GSE40718

Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis

Submitted by Ruth R Montgomery (Yale University School of Medicine, USA) on Sep 09 2012

Platform: ngs – Illumina Genome Analyzer II (Homo sapiens)

Pubmed: 23881275

Summary Background: West Nile virus is an emerging infection of biodefense concern and there are no available treatments or vaccines. Here we used a high-throughput method based on a novel gene expression analysis, RNA-Seq, to give a global picture of differential gene expression by primary human macrophages of 10 healthy donors infected in vitro with WNV.

Results: From a total of 50 million reads per sample, we employed a Bayesian hierarchical mixture model to identify 4,026 transcripts that were differentially expressed after infection. Both predicted and novel gene changes were detected, as were gene isoforms, and while many of the genes were expressed by all donors, some were unique. Knock-down of genes not previously known to be associated with WNV resistance identified their critical role in control of viral infection.

Conclusions: Our study distinguishes both common gene pathways as well as novel cellular responses. Such analysis will be valuable for translational studies of susceptible and resistant individuals -- and for targeting therapeutics -- in multiple biological settings.

20 Samples

ID	Title	Cell Type	Timepoint	Reported Virus	Virus Species
GSM999654	Subject1 Mock	macrophage	24 hrs	mock	Uninfected
GSM999655	Subject1 WNV	macrophage	24 hrs	WNV	West Nile virus
GSM999656	Subject2 Mock	macrophage	24 hrs	mock	Uninfected
GSM999657	Subject2 WNV	macrophage	24 hrs	WNV	West Nile virus
GSM999658	Subject3 Mock	macrophage	24 hrs	mock	Uninfected
GSM999659	Subject3 WNV	macrophage	24 hrs	WNV	West Nile virus
GSM999660	Subject4 Mock	macrophage	24 hrs	mock	Uninfected
GSM999661	Subject4 WNV	macrophage	24 hrs	WNV	West Nile virus
GSM999662	Subject5 Mock	macrophage	24 hrs	mock	Uninfected
GSM999663	Subject5 WNV	macrophage	24 hrs	WNV	West Nile virus
GSM999664	Subject6 Mock	macrophage	24 hrs	mock	Uninfected
GSM999665	Subject6 WNV	macrophage	24 hrs	WNV	West Nile virus
GSM999666	Subject7 Mock	macrophage	24 hrs	mock	Uninfected
GSM999667	Subject7 WNV	macrophage	24 hrs	WNV	West Nile virus
GSM999668	Subject8 Mock	macrophage	24 hrs	mock	Uninfected
GSM999669	Subject8 WNV	macrophage	24 hrs	WNV	West Nile virus
GSM999670	Subject9 Mock	macrophage	24 hrs	mock	Uninfected
GSM999671	Subject9 WNV	macrophage	24 hrs	WNV	West Nile virus
GSM999672	Subject10 Mock	macrophage	24 hrs	mock	Uninfected
GSM999673	Subject10 WNV	macrophage	24 hrs	WNV	West Nile virus