Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not reproducible in similar experiments. Meanwhile, new statistical methods for identifying DEGs continue to appear in the scientific literature. The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists.

Background: The acceptance of microarray technology in regulatory decision-making is being challenged by the existence of various platforms and data analysis methods. A recent report (E. Marshall, Science, 306, 630–631, 2004), by extensively citing the study of Tan et al. (Nucleic Acids Res., 31, 5676–5684, 2003), portrays a disturbingly negative picture of the cross-platform comparability, and, hence, the reliability of microarray technology. Results: We reanalyzed Tan's dataset and found that the intra-platform consistency was low, indicating a problem in experimental procedures from which the dataset was generated. Furthermore, by using three gene selection methods (i.e., p-value ranking, fold-change ranking, and Significance Analysis of Microarrays (SAM)) on the same dataset we found that p-value ranking (the method emphasized by Tan et al.) results in much lower cross-platform concordance compared to fold-change ranking or SAM. Therefore, the low cross-platform concordance reported in Tan's study appears to be mainly due to a combination of low intra-platform consistency and a poor choice of data analysis procedures, instead of inherent technical differences among different platforms, as suggested by Tan et al. and Marshall. Conclusion: Our results illustrate the importance of establishing calibrated RNA samples and reference datasets to objectively assess the performance of different microarray platforms and the proficiency of individual laboratories as well as the merits of various data analysis procedures. Thus, we are progressively coordinating the MAQC project, a community-wide effort for microarray quality control.

Previously, we have demonstrated that a variety of human cancers including the ovarian cancer express IL‐13Rα2, a high affinity receptor for IL‐13. Herein, we have examined if IL‐13 regulates invasion and metastasis of ovarian cancer through IL‐13Rα2 in vitro and in vivo in animal models of human ovarian cancer. We tested cell invasion and protease activity in IL‐13Rα2‐overexpressing and IL‐13Rα2‐negative ovarian tumor cell lines. IL‐13 treatment significantly augmented both cell invasion and enzyme activities in only IL‐13Rα2‐positive cells but not in IL‐13Rα2‐negative cells in vitro. Mechanistically, IL‐13 enhanced ERK1/2, AP‐1 and MMP activities only in IL‐13Rα2‐positive cells but not in IL‐13Rα2‐negative cells. In contrast, other signaling pathways such as IRS1/2, PI3K and AKT do not seem to be involved in IL‐13 induced signaling in ovarian cancer cell lines. Highly specific inhibitors for MMP and AP‐1 efficiently inhibited both invasion and protease activities without impacting the basal level invasion and protease activities in vitro. In orthotopic animal model of human ovarian cancer, IL‐13Rα2‐positive tumors metastasized to lymph nodes and peritoneum earlier than IL‐13Rα2‐negative tumors. Interestingly, the IL‐13Rα2‐positive tumor bearing mice died earlier than mice with IL‐13Rα2‐negative tumor. Intraperitoneal injection of IL‐13 further shortened survival of IL‐13Rα2‐positive tumor bearing mice compared to IL‐13Rα2‐negative tumor mice. IL‐13Rα2‐positive tumors and lymph node metastasis expressed higher levels of MMPs and higher ERK1/2 activation compared to IL‐13Rα2‐negative tumors. Taken together, IL‐13Rα2 is involved in cancer metastasis through activation of ERK/AP‐1 and that targeting IL‐13Rα2 might not only directly kill primary tumors but also prevent cancer metastasis.

The rapidly changing field of gene therapy promises a number of innovative treatments for cancer patients. Advances in genetic modification of cancer and immune cells and the use of oncolytic viruses and bacteria have led to numerous clinical trials for cancer therapy, with several progressing to late-stage product development. At the time of this writing, no gene therapy product has been approved by the United States Food and Drug Administration (FDA). Some of the key scientific and regulatory issues include understanding of gene transfer vector biology, safety of vectors in vitro and in animal models, optimum gene transfer, long-term persistence or integration in the host, shedding of a virus and ability to maintain transgene expression in vivo for a desired period of time. Because of the biological complexity of these products, the FDA encourages a flexible, data-driven approach for preclinical safety testing programs. The clinical trial design should be based on the unique features of gene therapy products, and should ensure the safety of enrolled subjects. This article focuses on regulatory considerations for gene therapy product development and also discusses guidance documents that have been published by the FDA.

BACKGROUND: Epithelial ovarian cancer demonstrates high mortality due to diagnosis at an advanced stage. In the search for a biomarker for early diagnosis and a target for therapy, the issue of whether interleukin‐13 receptor (IL‐13R), shown to be expressed on a variety of human cancers, is expressed in ovarian tumor samples was explored. In addition, whether this receptor serves as a biomarker and can be targeted by IL‐13 cytotoxin was examined.METHODS: IL‐13R expression in 15 normal and 68 ovarian tumor tissue samples was determined by immunohistochemistry. Correlation between clinicopathologic features and IL‐13R expression was analyzed. The efficacy of IL‐13R‐directed cytotoxin was determined in mice with subcutaneous, orthotopic, and peritoneal metastatic ovarian cancer.RESULTS: Immunohistochemical analyses revealed that 83% of ovarian cancer specimens express IL‐13Rα2, a high‐affinity IL‐13R subunit chain, whereas normal ovary samples expressed none or very low levels. The majority of clear cell ovarian carcinomas with the worst prognosis showed strong staining for IL‐13Rα2. IL‐13 cytotoxin was highly cytotoxic to the IGROV‐1 ovarian cancer cell line in vitro, and it mediated significant antitumor activity against a xenografted tumor model. The antitumor effects were confirmed by treating orthotopically implanted or peritoneal metastatic ovarian tumors, which showed significant extension of survival in immunodeficient mice. IL‐13 cytotoxin also prevented cachexia in treated mice. The soluble form of IL‐13Rα2 was detected in the serum of mice with peritoneal metastasis, and the level decreased to baseline in the treated group.CONCLUSIONS: IL‐13Rα2 is a promising target for ovarian cancer therapy, and the soluble form of IL‐13R may be a possible surrogate marker for disease monitoring. Cancer. Published 2006 by the American Cancer Society.