From Molecular Phenotyping to Targeted Therapies
Perhaps the most distinguished aspect of personalized medicine is the selection of a personalized treatment regimen which utilizes targeted therapy (1). In order to understand the concept of targeted therapy, one must understand the molecular causes of cancer since developing therapies attempt to target the causal aberration specifically (2). This review will briefly introduce how underlying genomic causes of lung cancer are detected, how they contribute to cell transformation, and how they guide development of targeted therapy.
Profiling the Underlying Genomic Causes
Development of personalized medicine begins with basic research that attempts to characterize the underlying genomic causes of cancer, and their effects on gene expression. Well characterized patterns of genomic alterations can serve as “biomarkers” for diagnostic, prognostic, therapeutic purposes (3). Such biomarkers include single-nucleotide polymorphisms (SNPs) and DNA copy number variations (CNVs) (4).
Genomic alterations such as deletions, duplications, or translocations can alter the number of copies of a segment of genomic DNA, resulting in CNVs (5). Altered DNA copy number may alter expression levels or expressed isoforms of genes involved in tumor induction or progression, as is the case with small cell lung cancer (SCLC) where induction of the focal adhesion pathway is often deregulated (6). SNPs are single nucleotide base alterations which occur at regular intervals in the genome and can be linked to phenotypes such as cancer susceptibility and drug response (5). For example SNP array studies of non-smoking lung-cancer patients have identified novel SNP patterns for diagnostic use (7).
Cytological, array-based, or sequencing techniques can detect and characterize biomarkers such as CNVs or SNPs to establish associations between specific biomarker patterns and specific phenotypes (2,5,8). Some of the aforementioned techniques and their limitations are discussed thoroughly in our techniques section. Biomarker signatures can distinguish different types of lung cancer, as is the case with established CNV signatures that distinguish squamous cell carcinoma from adenocarcinoma (9). Such distinct diagnosis guides selection of appropriate treatment regimens. Molecular phenotyping has also facilitated many therapeutic development projects as well, such as the annotation of a catalogue of all mutations implicated in cell transformation, based on the completion of the lung cancer genome sequence (2).
From Mutation to Cell Transformation
An individual genetic mutation alone rarely disrupts cellular function due to induction of compensatory mechanisms which sustain homeostasis (3). However, the accumulation of aberrations can eventually surpass the threshold of compensatory mechanisms to disrupt cellular activity (1). If the affected signalling pathways are those involved in cell proliferation, DNA repair, or tumor suppression, the cell may transform into a cancer cell (2).
Pathways involved in cell proliferation are often induced by growth factors such as epidermal growth factor (EGF) or vascular endothelial growth factor (VEGF) (9). EGF binds EGF receptor (EGFR) at the cell surface which homo-dimerizes with another EGFR bound to EGF. The two receptors then bind to and hydrolyze a molecule of ATP to autophosphorylate each other using their intracellular receptor tyrosine kinase (RTK) domains (10). Phosphorylation induces a conformational change in the intracellular domains of the receptors to expose binding sites for effector proteins. Effector proteins bind the receptors to induce signalling cascades involved in various cellular activities, such as resistance to apoptosis which can support tumorigenesis when deregulated (11).
Like EGFR, VEGF receptor (VEGFR) is a receptor tyrosine kinase which follows the same mechanism of activation after binding its ligand VEGF. VEGF can induce a variety of cellular activities, such as the creation of new blood vessels in a process called angiogenesis which can potentially support tumor growth when deregulated (12).Targeted therapies, such as monoclonal antibodies or small molecule inhibitors (SMIs) target factors in such pathways to inhibit propagation of the signalling cascade and suppress tumorigenesis (9).
Profiling the Underlying Genomic Causes
Development of personalized medicine begins with basic research that attempts to characterize the underlying genomic causes of cancer, and their effects on gene expression. Well characterized patterns of genomic alterations can serve as “biomarkers” for diagnostic, prognostic, therapeutic purposes (3). Such biomarkers include single-nucleotide polymorphisms (SNPs) and DNA copy number variations (CNVs) (4).
Genomic alterations such as deletions, duplications, or translocations can alter the number of copies of a segment of genomic DNA, resulting in CNVs (5). Altered DNA copy number may alter expression levels or expressed isoforms of genes involved in tumor induction or progression, as is the case with small cell lung cancer (SCLC) where induction of the focal adhesion pathway is often deregulated (6). SNPs are single nucleotide base alterations which occur at regular intervals in the genome and can be linked to phenotypes such as cancer susceptibility and drug response (5). For example SNP array studies of non-smoking lung-cancer patients have identified novel SNP patterns for diagnostic use (7).
