Model Organisms in Drug Discovery

58 C. ELEGANS FUNCTIONAL GENOMICS IN DRUG DISCOVERY
96-well pools and then screening the pools in a systematic manner. Once a
population of a single well has been found positive for a deletion, the progeny
can be grown up and individuals can be tested to obtain a mutant strain.
Caenorhabditis elegans hermaphrodites offer advantages when analyzed in this
fashion because isolation of individual hermaphrodites is sufficient to establish
a line. Although mutagenesis is a random event, a deletion knock-out can be
generated via sequential mutagenesis campaigns. The C. elegans gene knockout
consortium produces several hundred knock-outs per year for the
establishment of a genome-wide knock-out library.
Genome-wide expression profiling
The pathogenic status of a cell not only reflects changes in the activity of single
genes or proteins but also changes in the activities of a range of genes or
proteins that contribute to various pathways. The underlying rationale of
target hunts is the assumption that several genes in a network contribute to a
disease and, more importantly, that the modulation of several gene activities
can reverse the disease state. This opens several entry points for therapeutic
approaches and allows for the selection of the druggable genes. Instead of
generating knock-outs gene by gene and then testing for disease relevance, an
overall snap-shot of the activity of all genes may simultaneously identify all
relevant genes associated with a particular pathology. This can be achieved by
using DNA chips or DNA microarrays for expression profiling, allowing a
comparison of changes throughout the genome in pathogenic versus normal
cells. We will discuss here the use of DNA chips and microarrays for gene
identification but other applications are possible, such as in diagnostic,
pharmacogenomic and toxicogenomic studies.
Several DNA microarrays containing 17871 genes or 490% of the
C. elegans genome are available (Jiang et al., 2001). Caenorhabditis elegans
chips are made up of PCR fragments of 1–2 kb genomic DNA. The RNA
from one sample is used to prepare Cy3-labeled cDNA, and RNA from
another sample is used to prepare Cy5-labeled cDNA. These two cDNA
probes are simultaneously hybridized to a single DNA microarray and the
hybridization intensities are measured. Caenorhabditis elegans DNA chips
have been used to profile expression throughout development. Comparison of
RNA samples from each developmental stage to a mixed population sample
has revealed a twofold change in expression levels in about 12 486 of the
17 871 genes evaluated. Caenorhabditis elegans chips have been made available
to the C. elegans community and data from more than 30 collaborations have
been collected to develop a gene expression topomap (Kim et al., 2001b). Data
from 553 experiments have been used to create a correlation matrix of all
genes to establish functional groups of genes having similar expression