Using mRNA expression profiling to determine anticancer drug efficacy

Characterization of DNA reactive and non-DNA reactive anticancer drugs by gene expression profiling

Gene expression profiling technology is expected to advance our understanding of genotoxic mechanisms involving direct or indirect interaction with DNA. We exposed human lymphoblastoid TK6 cells to 14 anticancer drugs (vincristine, paclitaxel, etoposide, daunorubicin, camptothecin, amsacrine, cytosine arabinoside, hydroxyurea, methotrexate, 5-fluorouracil, cisplatin, 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea (CCNU), 1,3-bis (2-chloroethyl)-1-nitrosourea (BCNU), and bleomycin) for 4-h and examined them immediately or after a 20-h recovery period. Cytotoxicity and genotoxicity, respectively, were evaluated by cell counting and by in vitro micronucleus assay at 24h. Effects on the cell cycle were determined by flow cytometry at 4 and 24h. Gene expression was profiled at both sampling times by using human Affymetrix U133A GeneChips (22K). Bioanalysis was done with Resolver/Rosetta software and an in-house annotation program. Cell cycle analysis and gene expression profiling allowed us to classify the drugs according to their mechanisms of action. The molecular signature is composed of 28 marker genes mainly involved in signal transduction and cell cycle pathways. Our results suggest that these marker genes could be used as a predictive model to classify genotoxins according to their direct or indirect interaction with DNA.

Pharmacogenomics in lung cancer: an analysis of DNA repair gene expression in patients treated with platinum-based chemotherapy

Lung cancer is a worldwide epidemic and despite platinum-based chemotherapy being the cornerstone of non-small cell lung cancer treatment, patient response rates to these regimens remain very low. Although resistance to cisplatin is multifactorial, DNA repair plays a critical role in cisplatin resistance. One of the most important goals in translational research is to investigate the clinical use of DNA repair pathways that may influence cisplatin chemosensitivity. Trying to understand the role of genes involved in DNA repair and response to treatment has become one of the main objectives of individualised chemotherapy. It is well known that chemosensitivity is individually predetermined, and the upregulation of mRNA transcripts has been linked to differential response to cytotoxic drugs. In this article, the authors try to highlight the more relevant aspects regarding these issues, primarily focused on the potential role of ERCC1, RRM1, XPD and BRCA1 expression profiling as predictors of anticancer drug efficacy.

Breast cancer biomarkers

Substantial progress has been made over the past three decades in our understanding of the epidemiology, clinical course and basic biology of breast cancer. This chapter considers the existing ancillary tests and emerging molecular markers in breast cancer prognosis assessment and the prediction of response of breast cancer to treatment of the disease.

cDNA microarray analysis of differential gene expression in gastric cancer cells sensitive and resistant to 5-fluorouracil and cisplatin

PURPOSE

Gastric cancer is one of the most prevalent cancers worldwide. 5-fluorouracil (5-FU) and cisplatin are the most commonly used drugs for the treatment of gastric cancer. However, a significant number of tumors often fail to respond to chemotherapy.

MATERIALS AND METHODS

To better understand the molecular mechanisms underlying drug resistance in gastric cancer the gene expression in gastric cancer cells, which were either sensitive or resistant to 5-FU and cisplatin, were examined using cDNA microarray analysis. To confirm the differential gene expression, as determined using the microarray, semiquantitative RT-PCR was performed on a subset of differentially expressed cDNAs.

RESULTS

69 and 45 genes, which were either up-regulated (9 and 22 genes) or down-regulated (60 and 25 genes), were identified in 5-FU- and cisplatin-resistant cells, respectively. Several genes, such as adaptor-related protein complex 1 and baculoviral IAP repeat-containing 3, were up-regulated in both drug-resistant cell types. Several genes, such as the ras homolog gene family, tropomyosin, tumor rejection antigen, protein disulfide isomerase-related protein, melanocortin 1 receptor, defensin, cyclophilin B, dual specificity phosphatase 8 and hepatocyte nuclear factor 3, were down-regulated in both drug-resistant cell types.

CONCLUSION

These findings show that cDNA microarray analysis can be used to obtain gene expression profiles that reflect the effect of anticancer drugs on gastric cancer cells. Such data may lead to the assigning of signature expression profiles of drug-resistant tumors, which may help predict responses to drugs and assist in the design of tailored therapeutic regimens to overcome drug resistance.

Getting the right cells to the array: Gene expression microarray analysis of cell mixtures and sorted cells

BACKGROUND

Most biological samples are cell mixtures. Some basic questions are still unanswered about analyzing these heterogeneous samples using gene expression microarray technology (MAT). How meaningful is a cell mixture's overall gene expression profile (GEP)? Is it necessary to purify the cells of interest before microarray analysis, and how much purity is needed? How much does the purification itself distort the GEP, and how well can the GEP of a small cell subset be recovered?

METHODS

Model cell mixtures with different cell ratios were analyzed by both spotted and Affymetrix MAT. GEP distortion during cell purification and GEPs of purified cells were studied. CD34+ cord blood cells were purified and analyzed by MAT.

RESULTS

GEPs for mixed cell populations were found to mirror the cell ratios in the mixture. Over 75% pure samples were indistinguishable from pure cells by their overall GEP. Cell purification preserved the GEP. The GEPs of small cell subsets could be accurately recovered by cell sorting both from model cell mixtures and from cord blood.

CONCLUSIONS

Purification of small cell subsets from a mixture prior to MAT is necessary for meaningful results. Even completely hidden GEPs of small cell subpopulations can be recovered by cell sorting.

