Feng, Xiaodong_ Xie, Hong-Guang - Applying pharmacogenomics in therapeutics-CRC Press (2016)

Applying Pharmacogenomics in Drug Discovery and Development
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The chromosomal rearrangement (a reciprocal translocation) that creates the
Philadelphia chromosome in CML patients results in the fusion of two genes, Bcr and
Abl, and this causes Abl to be expressed at much higher levels than usual. Imatinib
targets the Abl protein and is effective in 89% of CML patients as a first-line therapy
if they harbor this genetic alteration. 26 Genomic analyses have the ability to identify
many different types of genetic alterations compared to histological and/or cytological
analyses, and can be used for large-scale screenings; it is widely believed that genomic
analyses have the potential to dramatically increase our ability to develop new and
effective drugs.
TARGET VALIDATION
Once an association between a disease and a genetic alteration (the potential drug
target) has been identified, a next step is to determine whether or not the genetic
alteration is causative in the disease process. The majority of genetic alterations—in
particular, SNPs—are not causal in the disease process, or only make a minimal contribution,
and therefore the majority of genetic alterations that are identified as being
associated with a disease are highly unlikely to be useful drug targets (although they
may still be useful biomarkers). 27 A significant amount of money is often needed to
conduct these studies, and it can take years to generate enough evidence to warrant
subsequent development of a suitable drug for the target.
Typically target validation experiments include both cell line and animal experiments.
If cell lines were used to identify the genetic alteration, patient samples may
also be assessed at this point to ensure that the potential target is clinically relevant.
Cell lines and animal models can be genetically engineered to express a particular
genetic alteration (“knock-in” experiments). The impact of the genetic alteration on
disease pathogenesis can then be assessed to establish whether a cause-and-effect
relationship exists. Alternatively, anti-sense technologies can be employed. These
technologies allow for “knock-out” of a particular genetic alteration that is present
within a cell line or animal model, and can be used to determine whether elimination
of the genetic alteration can provide “rescue” and prevent disease initiation
and/or progression in cell lines and animal models with endogenous expression of
the genetic alteration.
Cell line studies typically focus on the impact of “knocking-in” or “knocking-out”
the genetic alteration of signaling pathways that are known to be associated with
the potential target, and on physiological processes that pertain to a particular cell
type and the disease of interest. For example, if a genetic alteration in a component
of the mTOR signaling pathway (a pathway that can impact cell proliferation and survival)
is found to be associated with prostate cancer, an investigator would assess the
expression and activity levels of multiple components of the mTOR pathway to help
establish whether the genetic alteration does impact cell signaling. They would also
assess the impact of “knocking-in” or “knocking-out” the genetic alteration on cell
proliferation and survival, physiological processes relevant to cancer cells. In addition
to establishing the cause-and-effect relationship, cell line experiments are relatively
fast and cheap to perform, whereas animal experiments are also necessary as they take
into account systemic effects similar to patients. As with cell line studies, the impact