GENE EXPRESSION ANALYSIS IN MEASLES VIRUS RESEARCH
Embargo until
Date
2007-03-26T19:46:14Z
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Johns Hopkins University
Abstract
The sequencing of the human genome ushered in the era of high-throughput
biology. Rapid, whole cell analysis is replacing the molecular reductionist approach of
the last century. Microarrays are one of the main high-throughput technologies in this
field, allowing researchers to query the whole transcriptome of the cell in one
experiment. Learning to harness the power of this technology is a significant research
problem that requires expertise in biology, statistics and computation. Towards that goal,
this work examines three projects exploring the role of microarray analysis in biological
research: an in vitro infection model, acute disease in humans and vaccination in mice.
To test the technology in a highly controlled system, an in vitro infection model
was developed where monocyte-derived dendritic cells were infected with measles virus
and RNA was extracted over 24 hours. There were 1553 significantly regulated genes
during this time, with nearly 60% of them down regulated. The results were compared to
other in vitro infection systems, which highlighted a group of genes that formed a core
response to all the pathogens, including 2’5’ oligoadenylate synthetase, Mx and
interferon response factors 1 and 7. The analysis also showed that measles virus is the
only pathogen that does not induce dsRNA-dependent protein kinase above its
constitutive expression level. Measles also induced a robust interferon-α response in
contrast to the other pathogens. These results showed that microarray analysis could
provide a modular view of the immune response.
Since microarrays worked well in vitro, they were tested in vivo on peripheral
blood mononuclear cells from children with acute measles. We found 13 up regulated
genes and 206 down regulated genes in children at discharge from the hospital and at 1-
iii
month follow-up. All of the up regulated genes peaked at discharge but did not return to
baseline by the time of follow-up. The same pattern was found in the down regulated
genes. A number of immune factors were up regulated including interleukin-1β,
interleukin-8, TNF-α, CXCL2 and CCL4. The down regulated genes were involved in
three main biological processes: transcription, signal transduction and the immune
response, but also included the chemokine receptors CCR2 and CCR7.
Finally, a vaccine model in mice compared a formalin-inactivated measles
vaccine (FIMV) with an alphavirus replicon particle vaccine expressing the H protein
(VCR-H) from measles virus. Although both vaccines induced comparable antibody
titers to measles virus, VCR-H induced many more interferon-γ producing cells. Gene
expression analysis found many genes significantly regulated at day 4 post-vaccination in
CD8+ T cells from VCR-H vaccinated mice, while FIMV vaccinated mice did not show
any gene regulation until day 28. Many of the genes regulated by both vaccines were
involved in transcription and signal transduction.
High-throughput techniques are changing the nature of biological research by
providing a new view of the cell. This increased data load requires more computational
power and statistical expertise to effectively manage the information and extract
knowledge. As scientists learn to harness the power of these new technologies, basic
understanding of the cell and the fight against disease will benefit.
Description
Keywords
Microarrays, Dendritic cells, Measles virus, Vaccines