Drug Metabol Pers Ther 2016; aop

Mini Review

Ana E. Rodríguez-Vicentea, Eva Lumbrerasa, Jesus M. Hernándeza, Miguel Martín,

Antonio Calles, Carlos López Otín, Salvador Martín Algarra, David Páez and Miquel Taron*

Pharmacogenetics and pharmacogenomics

as tools in cancer therapy
DOI 10.1515/dmpt-2015-0042
Received November 24, 2015; accepted January 4, 2016
Abstract: Pharmacogenetics and pharmacogenomics
(PGx) are rapidly growing fields that aim to elucidate the
genetic basis for the interindividual differences in drug
response. PGx approaches have been applied to many
anticancer drugs in an effort to identify relevant inherited
or acquired genetic variations that may predict patient
response to chemotherapy and targeted therapies. In
this article, we discuss the advances in the field of can-
cer pharmacogenetics and pharmacogenomics, driven by
the recent technological advances and new revolutionary
massive sequencing technologies and their application
to elucidate the genetic bases for interindividual drug
response and the development of biomarkers able to per-
sonalize drug treatments. Specifically, we present recent
progress in breast cancer molecular classifiers, cell-free
a
Ana E. Rodríguez-Vicente, Eva Lumbreras and Jesus M. Hernández:
These authors contributed equally.
*Corresponding author: Miquel Taron, Amadix SL, Acera de
Recoletos 2, 1B, Valladolid 47004, Spain,
E-mail: taron.miquel@gmail.com
Ana E. Rodríguez-Vicente: Department of Molecular and Clinical
Pharmacology, University of Liverpool, Liverpool, UK; and IBSAL,
IBMCC, Centro de Investigación del Cáncer, Universidad de
Salamanca, CSIC, Hospital Universitario de Salamanca, Salamanca,
Spain
Eva Lumbreras and Jesus M. Hernández: IBSAL, IBMCC, Centro de
Investigación del Cáncer, Universidad de Salamanca, CSIC, Hospital
Universitario de Salamanca, Salamanca, Spain
Miguel Martín: Instituto de Investigación Sanitaria Gregorio
Marañón, Universidad Complutense, Madrid, Spain
Antonio Calles: Medical Oncology Department, Hospital
Universitario HM Sanchinarro, Madrid, Spain
Carlos López Otín: Departamento de Bioquímica y Biología
Molecular, Facultad de Medicina, Instituto Universitario de
Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
Salvador Martín Algarra: Medical Oncology Department, Clínica
Universidad de Navarra, Pamplona, Spain
David Páez: Medical Oncology Department, Hospital de la Santa
Creu i Sant Pau, Barcelona, Spain
circulating DNA as a prognostic and predictive biomarker
in cancer, patient-derived tumor xenograft models,
chronic lymphocytic leukemia genomic landscape, and
current pharmacogenetic advances in colorectal cancer.
This review is based on the lectures presented by the
speakers of the symposium “Pharmacogenetics and Phar-
macogenomics as Tools in Cancer Therapy” from the VII
Conference of the Spanish Pharmacogenetics and Phar-
macogenomics Society (SEFF), held in Madrid (Spain) on
April 21, 2015.
Keywords: circulating free DNA; mouse models; next-­
generation sequencing; polymorphisms; somatic ­mutations;
tumor profiling.
Introduction
In the past decade, advances in pharmacogenetics have
gradually unveiled more of the genetic basis of interindi-
vidual differences to drug responses. A large portion of
these advances has been made in the field of anticancer
therapy. Since entering the postgenomic era, the term
pharmacogenetics has gradually evolved into pharma-
cogenomics, and today, the two terms are interchangeable
in many scenarios. In this paper, pharmacogenetics and
pharmacogenomics are uniformly referred as PGx.