[Pharmacogenetics and pharmacogenomics of cancers]

Sequencing the human genome brings new tools for the individualisation of cancer chemotherapy, firstly thanks to the identification of polymorphisms of genes involved in anticancer drug metabolism or activity (Pharmacogenetics), and secondly thanks to the determination of tumour gene expression profiles and their relationship to chemosensitivity and chemoresistance (Pharmacogenomics). A few functional polymorphisms have been known for a long time (thiopurine methyltransferase, glutathion S-transferases), but several new ones have been identified recently, at the level of the genes encoding drug targets (thymidylate synthase), at the level of DNA repair enzymes (XPD) or at the level of transport proteins (MDR1). On the other hand, the research of correlations between gene expression profiles and chemosensitivity has been performed on the in vitro models of the National Cancer Institute and may allow crucial improvements in the identification of patients who would best take advantage of a specific chemotherapy. Clinical trials, first on a retrospective basis, then on a prospective one, are implemented to validate this approach.

Pharmacogenomics

The discovery of the human genome and subsequent expansion of proteomics research combined with emerging technologies such as functional imaging, biosensors and sophisticated computational biology are producing unprecedented changes in today's healthcare. The expanding knowledge of the molecular basis of cancer has shown that significant differences in gene expression patterns can guide therapy not only for neoplastic conditions, but also for a variety of diseases including inflammatory disorders, cardiovascular disease and neurodegenerative processes. As a result, the fields of pharmacogenetics and pharmacogenomics have emerged as potential new testing platforms for the individualized management of patients. An individual's response to a drug is the complex interaction of both genetic and non-genetic factors. Genetic variants in the drug target itself, disease pathway genes, or drug metabolizing enzymes may all be used as predictors of drug efficacy or toxicity. In oncology, the SNP technology has focused on detecting the predisposition for cancer, predicting of toxic responses to drugs and selecting the best individual and combinations of anti-cancer drugs. Pharmacogenomics involves the application of whole genome technologies (e.g., gene and protein expression data) for the prediction of the sensitivity or resistance of an individual's disease to a single or group of drugs. Genomic microarrays and transcriptional profiling have the ability to generate hundreds of thousands of data points requiring sophisticated and complex information systems necessary for accurate and useful data analysis. This technique has generated a wealth of new information in the fields of leukemia/lymphoma, and solid tumor classification and prediction of metastasis, drug and biomarker target discovery and pharmacogenomic drug efficacy testing.

Chemical discovery and global gene expression analysis in zebrafish

The zebrafish (Danio rerio) provides an excellent model for studying vertebrate development and human disease because of its ex utero, optically transparent embryogenesis and amenability to in vivo manipulation. The rapid embryonic developmental cycle, large clutch sizes and ease of maintenance at large numbers also add to the appeal of this species. Considerable genomic data has recently become publicly available that is aiding the construction of zebrafish microarrays, thus permitting global gene expression analysis. The zebrafish is also suitable for chemical genomics, in part as a result of the permeability of its embryos to small molecules and consequent avoidance of external confounding maternal effects. Finally, there is increasing characterization and analysis of zebrafish models of human disease. Thus, the zebrafish offers a high-quality, high-throughput bioassay tool for determining the biological effect of small molecules as well as for dissecting biological pathways.

[Perspectives for molecular diagnostics exemplified by urothelial bladder carcinoma]

The rapidly growing knowledge of molecular mechanisms will change the daily routine of clinicians in the near future. Regarding urothelial bladder carcinoma, one may expect that molecular diagnostics will identify patients susceptible to disease development by screening their genotype. Furthermore, in addition to histopathologic findings, prognostic markers will be used for disease management. In an ongoing multicenter trial, the decision on whether or not to treat patients with adjuvant chemotherapy after cystectomy is based on their p53 status. In the near future, cytostatic medications are expected to be chosen according to genetic profiles of the tumor or patient. New medications, which target tumor-specific alterations of cell-signaling cascades in bladder or other cancers, prominently inhibitors of the ERBB membrane receptor family, are currently under clinical investigation and will undoubtedly form an important part of therapeutic oncologic regimens. In conclusion, evaluation of gene profiles of tumors and patients will gain importance for clinicians.

Integration of molecular diagnostics with therapeutics: implications for drug discovery and patient care

The Introduction of targeted therapeutics into clinical practice has created major opportunities for further development of the molecular diagnostics industry. Emerging genomic and proteomic technologies and information are now resulting in the molecular subclassification of disease as the basis for diagnosis, prognosis and therapeutic selection. The ultimate goals of personalized medicine are to take advantage of a molecular understanding of disease, both to optimize drug development and direct preventive resources and therapeutic agents at the right population of people while they are still well. Single nucleotide polymorphisms identification and genotyping have uncovered predisposition markers from cancer and heart disease as well in the prediction of both drug efficacy and toxicity. Pharmacogenomic and pharmacodynamic assays are being developed to enhance the speed and decrease the cost of drug development, as well as reduce side effects and increase response rates in a variety of diseases. The traditional trial and error practice of medicine is progressively eroding in favor of more precise marker-assisted diagnosis and safer and more effective molecularly guided treatment of disease. For the diagnostics industry this represents an unprecedented opportunity for integration, increased value and commercial opportunities for molecularly-derived tests.

Integrating diagnostics and therapeutics: revolutionizing drug discovery and patient care

Over the next five years it is widely anticipated that the molecular diagnostics industry will continue to grow at double-digit pace to meet increasing demand for personalized medicine. A wide variety of drugs in late preclinical and early clinical development is now being targeted to disease-specific gene and protein defects that will require co-approval of diagnostic and therapeutic products by regulatory agencies. For clinical laboratories and pathologists, this integration of diagnostics and therapeutics represents a major new opportunity to emerge as leaders of the new medicine, guiding the selection, dosage, route of administration and multi-drug combinations, and producing increased efficacy and reduced toxicity of pharmaceutical products.