TMD offers pre-clinical services to elucidate the mechanism of action of a therapeutic and potentially differentiate your compound in the market. TMD’s genetic biomarker discovery by transcriptome analysis includes the following:
TMD can evaluate a drug’s influence on gene expression in tumor cell lines by extracting high-quality RNA from drug-treated tumor cells in culture followed by high-density transcriptome analysis (~33-35,000 genes). The microarray chip hybridizations and data acquisition are performed in collaboration with the GLP-genomics facility of the University of California in Los Angeles.
Once a microarray analysis has been performed, TMD can process the data through Ingenuity Pathway Analysis (IPA) from Ingenuity Systems that will allow TMD to evaluate the genes that significantly changed upon drug treatment in the context of high-level network analysis and their contributions to human signaling and metabolic pathways. Furthermore, complex network analysis allows TMD to identify logical drug combinations that would capitalize on the observed transcriptome changes induced by single agent therapy.
After TMD has evaluated the high-level network analysis from the microarray study and has chosen several genes of interest, TMD can validate the expression of these identified genes by qRT-PCR using our Applied Biosystem (ABI) 7900HT and the gene expression assays commercially available through ABI.
TMD currently applies the above technologies to Her1/Her2 and HDAC inhibitors. We have performed transcriptome analysis on a variety of breast cancer cell lines treated with these compounds, analyzed the changes in gene expression with IPA and have validated several genes of interest that form the basis of a gene signature that may predict for patient response.
Contact TMD for a free consultation to assess the usefulness of TMD’s Transcriptome Genetic Biomarker Discovery for your development programs.
