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Page 228 Crisafulli et al. Cancer Drug Resist 2019;2:225-41 I http://dx.doi.org/10.20517/cdr.2018.008
[42]
cancer to 5-Fluorouracil . Mutations of the PIK3CA gene are predictors of response to AKT and mTOR
[43]
inhibitors . Hence, taking into account the above caveats, cancer drivers can constitute rather attractive
targets for pharmacogenetic investigation.

As whole-genome information is rapidly accumulating [Figure 1], it is likely that more and more
genetic factors, or clusters of them, will be discovered that may affect both tumor progression, drug
pharmacodynamics and overall response to therapy. Such cross-feeding amid convergent research fields is
expected to foster better knowledge about gene-gene interactions vs. therapeutic drug metabolism.

Candidate polymorphism search
This type of analysis seeks polymorphic DNA sequences within specific genes, known to impact on the
pharmacokinetics or pharmacodynamics of a compound. Such information may aid in the selection among
different therapeutic strategies. When sufficiently large clinical data are available, they may also aid in drug
dosage selection.

A potential functional impact of genes mapping near polymorphic sites can be explored through gene
silencing. Gene silencing can be obtained through RNA interference via short hairpin RNA (shRNA;
preceding methods relied on siRNA) [44-46] . shRNA have been proposed for use as pharmacological
[47]
compounds . More recent applications include Clustered Regularly Interspaced Short Palindromic Repeats
(CRISPR) technology, which can be utilized to ablate target transcription factors, chromatin-modifying
factors, and noncoding RNA, thus providing powerful instruments for gene silencing purposes [48-51] .

Candidate pathway strategy
This strategy covers a wider range than the previous one. It still retains some of the limitation of the
candidate-gene approach, namely the need of previous knowledge regarding the biological cascades
correlated to a compound action. However, the pathway approach extends such an analysis to larger
numbers of related genes, whose altered function may impact on treatment efficacy. This approach may add
significant chances to explain inter-individual variation in drug efficacy/toxicity, as it includes evaluation
[51]
of potential epistatic effects and of the influence of other cis-regulatory elements . These studies may also
discover gene-gene interactions as pharmacological targets.

Newly added research strategies in this field are based on the concept of synthetic lethality. A synthetic
lethality event occurs when two or more genes are simultaneously perturbed and exposure to a drug results
in cellular or organism death/impairment . Large-scale analysis in yeast for interactions among orthologs
[52]
of human tumor suppressor genes allowed to evaluate thousands of genotype-drug combinations, that were
then transferred to cancer cells in vitro. This resulted in the identification of networks of conserved, synthetic
lethal interactions. Among them, the interaction of topoisomerases with RAD17 and of checkpoint kinases
with BLM were validated by patient survival data . These techniques inform on gene-gene and gene-drug
[53]
[54]
dependencies, taking advantage of better knowledge on control gene pathways , candidate for targeted
drug design . PARP inhibitor efficacy in BRCA1 and BRCA2 mutation carriers is limited by inherent and
[51]
acquired resistance. By using synthetic lethality in combination with PARP inhibitors, BRCA2-mutant cells
were found to be dependent on base excision repair, Atr activation and mRNA splicing. Subsequently, FEN1
[55]
and APEX2 were identified as BRCA2 synthetic lethal targets .

Whole-genome strategies
The previously described approaches suffer from a critical limitation, i.e., they only focus on pre-specified
sets of genes (knowledge-based), thereby ignoring potential candidates whose effect has not been linked,
yet, to treatment efficacy/toxicity. This limitation can be overcome by global strategies, whereby the focus
of the search is extended to the entire genome, transcriptome or proteome of an individual or group of
individuals. Since the completion of the human genome project and the early efforts to map human genetic