Tumor necrosis factor-α related gene response to Epothilone B in ovarian cancer

Cancer Drug Sensitivity Prediction Based on Deep Transfer Learning

In recent years, many approved drugs have been discovered using phenotypic screening, which elaborates the exact mechanisms of action or molecular targets of drugs. Drug susceptibility prediction is an important type of phenotypic screening. Large-scale pharmacogenomics studies have provided us with large amounts of drug sensitivity data. By analyzing these data using computational methods, we can effectively build models to predict drug susceptibility. However, due to the differences in data distribution among databases, researchers cannot directly utilize data from multiple sources. In this study, we propose a deep transfer learning model. We integrate the genomic characterization of cancer cell lines with chemical information on compounds, combined with the Encyclopedia of Cancer Cell Lines (CCLE) and the Genomics of Cancer Drug Sensitivity (GDSC) datasets, through a domain-adapted approach and predict the half-maximal inhibitory concentrations (IC50 values). Afterward, the validity of the prediction results of our model is verified. This study effectively addresses the challenge of cross-database distribution discrepancies in drug sensitivity prediction by integrating multi-source heterogeneous data and constructing a deep transfer learning model. This model serves as a reliable computational tool for precision drug development. Its widespread application can facilitate the optimization of therapeutic strategies in personalized medicine while also providing technical support for high-throughput drug screening and the discovery of new drug targets.

Therapeutic potential of patupilone in epithelial ovarian cancer and future directions

Ovarian cancer is the most lethal gynecologic malignancy worldwide with extremely poor patient prognosis. Elucidation of the detailed mechanisms of action of drugs targeting this cancer type is necessary to optimize treatment efficacy. Epothilones, a new class of microtubule-stabilizing anticancer drugs, show strong cytotoxic properties in vitro and in vivo and are additionally effective in taxane-resistant cells. In this report, we focus on inhibitors of microtubule depolymerization, taxanes, and the novel antimicrotubule agents, epothilones. Current knowledge regarding the effects of epothilone B on ovarian tumor cell metabolism is reviewed, along with recent advances in therapeutic strategies, such as novel agents and biologic drug combinations containing epothilone that target aberrant pathways in ovarian cancer.

Effect of epothilone B on cell cycle, metabolic activity, and apoptosis induction on human epithelial cancer cells-under special attention of combined treatment with ionizing radiation

In recent studies, epothilone B was shown to have a cytotoxic and radiosensitizing effect on cells. The aim of our investigation was to explain this impact by examining the mode of action of epothilone B on FaDu and A549 tumor cells. Flow cytometry was used for cell cycle distribution and for the evaluation of apoptosis. Metabolic activity was studied by proliferation assay. Influence on nuclei morphology was investigated by DNA-staining. We showed that epothilone B-induced G2/M accumulation is the main rationale for drug-induced radiosensitivity. The cytotoxic effect resulted in apoptotic cell death, decreased metabolic activity, and formation of multinucleated cells.

The effects of the histone deacetylase inhibitor romidepsin (FK228) are enhanced by aspirin (ASA) in COX-1 positive ovarian cancer cells through augmentation of p21

Histone deacetylase (HDAC) inhibitors have shown preclinical efficacy in solid tumors, including ovarian cancers. Our group has published that the HDAC inhibitor, romidepsin (FK228) suppresses ovarian cancer cell growth at nanomolar concentrations in vitro. HDAC inhibitors appear to be even more effective when used in combination with other antitumor agents. However, it remains unclear which antitumor agents are best suited for combination therapy. A recent report suggested that aspirin (acetylsalicylic acid, ASA ) is synergistic with HDAC inhibitors in ovarian cancer cells. ASA is a relatively selective inhibitor of cyclooxygenase-1 (COX-1) and has anti-proliferative effects in ovarian cancer cells. The goal of this study was to investigate the impact of ASA on the activity of the HDAC inhibitor, FK228 in COX-1 positive (OVCAR-3) and COX-1 negative (SKOV-3) human ovarian cancer cell lines. The growth inhibitory effects of FK228 were enhanced by ASA in COX-1 positive ovarian cancer cells. In contrast, ASA had no influence on the results of FK228 treatment in COX-1 negative ovarian cancer cells. Upregulation of the cell cycle control protein p21 was induced robustly by FK228 in both cell lines. In the COX-1 positive cells, p21 expression was augmented by the addition of ASA to FK228 treatment. Furthermore, COX-1 siRNA attenuated the effects of combined ASA and FK228 on the levels of p21 expression and the amount of growth inhibition. The additional increase in p21 by ASA in FK228-treated cells was not observed at the promoter or transcriptional levels. However, a significant delay in p21 protein degradation in the presence of ASA and FK228 in COX-1 positive cells was associated with inhibition of proteasome activity. Our study provides a potential rationale for combining ASA with HDAC inhibitors in a subset of ovarian cancers.

