using a complementary DNA microarray containing 4451 cancer-related, sequence-verified features, we identified a subset of EOC characterized by the expression of numerous genes related to the extracellular matrix (ECM) and its remodeling, along with elements of the fibroblast growth factor 2 (FGF2) signaling pathway. A total of 10 genes were validated by quantitative real-time polymerase chain reaction, and coexpression of FGF2 and fibroblast growth factor receptor 4 in tumor cells was revealed by immunohistochemistry, confirming the reliability of gene expression by cDNA microarray. Since the functional relationships among these genes clearly suggested involvement of the identified molecular signature in processes related to epithelial-stromal interactions and/or epithelial-mesenchymal cellular plasticity, we applied supervised learning analysis on ovarian-derived cell lines showing distinct cellular phenotypes in culture. This procedure enabled construction of a gene classifier able to discriminate mesenchymal-like from epithelial-like cells. Genes overexpressed in mesenchymal-like cells proved to match the FGF2 signaling and ECM molecular signature, as identified by unsupervised class discovery on advanced tumor samples. In vitro functional analysis of the cell plasticity classifier was carried out using two isogenic and immortalized cell lines derived from ovarian surface epithelium and displaying mesenchymal and epithelial morphology, respectively. The results indicated the autocrine, but not intracrine stimulation of mesenchymal conversion and cohort/scatter migration of cells by FGF2, suggesting a central role for FGF2 signaling in the maintenance of cellular plasticity of ovary-derived cells throughout the carcinogenesis process. These findings raise mechanistic hypotheses on EOC pathogenesis and progression that might provide a rational underpinning for new therapeutic modalities.

Cell Line, Tumor↗

PubMed2004

Alternative mutations of BRAF, RET and NTRK1 are associated with similar but distinct gene expression patterns in papillary thyroid cancer.

Papillary thyroid carcinoma (PTC) is associated with RET and NTRK1 rearrangements and BRAF mutations. A series of 60 PTCs collected in a single center from Italian patients were histologically re-examined and subclassified as well differentiated or tall cell variant. The sample collection was analysed for the presence of all the reported PTC-associated genetic alterations through DNA or cDNA amplification, followed by automated sequencing. The analysis of exons 11 and 15 of BRAF gene revealed the T1796A (V599E) mutation in 32% of cases, and this alteration is significantly associated with PTC tall cell variant. Oncogenic rearrangements of RET and NTRK1 receptors were found in 33 and 5% of cases, respectively. No Ras mutations were detected. Overall, genetic alterations were detected in two-thirds of samples, and in no single case more than one mutational event was found simultaneously. Gene expression profiling of a subset of 31 tumors performed using cDNA microarray chips showed no strong differences in global gene expression among the different cases. However, a supervised analysis of the obtained data identified a subset of genes differentially expressed in tumors carrying BRAF mutation or RTK rearrangement.

Adenocarcinoma, Papillary↗

PubMed2004

CTAB-urea method purifies RNA from melanin for cDNA microarray analysis.

Melanin represents a major problem for the study of melanoma by microarrays since it is retained during RNA extraction and inhibits the enzymatic reactions used for probe preparation. Here we report a new method for cleaning RNA from melanin, based on the use of the cationic detergent cetyl-trimethylammonium bromide (CTAB)-urea for RNA precipitation. This method is easy to perform and has a low cost. Purified RNA is recovered with high quality and good yield. CTAB-urea treated RNA from highly pigmented melanoma cells can be successfully reverse transcribed and labeled to obtain probes which can be subsequently used in cDNA microarray experiments, giving consistent and reproducible results.

Biotechnology↗