Considering the significant heterogeneity associ-
ated with patient responses to anticancer agents and
their narrow therapeutic index, these disciplines have
the potential to offer individualized oncologic treatment
regimens. Although the initial markers of interest were
proteins, such as the estrogen or HER2 receptors in breast
cancer, many of the more recent predictive biomarkers
currently used to guide treatment are genomic. Aberra-
tions in the tumor’s somatic genome that drive malignant
conversion are being comprehensively cataloged for most
tumor types, and disrupting these oncogenic processes
is a promising strategy for combating cancer. Enhanced
understanding of cancer genetics has enabled the rapid

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2      Rodríguez-Vicente et al.: Pharmacogenetics and pharmacogenomics as tools in cancer therapy
development of more effective and less toxic targeted
agents for precision therapy. Clearly, a better under-
standing of the genetic determinants of anticancer drug
response will enable prospective identification of patients
at risk for severe toxicity or those most likely to benefit
from a particular treatment regimen.
In recent years, PGx has moved beyond candidate
gene approaches and genomewide association studies
(GWASs) toward personalized genomics, which is now
being driven by massively parallel sequencers that are
high definition genetic analyzers capable of sequencing
an entire human genome in a few days. Next-generation
sequencing has the potential to accelerate the early detec-
tion of disorders and the identification of PGx markers to
customize treatments.
In this article, we aim to present an overview of the
trends in this field, based on the lectures presented in the
Symposium “Pharmacogenetics and Pharmacogenom-
ics as Tools in Cancer Therapy” at the VII Conference of
the Spanish Pharmacogenetics and Pharmacogenomics
Society (SEFF), on April 21, 2015.
Tumor profiling: personalizing
treatment for breast cancer
The clinical application of RNA microarrays has been
largely explored in the last years. Perou et al. [1] divided
breast cancer in four subtypes according to their gene
expression profile. In 2012, the Cancer Genome Atlas
network analyzed primary breast cancers by multiple
genomic platforms: DNA copy number arrays, DNA meth-
ylation, exome sequencing, messenger RNA arrays, micro-
RNA sequencing, and reverse-phase protein arrays. The
ability to integrate information across platforms provided
Table 1: Summary of the multigene tests utilised in breast cancer.
Test   Origin   No. of  Technology  FDA  
markers approved
MammaPrint   Fresh/FFPE  70  Gene chip   Yes  
PAM50   FFPE   50  qRT-PCR   Yes  
Oncotype DX  FFPE   16  qRT-PCR   No  
EndoPredict   Fresh/FFPE  8  qRT-PCR   No  
FFPE, Formalin-fixed paraffin-embedded; qRT-PCR, quantitative reverse-transcriptase PCR; N0, lymph node negative; ER, estrogen receptor;
BC, breast cancer.
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key insights into previously defined gene expression sub-
types and confirmed the existence of four main breast
cancer classes, caused by different subsets of genetic
and epigenetic abnormalities. The signature of each
subtype has increased our knowledge of breast cancer
and improved the prognostication and the prediction of
response to therapy [2].
Breast cancer is detected in most cases by screening
examinations, being early detection a key point for the
prognostication. Previous tools can cause pitfalls in the
therapy outcome because two major factors: (1) low accu-
racy in the identification of patients that will not benefit
from chemotherapy [2] and (2) insufficient accuracy iden-
tifying patients with apparent low risk that actually would
be benefited from chemotherapy [3].
Genomic platforms are based on multigene RNA
expression profiles to predict the response to thera-
pies supported by molecular classifiers. They are
mainly based on estrogen receptor (ER)-related and
proliferation-related genes and provide useful com-
­
plementary information to the tumor size and grade
in early breast cancer patients ER+/HER2-. Table  1
summarizes the tests used for breast cancer detection.
These platforms have evolved in recent years, and there
are two generations. The first-generation prognostic
breast cancer signatures include MammaPrint (Agendia
AG, Amsterdam, The Netherlands) and Oncotype DX
(Genomic Health, Redwood City, CA, USA) and provide
an estimate risk of recurrence [4, 5]. MammaPrint ana-
lyzes 70 genes to calculate a recurrence score (low or
high risk). This assay has been developed for breast
cancer patients younger than 61  years with stage I/II,
lymph node-negative, or one to three lymph node-posi-
tive disease [4, 6, 7]. Oncotype DX analyzes 21 genes and
then calculates a recurrence score based on the value
of each gene group (proliferation, estrogen, HER2, and
Clinical indication   Results
Prognosis in N0,  < 5 cm, stage I/II, ER+ or ER- BC   Good versus poor prognosis
Prognosis of breast cancer. Prediction of   Classification into luminal
response to anthracycline-based chemotherapy A, luminal B, HER2
versus CMF enriched, and basal like
Prognosis and prediction of benefit from   Risk stratification (low,
chemotherapy (ER+, N0/1-3N+ BC) on tamoxifen intermediate, and high)
ER+/HER2-negative patients treated with   Low and high risk
endocrine therapy
 Rodríguez-Vicente et al.: Pharmacogenetics and pharmacogenomics as tools in cancer therapy      3
invasion) and the expression of specific genes (CD68,
GSTM1, and BAG1). The score places the patient on a risk
group (low, intermediate, and high) that is the likeli-
hood of recurrence at 10 years [5]. Both are substantially
more accurate to predict recurrence within the first
5 years than in later years.
