Biology Reference
In-Depth Information
Chapter 7
DNA Microarray to Analyze Adenovirus-Host Interactions
Stefania Piersanti , Enrico Tagliafi co , and Isabella Saggio
Abstract
Defi ning the molecular toxicity of viral vectors that
are
or
will be
in use for clinical trials is a prerequisite
for their safe application in humans. DNA chips allow high-throughput evaluation of the profi le of trans-
duced cells and have contributed to underlining specifi c aspects of vector toxicity both in in vitro and in
vivo assets. With gene chips we have been able to identify vector-specifi c properties, such as the cell cycle
alteration induced by vector genomic DNA, along with the activation of specifi c innate immune pathways
that can be ascribed to viral particles. We herein describe a detailed protocol for the use of gene chips to
dissect the toxicogenomic signature of human and canine helper-dependent adenoviral vectors. We suggest
specifi c procedures suited for the study of these viral vectors, but we also give indications that can be
applied to different experimental contexts. In addition, we discuss the in silico elaboration of gene chip raw
data which is a crucial step to extrapolate biological information from gene chip studies.
Key words
DNA chip, Transcriptome, Microarray, Gene therapy, Viral vectors, Adenovirus,
Toxicogenomics
1
Introduction
For a correct use of adenoviral vectors in the clinic, comprehen-
sive knowledge of their impact on the target host cell, organ, or
organism is required. Viral vector induced activation of the
immune system has been extensively analyzed, along with vector
direct toxicity on tissues following in vivo administration ([
1
] and
references therein). One further approach to deepen the informa-
tion on adenoviral vector is to study the molecular impact of ade-
noviral transduction on the host cell transcriptome. In the last
years, DNA microarrays (also called DNA chips or gene chips),
consisting of a highly ordered matrix of thousands of different
DNA sequences with known identities, have become invaluable
tools for the global analysis of gene expression, and besides their
use in the study of disease states, of development, or of the conse-
quences of gene disruptions and drug treatments ([
2
] and refer-
ences therein), they have also been proposed as a means to defi ne
the toxicogenomic signature of different gene therapy vectors in
