A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling
| Autor: | Peter J. Shepard, Bruce Seligmann, Diana E. Goyena, Harper C. VanSteenhouse, Joel Mccomb, Joanne M. Yeakley |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Molecular biology Cellular differentiation lcsh:Medicine Gene Expression Artificial Gene Amplification and Extension Hydroxamic Acids Biochemistry Polymerase Chain Reaction Transcriptome Sequencing techniques 0302 clinical medicine Gene expression Ligation Assay lcsh:Science RNA structure Multidisciplinary Physics RNA sequencing Genomics Gene Pool Nucleic acids Physical sciences 030220 oncology & carcinogenesis Nucleic acid thermodynamics MCF-7 Cells RNA annealing RNA extraction Transcriptome Analysis Research Article medicine.drug Annealing (genetics) Biophysics Computational biology Biology Sensitivity and Specificity 03 medical and health sciences Complementary DNA Genetics medicine Humans RNA folding Gene Evolutionary Biology Molecular Biology Assays and Analysis Techniques Population Biology Gene Expression Profiling lcsh:R Reproducibility of Results Biology and Life Sciences Computational Biology Genome Analysis Research and analysis methods Gene expression profiling Macromolecular structure analysis Molecular biology techniques 030104 developmental biology Trichostatin A RNA lcsh:Q Population Genetics |
| Zdroj: | PLoS ONE PLoS ONE, Vol 12, Iss 5, p e0178302 (2017) |
| ISSN: | 1932-6203 |
| Popis: | The use of gene expression signatures to classify compounds, identify efficacy or toxicity, and differentiate close analogs relies on the sensitivity of the method to identify modulated genes. We used a novel ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq®, to determine whether previously unreported compound-responsive genes could be identified and incorporated into a broad but specific compound signature. TempO-Seq exhibits 99.6% specificity, single cell sensitivity, and excellent correlation with fold differences measured by RNA-Seq (R2 = 0.9) for 20,629 targets. Unlike many expression assays, TempO-Seq does not require RNA purification, cDNA synthesis, or capture of targeted RNA, and lacks a 3' end bias. To investigate the sensitivity of the TempO-Seq assay to identify significantly modulated compound-responsive genes, we derived whole transcriptome profiles from MCF-7 cells treated with the histone deacetylase inhibitor Trichostatin A (TSA) and identified more than 9,000 differentially expressed genes. The TSA profile for MCF-7 cells overlapped those for HL-60 and PC-3 cells in the Connectivity Map (cMAP) database, suggesting a common TSA-specific expression profile independent of baseline gene expression. A 43-gene cell-independent TSA signature was extracted from cMAP and confirmed in TempO-Seq MCF-7 data. Additional genes that were not previously reported to be TSA responsive in the cMAP database were also identified. TSA treatment of 5 cell types revealed 1,136 differentially expressed genes in common, including 785 genes not previously reported to be TSA responsive. We conclude that TSA induces a specific expression signature that is consistent across widely different cell types, that this signature contains genes not previously associated with TSA responses, and that TempO-Seq provides the sensitive differential expression detection needed to define such compound-specific, cell-independent, changes in expression. |
| Databáze: | OpenAIRE |
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