In recent years, the second-generation tests, Endo-
Predict (Sividon Diagnostics GmbH, Germany) and
PAM50 (NanoString Technologies, Seattle, WA, USA),
have been released. EndoPredict is based on the anal-
ysis of 12 genes (eight tumor genes, three normaliza-
tion genes, and one DNA control gene). The result of
this molecular fingerprint (EP-Score) plus the clinical
pathological parameters (tumor size and nodal status)
provides the EPclin-Score (low or high risk). This new
molecular test has the strong potential to assist in
optimizing adjuvant therapy and thus might improve
management of patients with early-stage breast cancer
[8]. PAM50 is designed to identify breast cancer sub-
types by analyzing 50 genes to classify tumors into
one of four intrinsic subtypes (Luminal A, Luminal B,
HER2-enriched, and Basal-like). Each subtype provides
prognostic information to guide clinical decisions [9].
These new tests showed a better prognostic value for
late recurrences while also remaining predictive of early
relapse [10].
These tests also provide insights on clinical out-
comes, adding value to the clinical decision. Low-risk
patients get no benefits from tamoxifen or chemotherapy
plus tamoxifen, and they have more adverse effects and
lower quality of life. In addition, the benefit of chemo-
therapy in intermediate-risk patients is unclear, and they
will need increased follow-up by clinicians. However,
patients in the high-risk group have an absolute benefit
of chemotherapy followed by tamoxifen [11]. In the last
years, many efforts have been put to accomplish the per-
sonalized medicine in breast cancer. Thus, the IMPAKT
2012 Working Group proposed the following recommen-
dations: (i) a need to develop models that integrate clin-
icopathologic factors along with genomic tests, (ii) the
creation of registries for patients who are subjected to
genomic testing in the daily practice, and (iii) the demon-
stration of clinical utility should be made in the context
of a prospective randomized trial [12]. Future clinical
trials should be conducted to definitively demonstrate
the value of the genetic signature in the outcome assess-
ment of breast cancer patients.
This information is based on the lecture that
Miguel  Martín gave on “Genomic Expression on Breast
Cancer: Personalized Treatment” from the VII SEFF
Conference.
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Circulating free DNA as a prognostic
and predictive biomarker in cancer
Circulating free DNA (cfDNA) consists of small fragments
of DNA released into the blood stream through several
possible mechanisms, including the release of DNA from
macrophages after they engulf apoptotic and necrotic
cells or the spontaneous release of DNA fragments by
cells from the primary cancer site, metastases, or circu-
lating tumor cells. In cancer patients, circulating DNA
carries tumor-related genetic and epigenetic alterations
that are relevant to cancer development, progression, and
resistance to therapy. Detecting cfDNA in plasma or serum
could serve as a “liquid biopsy”, which would be useful
for numerous diagnostic applications and would avoid
the need for tumor tissue biopsies. The use of such a liquid
biopsy delivers the possibility of collecting repeated blood
samples, consequently allowing the changes in cfDNA
to be traced during the natural course of the disease or
during cancer treatment.
Cancer patient treatment is driven today by molecu-
lar analysis of different key genes involved in tumorigenic
pathways. Targeted therapies are a must in the treatment
of certain tumors such as advanced non-small cell lung
cancer (NSCLC) with epidermal growth factor receptor
(EGFR) mutations and tyrosine kinase inhibitors (TKIs) or
advanced colorectal cancer (CRC) with k-ras wild-type and
monoclonal antibodies (mAbs) anti-EGFR.
