Biomedical Engineering Reference
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the discovery of the mode of action of novel compounds having interesting pharma-
cological features (i.e., antifungal or anticancer drugs). In any case, useful insights
on the mode of action of novel compounds can be achieved using this approach.
Indeed, the observation of increased fitness of a homozygous deletant strain treated
with a cytotoxic compound can be ascribed to the lack of an entity downstream in the
pathway encompassing the direct target of the molecule. On the other hand, the HOP
approach can also be exploited for the identification of genes involved in pathways
buffering the compound or drug effects. Indeed, if a compound is lethal for the cell,
the presence of a gene coding for a protein involved in its elimination (i.e., efflux or
metabolism) grants to the cell the possibility of surviving the treatment. The deletion
of this response-associated gene reduces the cell defenses, making the deletant yeast
cells more susceptible to the compound with respect to wild-type cells. Using this
approach, the mechanisms driving a cell's response to nickel compound toxicity were
defined by the identification of functional categories overrepresented in the group of
hypersensible deletant strains [40]. The use of S. cerevisiae as a model for drug
discovery can be affected by the presence of several multidrug resistance (MDR)
mechanisms, which can prevent the identification of biologically active compounds
just because of the abnormal (with respect to other eukaryotic cells) extrusion of
chemical compounds from the cell. The use of HOP, and in particular of homozygous
strains deleted in genes involved in MDR, is therefore useful as an initial screen for
the selection of novel bioactive compounds [41].
Taking advantage of the HOP approach, Dudley et al. were able to generate a
profile of pleiotropy genes [42]. Pleiotropy occurs when a single gene influences sev-
eral phenotypic traits. As a consequence, a mutation or inactivation (i.e., caused by a
chemical compound) of this gene may have an effect on some or all traits simultane-
ously. This is a considerable disadvantage for forward chemical genetics approaches,
since the noisy background of the effect of the targeting forbids identification of
the drug target. In addition, a major challenge in the analysis of pleiotropic genes is
determining whether every phenotype associated with a mutation results from the loss
of a single function or of multiple functions encoded by the same gene. Dudley et al.
succeeded in identifying genes whose deletion made the cell resistant to the pertur-
bation (both chemical and physical perturbations) by observing both dimension and
density of the colonies generated by the deletant cells separately undergoing several
stresses. The definition of a response pattern to the broad and diversified collection
of conditions studied for each gene deletion made it possible to propose a functional
gene grouping criterion; if treatment with a specific perturbation induces the same
phenotype on two or more different deletant strains, the genes for which these strains
are deleted are probably involved similarly in the process affected by the treatment.
14.2.1.3 Multicopy Suppression Profiling: Dosage Suppression The multicopy
suppression profiling (MSP) approach (Figure 14.5) is based on the principle that
cells bearing an increased copy number of a specific gene express an increased level of
the gene product. If the gene encodes for the target of a specific cytotoxic compound,
the overexpressing cell should tolerate higher drug levels. For this application, a new
strain library was generated; a yeast chromosomal library harbored on a multicopy
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