Currently, cancer therapy remains limited by a “one-size-fits-all” approach, whereby treatment decisions are based mainly on the clinical stage of disease, yet fail to reference the individual's ...underlying biology and its role driving malignancy. Identifying better personalized therapies for cancer treatment is hindered by the lack of high-quality “omics” data of sufficient size to produce meaningful results and the ability to integrate biomedical data from disparate technologies. Resolving these issues will help translation of therapies from research to clinic by helping clinicians develop patient-specific treatments based on the unique signatures of patient's tumor. Here we describe the Georgetown Database of Cancer (G-DOC), a Web platform that enables basic and clinical research by integrating patient characteristics and clinical outcome data with a variety of high-throughput research data in a unified environment. While several rich data repositories for high-dimensional research data exist in the public domain, most focus on a single-data type and do not support integration across multiple technologies. Currently, G-DOC contains data from more than 2500 breast cancer patients and 800 gastrointestinal cancer patients, G-DOC includes a broad collection of bioinformatics and systems biology tools for analysis and visualization of four major “omics” types: DNA, mRNA, microRNA, and metabolites. We believe that G-DOC will help facilitate systems medicine by providing identification of trends and patterns in integrated data sets and hence facilitate the use of better targeted therapies for cancer. A set of representative usage scenarios is provided to highlight the technical capabilities of this resource.
Very little is known regarding regulation of microRNA (miRNA) biogenesis in normal tissues, tumors, and cell lines. Here, we profiled the expression of 225 precursor and mature miRNAs using real-time ...PCR and compared the expression levels to determine the processing patterns. RNA from 22 different human tissues, 37 human cancer cell lines, and 16 pancreas and liver tissues/tumors was profiled. The relationship between precursor and mature miRNA expression fell into the following four categories: (1) a direct correlation exists between the precursor and mature miRNA expression in all cells/tissues studied; (2) direct correlation of the precursor and mature miRNA exists, yet the expression is restricted to specific cell lines or tissues; (3) there is detectable expression of mature miRNA in certain cells and tissues while the precursor is expressed in all or most cells/tissues; or (4) both precursor and mature miRNA are not expressed. Pearson correlation between the precursor and mature miRNA expression was closer to one for the tissues but was closer to zero for the cell lines, suggesting that processing of precursor miRNAs is reduced in cancer cell lines. By using Northern blotting, we show that many of these miRNAs (e.g., miR-31, miR-105 and miR-128a) are processed to the precursor, but in situ hybridization analysis demonstrates that these miRNA precursors are retained in the nucleus. We provide a database of the levels of precursor and mature miRNA in a variety of cell types. Our data demonstrate that a large number of miRNAs are transcribed but are not processed to the mature miRNA.
Approximately 80% of Stage II colon cancer patients are cured by appropriate surgery. However, 20% relapse, and virtually all of these people will die due to metastatic disease. Adjuvant chemotherapy ...has little or no impact on relapse or survival in Stage II colon cancer, and can only add toxicity without benefit for 80% of the target population that has been cured by surgery. Despite much effort, it is difficult to identify clinical or molecular determinants of outcome in Stage II colon cancer, defeating attempts to target treatments to the 20% of individuals who are destined to relapse. We hypothesized that a multidimensional molecular analysis will identify a combination of factors that serve as prognostic biomarkers in Stage II adenocarcinoma of the colon. The Georgetown informatics team generated and analyzed multi-omics profiling datasets in stage II CRC patients with or without relapse to identify molecular signatures in CRC that may serve both as prognostic markers of recurrence, and also allow for identification of the subgroup of patients who might benefit from adjuvant chemotherapy. The datasets were loaded to GDOC® (Georgetown Database of Cancer) for further mining and analysis. The G-DOC web portal (http://gdoc.georgetown.edu) includes a broad collection of bioinformatics and systems biology tools for analysis and visualization of four major "omics" types: DNA, mRNA, microRNA, and metabolites. Through technology re-use, the G-DOC infrastructure will accelerate progress for a variety of ongoing programs in need of integrative multi-omics analysis, and advance our opportunities to practice effective personalized oncology in the near future.
The aim of this study was to perform comparative analysis of multiple public datasets of gene expression in order to identify common genes as potential prognostic biomarkers. Additionally, the study ...sought to identify biological processes and pathways that are most significantly associated with early distant metastases (<5 years) in women with estrogen receptor-positive (ER+) breast tumors. Datasets from three published studies were selected for in silico analysis of gene expression profiles of ER+ breast cancer, using time to distant metastasis as the clinical endpoint. A subset of 44 differently expressed genes (DEGs) was found common to all three studies and characterized by mitotic checkpoint genes and pathways that regulate mitotic spindle and chromosome dynamics. DEG promoter regions were enriched with NFY binding sites. Analysis of miRNA target sites identified significant enrichment of miR-192, miR-193B, and miR-16–1 targets. Aberrant mitotic regulation could drive increased genomic instability leading to a progression towards an early onset metastatic phenotype. The relative importance of mitotic instability may reflect the clinical utility of mitotic poisons in metastatic breast cancer, including poisons such as the taxanes, epothilones, and vinca alkaloids.
Immunohistochemistry is a method that can provide complementary diagnostic and prognostic information to morphological observations and soluble assays. Sensitivity, specificity, or requirements for ...arduous sample preparation or signal amplification procedures often limit the application of this approach to routine clinical specimens. Rolling circle amplification (RCA) generates a localized signal via an isothermal amplification of an oligonucleotide circle. The application of this approach to immunohistochemistry could extend the utility of these methods to include a more complete set of immunological and molecular probes. RCA-mediated signal amplification was successfully applied to the sensitive and specific detection of a variety of cell surface antigens (CD3, CD20, and epithelial membrane antigen) and intracellular molecules (vimentin and prostate-specific antigen) within a variety of routinely fixed specimens, as well as samples prepared for flow cytometry. RCA technology, which has an intrinsically wide dynamic range, is a robust and simple procedure that can provide a universal platform for the localization of a wide variety of molecules as a function of either antigenicity or nucleic acid sequence. The use of RCA in this way could enhance the use of markers of current interest as well as permit the integration of emerging information from genomics and proteomics into cell- and tissue-based analyses.
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