An extension of the trial EURTAC 2007–2011 (EURo-
pean TArceva vs. Chemotherapy) conducted by the
Spanish Lung Cancer Group demonstrated the greater
efficacy of erlotinib compared with chemotherapy for the
first-line treatment of European patients with advanced
NSCLC harboring oncogenic EGFR mutations (exon 19
deletion or L858R mutation in exon 21). In this study, they
analyzed cfDNA from 97 blood samples as a surrogate for
tumor biopsy, determining EGFR mutation status and cor-
relating it with outcome [13, 14]. EGFR mutations could be
detected in cfDNA from 76 (78%) of 97 samples.
The use of TKIs to target EGFR in patients with NSCLC
is effective but limited by the emergence of drug resist-
ance mutations. A single secondary EGFR mutation,
T790M, confers acquired resistance to current drugs.
Several studies suggest that T790M might be particu-
larly advantageous to tumor cells after drug selection,
as it confers both drug resistance and gain of transform-
ing activity. The analysis of cfDNA identified the T790M
drug resistance mutation in the majority of patients who
had clinical tumor progression while receiving therapy
with TKIs [15].
4      Rodríguez-Vicente et al.: Pharmacogenetics and pharmacogenomics as tools in cancer therapy
KRAS mutations are associated with the onset of
acquired resistance to anti-EGFR treatment in CRCs. Misale
et al. demonstrated that the KRAS mutant alleles found in
the tumors of patients collected after radiographic disease
progression can be detected in plasma using highly sensi-
tive DNA analysis methods. This study suggested that the
blood-based noninvasive monitoring of patients undergo-
ing treatment with anti-EGFR therapies for the emergence
of KRAS mutant clones could allow the early initiation of
combination therapies that may delay or prevent disease
progression [16].
CRC is the second most common cancer in women
and third in men in the US, UE, and Japan, and it is the
fourth cause of death from cancer (45% of diagnosed
patient); in Spain, it is the first common cancer and the
second common cause of death from cancer. When the
cancer is detected early, the survival at 5  years reaches
90%, whereas if it is in an advanced stage, 5-year sur-
vival drops to 12%. The current options for CRC screening
are colonoscopy, fecal occult blood testing (not sensitive
for advanced adenoma [AA]), and DNA screenings tests.
Giraldez et al. [17] showed that a noninvasive test based
on a six-miRNA profile can identify patients with CRC and
AA in average-risk population. In this study, they ana-
lyzed 196 plasma samples from 123 patients newly diag-
nosed with sporadic colorectal neoplasia (63 with CRC
and 60 with AA) and 73 healthy individuals (controls).
The miRNAs from plasma were analyzed using a genom-
ewide miRNA expression profiling assay and RT-qPCR.
The results obtained in this study showed that miRNA
expression profile can be used as a biomarker in CRC,
although it has limited value in identifying patients with
premalignant neoplastic lesions.
As the individual genomic profiles of a patient’s tumor
become more readily available, the use of cfDNA assays
can be better exploited for personalized medicine and for
monitoring treatment efficacy.
The information provided here summarizes Miquel
Taron’s lecture at the 2015 SEFF VII meeting.
Avatar mouse models for
­personalized cancer treatment
Among the large repertoire of in vivo systems used to
study cancer, mouse models represent the most widely
used system. The ease of genetic manipulation, the short
gestation period, and the low maintenance cost are some
of the advantages associated with the use of murine
systems.
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“Mouse avatars” represent a patient-derived tumor
xenograft (PDTX) model to aid in the selection of appro-
priate chemotherapeutic agents [18]. These avatars allow
for each patient to have their own tumor growing in an in
vivo system, thereby allowing the identification of a per-
sonalized therapeutic regimen, eliminating the cost and
toxicity associated with nontargeted chemotherapeutic
measures. They allow a quick assessment of the safety
and efficacy profiles of an investigational drug or novel
drug combinations. These systems are particularly useful
in cases where patients are not eligible for clinical trials or
there are no ongoing clinical trial options [19]. Generally,
mouse avatars involve three steps, as follows:
1. The tumor is obtained by surgical resection.
2. Fresh pieces of the tumor are implanted into mice
(“first-generation” avatar mice). If necessary, these
tumors can be extracted, divided into pieces, and
implanted again in multiple avatar mice, repeating
this process several times to obtain a large number of
avatar mice from a single patient.
