ABSTRACT
Despite the individually different molecular alterations in tumors, the malignancy associated biological traits are strikingly similar. Results of a previous study using renal cell carcinoma (RCC) as a model pointed towards cancer-related features, which could be visualized as three groups by microarray based gene expression analysis. In this study, we used a mathematic model to verify the presence of these groups in RCC as well as in other cancer types. We developed an algorithm for gene-expression deviation profiling for analyzing gene expression data of a total of 8397 patients with 13 different cancer types and normal tissues. We revealed three common Cancer Transcriptomic Profiles (CTPs) which recurred in all investigated tumors. Additionally, CTPs remained robust regardless of the functions or numbers of genes analyzed. CTPs may represent common genetic fingerprints, which potentially reflect the closely related biological traits of human cancers.
Subject(s)
Gene Expression Regulation, Neoplastic/genetics , Neoplasms/genetics , Algorithms , Carcinoma, Renal Cell/classification , Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/metabolism , Gene Expression Profiling , Genes, Neoplasm/genetics , Genome-Wide Association Study , Humans , Kidney Neoplasms/classification , Kidney Neoplasms/genetics , Kidney Neoplasms/metabolism , Models, Theoretical , Neoplasms/classification , Neoplasms/metabolism , Oligonucleotide Array Sequence AnalysisABSTRACT
Small molecule screening, the systematic encounter of biology space with chemical space, has provoked the emergence of a whole industry that recreates itself by constant iterative improvements to this process. The authors describe an approach to tackle the problem for one of the most time-consuming steps in the execution of a screening campaign, namely, the reformatting of high-throughput screening test compounds from master plates to daughter assay plates used in the execution of the screen. Through an engineered storage procedure, they prepare plates ahead of the screening process with the respective compounds in a ready-to-use format. They show the biological inertness of the method and how it facilitates efficient recovery of compound activity. This uncoupling of normally interconnected processes provides time and compound savings, avoids repeated freeze-thaw cycles of compound solutions, and removes the problems associated with the DMSO sensitivity of certain assays types.