The efficacy and safety of ixabepilone monotherapy in the treatment of breast and gynecologic malignancies

Ixabepilone is a semisynthetic analogue of epothilone B, a novel microtubule-stabilizing agent. Preclinical data suggest that its mechanisms of actions are different from those of the most commonly used microtubule-stabilizing agent, paclitaxel. This information in addition to the cytotoxicity of this drug in taxane-resistant cell lines in multiple solid tumors supports the fact that ixabepilone may be active in taxane-resistant tumors. Breast and gynecologic malignancies are leading causes of morbidity and mortality in women. Clinical studies demonstrate significant activity of ixabepilone monotherapy in these heavily pretreated patients. The toxicity profile of ixabepilone seems to be similar to that of taxanes and manageable by supportive methods.

Safety and efficacy of patupilone in patients with advanced ovarian, primary fallopian, or primary peritoneal cancer: a phase I, open-label, dose-escalation study

PURPOSE To evaluate the safety, maximum tolerated dose (MTD), and pharmacokinetics of patupilone administered once every 3 weeks with proactive standardized diarrhea management in patients with resistant or refractory ovarian, fallopian, or peritoneal cancer. PATIENTS AND METHODS Patients received patupilone (6.5 to 11.0 mg/m(2)) every 3 weeks via 20-minute infusion. Adverse events, dose-limiting toxicities (DLT), MTD, and tumor response were determined. The tumor response was measured by Response Evaluation Criteria in Solid Tumors (RECIST) and cancer antigen 125 levels. Results Forty-five patients were enrolled. Adverse events were mild to moderate in intensity, and grade 3 diarrhea (13%) was the most commonly reported serious adverse event. Grade 3 peripheral neuropathy was noted in two patients (4%). Diarrhea, peripheral neuropathy, and fatigue were the most common DLTs; however, these were uncommon in the first cycle and the MTD was therefore not reached in this study. Overall response (OR; complete and partial responses; median cycles, 8) per RECIST in patients with measurable disease (n = 36) was 19.5%. Median duration of disease stabilization (complete and partial responses and stable disease) was 15.8 months. These results appear improved from a previous study in a similar patient population using a weekly schedule (2.5 mg/m(2)/week; N = 53; OR, 5.7%). CONCLUSION Patupilone once every 3 weeks was well-tolerated at doses up to 11.0 mg/m(2). Patupilone demonstrated promising antitumor activity in patients with drug-resistant/refractory disease. An ongoing phase III study in this patient population is testing the 10.0 mg/m(2) dose.

Gene-expression profiling in epithelial ovarian cancer

DNA-microarray technology has made it possible to simultaneously analyze the expression of thousands of genes in a small sample of tumor tissue. In epithelial ovarian cancer, gene-expression profiling has been used to provide prognostic information, to predict response to first-line platinum-based chemotherapy, and to discriminate between different histologic subtypes. Furthermore, DNA-microarray technology might permit identification of novel markers for early detection of disease and provide insights into the mechanisms of cancer growth and chemotherapy resistance. In this Review, we summarize the contributions of gene-expression profiling to the diagnosis and management of epithelial ovarian cancer and discuss ways in which this technique could become a useful tool in clinical management.

Molecular prognostic markers in ovarian cancer: toward patient-tailored therapy

In ovarian cancer the ceiling seems to be reached with chemotherapeutic drugs. Therefore a paradigm shift is needed. Instead of treating all patients according to standard guidelines, individualized molecular targeted treatment should be aimed for. This means that molecular profiles of the distinct ovarian cancer subtypes should be established. Until recently, most studies trying to identify molecular targets were single-marker studies. The prognostic role of key components of apoptotic and prosurvival pathways such as p53, EGFR, and HER2 has been extensively studied because resistance to chemotherapy is often caused by failure of tumor cells to go into apoptosis. However, it is more than likely that different ovarian cancer subtypes with extensive molecular heterogeneity exist. Therefore, exploration of the potential of specific tumor-targeted therapy, based on expression of a prognostic tumor profile, may be of interest. Recently, new profiling techniques, such as DNA and protein microarrays, have enabled high-throughput screening of tumors. In this review an overview of the current status of prognostic marker and molecular targeting research in ovarian cancer, including microarray studies, is presented.

Emerging issues of the expression profiling technologies for the study of gynecologic cancer

Evaluation of the prognostic parameters of gynecologic cancer has shown their failure for classification according to the clinical behavior or the prediction of its outcome. This weakness has important implications on prognosis and treatment. The increasing understanding of the complexity of the human genome, coupled with the development of high throughput analysis techniques and bioinformatics tools, has changed our concepts on cancer biology, by shifting our targets to a global analysis of the transcriptome and the proteome, linking genes and their products into functional pathways. These approaches permit the documentation of expression patterns of thousands of genes within a cell. With the use of DNA microarray technology, it is feasible to identify signature patterns of expression in tumor samples that faithfully correlate with its biology, providing accurate prognosis for each cancer patient and thus a rational customized treatment. At this stage, there is a need for systematic studies for the validation of these novel approaches. In this review, we provide a basic background of the concept of the technology, highlight several emerging issues from their applications on gynecologic cancer, discuss a series of important themes and problems regarding their interpretation and relevance for the clinicians, and comment on future areas of research.