3. Once the desired number of avatar mice has been
achieved, the mice are treated with the available
options of chemotherapy, and the response of the
tumors in the avatar mice is examined to choose the
most efficient one.
The rationale for implementing PDTX models relies on the
fact that these models are predictive of clinical outcome.
This has been shown in several retrospective studies and
more recently in prospective clinical trials. Several reports
in CRC, NSCLC, squamous cell carcinoma of the head and
neck, human breast cancer, and renal cell carcinoma have
tested the response rate of drugs used as standard of care
in medical oncology in PDTX models. These experiments
show that the response rates in PDTX models correlate
with those observed in the clinic, both for targeted agents
and for classic cytotoxics.
The therapeutic benefits of the avatar mice have been
demonstrated by several groups [20, 21]. When used in
the study of advanced solid cancers with very poor prog-
nosis, such as gemcitabine-resistant pancreatic cancer,
gastroesophageal adenocarcinoma, or colon cancer, the
xenograft model allowed the identification of an effective
treatment regimen [20, 22].
Avatar models also proved useful for a direct assess-
ment between potential targeted therapies based on
genomic information and potentially active chemotherapy
regimens selected from a long list of phase II studies, for
instance, NSCLC and everolimus and nab-paclitaxel [23].
Moreover, there is an increase in robustness and accu-
racy of these systems in predicting clinical outcome when
 Rodríguez-Vicente et al.: Pharmacogenetics and pharmacogenomics as tools in cancer therapy      5
applied in combination with other molecular biology and
bioinformatics tools, such as gene expression arrays and
exome sequencing.
This is a summary of the lecture given by Antonio
Calles at the VII 2015 SEFF Conference.
The genomic landscape of cancer:
the chronic lymphocytic leukemia
experience and beyond
Chronic lymphocytic leukemia (CLL), the most common
hematological neoplasm in the Western world, is among
the first human neoplasia whose study has benefited
from the recent introduction of high-throughput sequenc-
ing technologies of outstanding efficiency. The Interna-
tional Cancer Genome Consortium (ICGC) and the Cancer
Genome Atlas (http://cancergenome.nih.gov/) were
formed to sequence the genomes, transcriptomes, and
epigenomes of large cohorts of paired tumor and normal
samples from the most prevalent cancer types. Given the
clinical and societal effects of CLL and the gaps in our
knowledge of its genomic determinants, it was included
among the 50 tumors prioritized by the ICGC for large-
scale sequencing.
Whole-genome sequencing and whole-exome
sequencing studies in CLL patients have identified
recurrently mutated genes such as NOTCH1, SF3B1,
TP53, BIRC3, and POT1 [24–26]. Protection of telomeres
1 (POT1) encodes a component of the shelterin complex
that is critical for the maintenance of telomere integ-
rity. In terms of telomere dysfunction, CLL is perhaps
the most well-studied hematological malignancy,
where investigations have shown telomere dysfunction
to be a key determinant of the pathophysiology of the
disease. Ramsay et al. [27] performed exome sequencing
in 127 samples and Sanger sequencing in 214 samples
from matched tumor and normal blood collected from
patients with CLL, detecting heterozygous mutations in
POT1 in 3.5% of all samples. Mutant POT1 proteins pro-
moted telomere elongation independently of telomerase
activity and resulted in telomeric aberrations and an
elevated frequency of chromosome breaks and fusions.
These findings establish POT1 as the first shelterin gene
found to be mutated in human cancer and suggest that
it may be a potential driver of genomic instability during
CLL progression. Moreover, mutations in POT1 have been
recently identified in other cancers, such as melanoma
and glioma [28, 29].
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Furthermore, recent studies have profiled the tran-
scriptome and the DNA methylome of many CLL cases [30,
31]. These studies have not identified a principle driver
mutation in the vast majority of patients. However, they
have identified recurrent mutations at lower frequencies
and the genomic context in which they exist. The mutated
genes tend to cluster in different pathways that include
NOTCH1 signaling, RNA splicing and processing machin-
ery, innate inflammatory response, Wnt signaling, and
DNA damage and cell cycle control, among others. These
results highlight the molecular heterogeneity of CLL and
may provide new biomarkers and potential therapeutic
targets for the diagnosis and management of the disease.
