Technical considerations in quantitating gene expression.
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Gene Expression↗
Biomedical subjects
Richard A Shimkets
Publications and source records attributed to Richard A Shimkets.
GeneCalling: transcript profiling coupled to a gene database query.
We describe the GeneCalling method for the discovery of differentially expressed genes, both known and novel, from any species including useful sequence information to determine the potential function of novel genes captured. The method relies on transcript visualization coupled to a database query to rapidly and quantitatively identify differentially expressed transcripts. The method has been applied to a wide variety of disease models in a variety of species, addressing problems as diverse as identifying novel human cancer gene targets, understanding how drugs and diet affect animal models of disease, and understanding the basis of trait differences in related strains of corn.
Animals↗
Gene expression quantitation technology summary.
Scientists routinely talk and write about gene expression and the abundance of transcripts, but in reality they extrapolate this information from the various measurements that a variety of different technologies provide. Indeed, there are many reasons why applying different technologies to the problem of transcript abundance may give different results, owing to an incomplete understanding of the gene in question or from shortcomings in the applications of the technologies. There are nine basic considerations for making a technology choice for quantitating gene expression that will impact the overall outcome: architecture, specificity, sensitivity, sample requirement, coverage, throughput, cost, reproducibility, and data management. These considerations will be discussed in the context of available technologies.
Computational Biology↗
Angioarrestin: an antiangiogenic protein with tumor-inhibiting properties.
The angiopoietins comprise a family of proteins that have pro or antiangiogenic activities. Through a proprietary technology designed to identify transcripts of all expressed genes, we isolated a cDNA encoding an angiopoietin-related protein that we designate angioarrestin. The mRNA expression profile of angioarrestin was striking in that it was down-regulated in many tumor tissues when compared with adjacent nontumor tissue, suggesting a role for this protein in tumor inhibition. To test this hypothesis, we ectopically expressed angioarrestin in HT1080 tumor cells and measured pulmonary tumor nodule formation in nude mice. HT1080 cells expressing angioarrestin showed a marked reduction in the number and size of tumor nodules. In vitro, the recombinant protein was systematically tested in a number of endothelial cell assays and found to block critical processes involved in the angiogenic cascade, such as vascular endothelial growth factor/basic fibroblast growth factor-mediated endothelial cell proliferation, migration, tubular network formation, and adhesion to extracellular matrix proteins. These findings reveal a novel function for angioarrestin as an angiogenesis inhibitor and indicate that the molecule may be a potential cancer therapeutic.
3T3 Cells↗