Minority Gene Expression Profiling: Probing the Genetic Signatures of Pathogenesis Using Ribosome Profiling
- 27 March 2020
- journal article
- research article
- Published by Oxford University Press (OUP) in The Journal of Infectious Diseases
- Vol. 221 (Supplement), S341-S357
- https://doi.org/10.1093/infdis/jiz565
Abstract
Minority Gene Expression Profiling (MGEP) refers to a scenario where the expression profiles of specific genes of interest are concentrated in a small cellular pool that is embedded within a larger, non-expressive pool. An example of this is the analysis of disease-related genes within sub-populations of blood or biopsied tissues. These systems are characterized by low signal-to-noise ratios that make it difficult, if not impossible, to uncover the desired signatures of pathogenesis in the absence of lengthy, and often problematic, technical manipulations. We have adapted ribosome profiling (RP) workflows from the Illumina to the Ion Proton platform and used them to analyze signatures of pathogenesis in an MGEP model system consisting of human cells eliciting <3% productive dengue infection. We find that RP is powerful enough to identify relevant responses of differentially expressed genes, even in the presence of significant noise. We discuss how to deal with sources of unwanted variation, and propose ways to further improve this powerful approach to the study of pathogenic signatures within MGEP systems.Keywords
Funding Information
- In-House Laboratory Independent Research Program of the Naval Medical Research Center (ILIR-4514)
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