A comprehensive evaluation of the genomic land-
scape of 452 CLL cases and 54 patients with monoclonal
B-lymphocytosis, a precursor disorder, recently per-
formed by the CLL-ICGC Spanish Consortium, has allowed
the identification of novel recurrent mutations in non-
coding regions, including the 3′-UTR of NOTCH1 and the
PAX5 enhancer [32]. The analysis of structural variants
confirmed the presence of known CNAs such as loss of
13q14, 11q22-q23, 17p, 6q15-q21, and trisomy 12. In addi-
tion, this work identified novel candidate CLL driver genes
in regions of recurrent chromosomal alterations, includ-
ing deletions that involve ZNF292 at 6q15 (2.4%), deletions
of 2q37 encompassing SP140 and SP110, loss of 3p21 (2%)
affecting SMARCC1 and SETD2, and loss of 10q24 (1.8%)
involving NFKB2. The accumulative number of driver
alterations (0 to  ≥ 4) discriminated between patients with
differences in clinical behavior.
These studies on CLL have been extended to the
genomic analysis of other human malignancies, including
head and neck carcinomas, with the finding of new tumor
suppressor genes such as CTNNA2 and CTNNA3, which
are recurrently mutated in these tumors [33].
The data presented here are based on the lecture that
Carlos López Otín gave on the genomic landscape of CLL,
at the VII SEFF meeting.
Personalized medicine on
metastatic melanoma
Melanoma is usually a cancer skin that begins in melano-
cytes. There are three categories of melanoma: cutane-
ous, mucosal, and ocular melanoma. Several risk factors
have been describe that can make a person more likely to
develop melanoma: ultraviolet light exposure, moles, skin
type, family history, weakened of the immune system,
older age, and male gender. The main prognostic factors
6      Rodríguez-Vicente et al.: Pharmacogenetics and pharmacogenomics as tools in cancer therapy
are tumor thickness, ulceration, mitotic rate lymph node
involvement, histological type, and molecular markers.
For decades, melanoma has held a designation of ill
repute because no cancer therapy has shown an improve-
ment in average survival. Typical treatments such as dac-
arbazine and temozolomide showed low response rates
and no survival improvement [34], whereas immunother-
apy (interferon or interleukin 2) also had low response
rates and high toxicity [35].
Fortunately, a new generation of therapies for meta-
static melanoma has arisen in the last few years, resulting
in improvements in response rates and overall survival
outcomes. These advancements have taken place primar-
ily on two separate fronts: (1) molecularly targeted inhibi-
tors and (2) immune checkpoint inhibitors that work by
enhancing T-lymphocyte function. These discoveries have
allowed the development of modern therapies such as
vemurafenib and ipilimumab [36].
Since the discovery that the oncogene BRAF is the most
frequently mutated protein in melanoma, there has been
a remarkable progress in the development of target thera-
pies. Mutations have been described at numerous sites in
the BRAF gene, although 90% results in the substitution
of glutamic acid (E) for valine (V) in exon 15. Melanoma is
dependent of the Raf/MEK/ERK pathway, suggesting that
the inhibition of BRAF kinase activity could benefit mela-
noma patients [37]. This pathway is key to cell prolifera-
tion, and targeted inhibitors can downregulate the activity
of this pathway and slow cell growth.
Vemurafenib (PLX4032) was developed using a struc-
ture-guided approach. It is a potent and selective inhibitor
that binds oncogenic BRAF V600 mutation. Vemurafenib
reported an inhibition of the tumor growth and a pro-
longed survival in BRAF mutation-positive xenograft in
preclinical models [38]. The next step was to use phase
I (dose escalation) in selected patients. Response was
observed at all sites of disease at day 15 compared with
baseline, including lung, liver, and bone. To confirm the
response rate and the antitumoral activity, phase 3 was
conducted by the comparison of vemurafenib with dac-
arbazine in patients with BRAF V600E mutation. The
study associated vemurafenib with a significant decrease
in death hazard and tumor progression. The treatment of
BRAF V600E mutant melanoma with vemurafenib marks
a paramount change in the clinical management of mela-
noma patients [39]. Dabrafenib, another BRAF inhibitor,
was also approved. The specific inhibition of BRAF leads
to an upregulation of the MAPK pathway through the pro-
motion of treatment resistance and cell proliferation and
the increased rate of RAS-related skin toxicities [40]. A
common toxic event is secondary cutaneous squamous
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cell carcinoma and keratoacanthomas owing to a para-
doxical activation of the MAPK pathway in keratinocytes,
which can be blocked with MEK inhibitor [41]. This dis-
covery leads to the development of MEK inhibitors such as
cobimetinib and trametinib. Clinical data suggest that the
inhibition of both MEK and mutant BRAF kinases might
result in a greater initial tumor response, prevent MAPK-
driven acquired resistance, and decrease the frequency
and severity of toxic events.
