by both genetic and non-genetic mechanisms. Genetic resistance appears when mutations
emerge that allow the cell to grow even in the presence of drug. Examples of this are
resistance to BRAF inhibitors by amplification of BRAF or mutations of NRAS in melanoma
[41], and hormone therapy resistance in breast cancer by mutation of the ER [42].
However, non-genetic mechanisms can also mediate resistance to targeted therapy. In a
recent study, Rambow and colleagues elegantly demonstrated that BRAF and MEK inhibition in a PDX model of melanoma resulted in the establishment of minimal residual disease
(MRD), whose mutational profile was not significantly different to that of the tumor before
treatment [22]. Furthermore, cells in MRD could be classified in four transcriptional states,
one of which, characterized by having a neural crest stem cell transcriptional program, went
on to establish tumor growth despite continuous treatment. This subpopulation could be
further targeted by a retinoid X receptor inhibitor, delaying the onset of resistance, and
demonstrating the power of these kinds of analyses to identify potential targets beyond the
findings from bulk genome and transcriptome sequencing.
Liquid biopsies are also useful for the monitoring of cancer evolution and progression,
as they can inform in real time how the tumor is responding to therapy and whether novel
mutations have been acquired that may provide resistance. The tumor mutational landscape
changes over time due to evolutionary and therapeutic selective pressure [26], thus, almost
all tumors acquire resistance to systemic treatment as a result of tumor heterogeneity, clonal
evolution, and selection. For example, in a study of 640 patients, Bettegowda and
colleagues found ctDNA fragments at relatively high concentrations in the circulation of
most patients with metastatic cancer and at lower fraction of patients with localized
cancers, as well as identifying mutations in ctDNA that conferred resistance to EGFR
blockade in colorectal cancer patients [43]. These and other similar results illustrate the
potential of this technology to aid in monitoring tumor evolution and therapy treatment.
2.7
International Collaborative Efforts in Cancer Sequencing
and Mutation Classification
In order to exploit the power of next-generation sequencing technologies in cancer
diagnosis, monitoring, and treatment, international collaborative consortia have been
formed to collect and sequence DNA and RNA of thousands of cancer tissues from
different countries and research institutions around the world.
2.7.1 The Cancer Genome Atlas (TCGA)
TCGA was launched in 2005 as an effort to generate sequencing data from a large
collection of tumors, as well as to analyze and interpret their molecular profiles to provide
a comprehensive overview of the underlying biology and potential therapeutic targets
[12]. Other secondary aims of this project are to release data freely to the scientific
30
C. Molina-Aguilar et al.
emerge that allow the cell to grow even in the presence of drug. Examples of this are
resistance to BRAF inhibitors by amplification of BRAF or mutations of NRAS in melanoma
[41], and hormone therapy resistance in breast cancer by mutation of the ER [42].
However, non-genetic mechanisms can also mediate resistance to targeted therapy. In a
recent study, Rambow and colleagues elegantly demonstrated that BRAF and MEK inhibition in a PDX model of melanoma resulted in the establishment of minimal residual disease
(MRD), whose mutational profile was not significantly different to that of the tumor before
treatment [22]. Furthermore, cells in MRD could be classified in four transcriptional states,
one of which, characterized by having a neural crest stem cell transcriptional program, went
on to establish tumor growth despite continuous treatment. This subpopulation could be
further targeted by a retinoid X receptor inhibitor, delaying the onset of resistance, and
demonstrating the power of these kinds of analyses to identify potential targets beyond the
findings from bulk genome and transcriptome sequencing.
Liquid biopsies are also useful for the monitoring of cancer evolution and progression,
as they can inform in real time how the tumor is responding to therapy and whether novel
mutations have been acquired that may provide resistance. The tumor mutational landscape
changes over time due to evolutionary and therapeutic selective pressure [26], thus, almost
all tumors acquire resistance to systemic treatment as a result of tumor heterogeneity, clonal
evolution, and selection. For example, in a study of 640 patients, Bettegowda and
colleagues found ctDNA fragments at relatively high concentrations in the circulation of
most patients with metastatic cancer and at lower fraction of patients with localized
cancers, as well as identifying mutations in ctDNA that conferred resistance to EGFR
blockade in colorectal cancer patients [43]. These and other similar results illustrate the
potential of this technology to aid in monitoring tumor evolution and therapy treatment.
2.7
International Collaborative Efforts in Cancer Sequencing
and Mutation Classification
In order to exploit the power of next-generation sequencing technologies in cancer
diagnosis, monitoring, and treatment, international collaborative consortia have been
formed to collect and sequence DNA and RNA of thousands of cancer tissues from
different countries and research institutions around the world.
2.7.1 The Cancer Genome Atlas (TCGA)
TCGA was launched in 2005 as an effort to generate sequencing data from a large
collection of tumors, as well as to analyze and interpret their molecular profiles to provide
a comprehensive overview of the underlying biology and potential therapeutic targets
[12]. Other secondary aims of this project are to release data freely to the scientific
30
C. Molina-Aguilar et al.