Despite all of the progress made in the treatment of
melanoma patients, is important to overcome the resist-
ance to BRAF inhibitors and to identify new therapeutic
pathways in patients without the BRAF V600 mutation.
This review is based on the lecture that Salvador
Martín Algarra presented in the VII Conference of the
Spanish Pharmacogenetics and Pharmacogenomics
Society (SEFF).
Pharmacogenetics in CRC
CRC is a major health problem because of its high inci-
dence and mortality. Currently, the standard treatment
of metastatic CRC is based on various chemotherapeutic
drugs (fluoropyrimidine, oxaliplatin, and irinotecan) and
mAbs against vascular endothelial growth factor as beva-
cizumab and EGFR as cetuximab and panitumumab. More
recently, two new antiangiogenic molecules, aflibercept
and regorafenib, have been incorporated to the treatment
of metastatic colorectal cancer (mCRC). However, the
improvements in CRC therapeutics are still far from sat-
isfactory, as the 5-year adjusted relative survival rate for
metastatic CRC patients in European countries is  < 10%.
Therefore, the search of PGx markers for this tumor is of
utmost interest.
The dihydropyrimidine dehydrogenase enzyme (DPD,
encoded by the gene DPYD) plays a key role in the metabo-
lism of fluoropyrimidines. Patients carrying the deleteri-
ous IVS14+1G > A (DPYD*2A) and 2846T > C variant alleles
display severe toxicities, which are fatal in homozygous
variant subjects. Although the frequency of DPYD*2A allele
is low, the screening for DPD mutation is clinically rel-
evant to avoid the severe toxicities or death in CRC patients
treated with fluoropyrimidine-containing regimens [42].
Fluorouracil/leucovorin (FU/LV) plus irinotecan
(FOLFIRI) is one of the standard first-line options for
patients with mCRC. Irinotecan is metabolized through
uridine diphosphate glucuronosyltransferase (UGT1A1).
The UGT1A1*28 allele has been associated with the risk of
developing severe toxicities. In contrast, the standard dose
of 180 mg/m2 for irinotecan is significantly lower than the
 Rodríguez-Vicente et al.: Pharmacogenetics and pharmacogenomics as tools in cancer therapy      7

dose that can be tolerated by patients with aUGT1A1 *1/*1
or *1/*28 genotype [43].
The functional activation of growth factors and recep-
tors of the EGFR family occurs in most epithelial cell
cancers, rendering EGFR as a target for cancer treatment.
Cetuximab and panitumumab are mAbs that target the
extracellular domain of the EGFR. EGFR activation via
ligand binding results in signaling through the several
pathways such as PI3K/AKT and Ras/Raf/Mek/Erk, which
contributes to cell proliferation, survival, angiogenesis,
and metastasis development. RAS mutations have an
adverse effect on the prognosis [44], and RAS mutation
status remains the most relevant biological marker of
response to anti-EGFR treatment. It has been suggested
recently that all patients with mCRC who are candidates
for anti-EGFR antibody therapy should have their tumor
tested for mutations in RAS [45]. Constitutive mutations
of RAS predict resistance to anti-EGFR MoAbs in CRC.
However, many patients (~40%) with a wild-type RAS
status do not respond to anti-EGFR mAbs. Mutations in
other downstream components of the EGFR signalling
pathway (BRAF, NRAS, and PIK3CA) have been recently
analyzed in a large cohort of patients [46]. This study con-
firmed the negative effect of KRAS mutations on outcome
after anti-EGFR therapy and showed that BRAF, NRAS and
PIK3CA mutations could account for an additional small
percentage of nonresponding patients.
BRAF V600E mutations are detected in 8–10% early
stage and 4–5% late stage CRC, being a strong indicator
of very poor prognosis. In addition, a negative predic-
tive effect for anti-EGFR mAbs has been reported in some
studies [46–48]. However, these mutations have not
shown a clear predictive effect related to anti-EGRF thera-
pies in randomized clinical trials such as the PRIME study
[49], and until now, no changes in the label by any regula-
tory authority have been made.
MET is a cell membrane growth factor receptor tyros-
ine kinase, which is the specific receptor for the hepato-
cyte growth factor (HGF). The high expression of MET in
CRC is associated with the development of distant metas-
tases and with shorter metastasis-free survival. MET and
HGF are implicated in resistance to target therapy, such as
gefitinib or erlotinib in NSCLC or to cetuximab and panitu-
mumab in CRC [50–53].
Moreover, in the EGFR pathway, polymorphisms in
EGFR and its ligand EGF have been studied as biomarkers
for anti-EGFR treatment. However, although other EGFR
ligands such as amphiregulin (AREG) and epiregulin
(EREG) have recently gained interest as novel biomarkers
of response in patients treated with anti-EGFR therapies,
their potential pharmacogenetic role has not been eluci-
dated. A recent work performed by a Spanish group ana-
lyzed the tagging SNPs (Tag SNPs) in the AREG and EREG
genes in a population of refractory mCRC patients with
KRAS and wild-type BRAF, treated with irinotecan-based
chemotherapy plus EGFR inhibitors [54]. The results dem-
onstrate, for the first time, that common variants in the
AREG gene region were associated with the outcome of
refractory mCRC patients. In addition, a functional SNP in
the EGFR gene was associated with PFS and OS [54]. The
potential effect of these SNPS as biomarkers for anti-EGFR
therapies must be validated in further studies.

Table 2: Main cancer biomarkers and their clinical role.

To evaluate risk of recurrence

 21-Gene signature (Oncotype DX®)   Breast cancer
 70-Gene signature (Mammaprint®)   Breast cancer
 12-Gene signature (EndoPredict®)   Breast cancer
 50-Gene signature (PAM50®)   Breast cancer
To select patients who are most likely to benefit from treatment with certain targeted therapies
 BRAF V600 mutations   Cutaneous melanoma and CRC
 KRAS mutation   CRC
 EGFR mutations: exon 19 deletion and L858R  NSCLC
 Polymorphisms in EGFR and its ligand EGF   CRC
To predict drug resistance
 EGFR T790M mutation   NSCLC
To predict toxicity  
 DPYD*2A   CRC
 UGT1A1*28   CRC
To select patients with worse prognosis
 RAS mutations   CRC
 Expression of MET   CRC

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8      Rodríguez-Vicente et al.: Pharmacogenetics and pharmacogenomics as tools in cancer therapy
The information provided here summarizes David
Páez’s lecture at the VII SEFF meeting (Madrid, April 21,
2015).
Conclusions
With the rapid evolution of genetic and genomic technolo-
gies revolutionizing our approach to prognosis, screen-
ing, and targeting of therapies, the age of personalized
and predictive medicine is defining how clinical practice
is evolving today and how it will be practiced in the future.
Moreover, in the field of oncology, clinical molecular diag-
nostics and biomarker discoveries are constantly advanc-
ing, with predictive biomarkers guiding both therapy and
monitoring of disease progression or remission. Table  2
shows the main biomarkers mentioned in this review and
their clinical role. Individualized tumor pharmacogenetic
analysis will continue to improve, and it is likely that in
the near future that more comprehensive PGx studies that
involved epigenetic factors, such as miRNA, DNA methyla-
tion, and histone modification, will be the new norm for
PGx discovery. Thus, considerable efforts are needed to
translate scientific discovery into clinical practice and in
new drug development.
Acknowledgments: AERV is supported by a grant from the
Fundación Ramón Areces.
Author contributions: All the authors have accepted
responsibility for the entire content of this submitted
manuscript and approved submission.
Research funding: None declared.
Employment or leadership: None declared.
Honorarium: None declared.
Competing interests: The funding organization(s) played
no role in the study design; in the collection, analysis, and
interpretation of data; in the writing of the report; or in the
decision to submit the report for publication.
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