Cytological, array-based, or sequencing techniques can detect and characterize biomarkers such as CNVs or SNPs to establish associations between specific biomarker patterns and specific phenotypes (2,5,8). Some of the aforementioned techniques and their limitations are discussed thoroughly in our techniques section. Biomarker signatures can distinguish different types of lung cancer, as is the case with established CNV signatures that distinguish squamous cell carcinoma from adenocarcinoma (9). Such distinct diagnosis guides selection of appropriate treatment regimens. Molecular phenotyping has also facilitated many therapeutic development projects as well, such as the annotation of a catalogue of all mutations implicated in cell transformation, based on the completion of the lung cancer genome sequence (2).
From Mutation to Cell Transformation
An individual genetic mutation alone rarely disrupts cellular function due to induction of compensatory mechanisms which sustain homeostasis (3). However, the accumulation of aberrations can eventually surpass the threshold of compensatory mechanisms to disrupt cellular activity (1). If the affected signalling pathways are those involved in cell proliferation, DNA repair, or tumor suppression, the cell may transform into a cancer cell (2).
Pathways involved in cell proliferation are often induced by growth factors such as epidermal growth factor (EGF) or vascular endothelial growth factor (VEGF) (9). EGF binds EGF receptor (EGFR) at the cell surface which homo-dimerizes with another EGFR bound to EGF. The two receptors then bind to and hydrolyze a molecule of ATP to autophosphorylate each other using their intracellular receptor tyrosine kinase (RTK) domains (10). Phosphorylation induces a conformational change in the intracellular domains of the receptors to expose binding sites for effector proteins. Effector proteins bind the receptors to induce signalling cascades involved in various cellular activities, such as resistance to apoptosis which can support tumorigenesis when deregulated (11).
Like EGFR, VEGF receptor (VEGFR) is a receptor tyrosine kinase which follows the same mechanism of activation after binding its ligand VEGF. VEGF can induce a variety of cellular activities, such as the creation of new blood vessels in a process called angiogenesis which can potentially support tumor growth when deregulated (12).Targeted therapies, such as monoclonal antibodies or small molecule inhibitors (SMIs) target factors in such pathways to inhibit propagation of the signalling cascade and suppress tumorigenesis (9).
Targeted Therapies: Monoclonal Antibodes and Small Molecular Inhibitors
Monoclonal antibody therapy can target tumor cells and suppress their proliferation. Monoclonal antibodies recognize and bind specifically to antigens present on the cell surface (9). Tumor cells display antigens that are abnormal to a certain cell type, or highly enriched. Antibodies can be raised against such antigens, and then used to target the cell. The bound antibody can mark tumor cell for immunological attack, deliver a cytotoxic agent to induce apoptosis, or bind to a surface receptor to inhibit signalling cascades implicated in tumor development (13). For example, non-small-cell lung cancer (NSCLC) patients diagnosed with aberrations in the VEGF pathway may be prescribed Bevacizumab, an FDA-approved monoclonal antibody that functions as a VEGF-A inhibitor by competitively binding the ATP-binding domain of VEGFR to inhibit ATP-dependent kinase activity (14). Three monoclonal antibodies currently in clinical trials for use as EGFR inhibitors in lung cancers are Cetuximab, Metuzumab, and Pantitumumab (15).
Monoclonal antibody therapy can be highly effective due to high specificity for molecular targets, and high stability in human serum(13). Monoclonal antibody therapy has several limitations as well including difficulty and expense of manufacture, and lack of cell-permeability which presents challenges for drug delivery (9). Researchers of small molecule inhibitors attempt to overcome such limitations in their design (10).
Small molecule inhibitors (SMIs) are organic compounds less than 800 Da, designed to bind competitively and reversibly to a potential protein-protein interface. Such compounds may target protein-protein interfaces to disrupt ligand-receptor binding in order to inhibit propagation of a specific signalling cascade (9). For example, RTK inhibitors may bind the dimerization domain to prevent dimerization of the receptors required to activate their kinase activity, or the inhibitors may target the ATP-binding domain which normally binds ATP to facilitate ATP-dependent kinase activity (10). The latter mechanism of action is used by Gefitinib and Erlotinib, two FDA-approved RTK inhibitors prescribed to NSCLC patients with detected EGFR mutations. These SMIs target the RTK domains of EGFR to inhibit deregulated activation of anti-apoptotic pathways (11). In addition to targeting EGF receptors, several SMIs targeting the VEGF receptors are currently in clinical trials for use in lung cancer therapy (15).
In conclusion, molecular phenotyping has been invaluable to the development of targeted therapies in lung cancer. In basic research, molecular phenotyping identifies genomic aberrations, and their involvement in disruption to pathways with oncogenic implications (2). Based on this information, compounds such as monoclonal antibodies or small molecular inhibitors are developed to target factors in the identified pathway to disrupt signal propagation in an attempt to suppress tumor growth (9). After drug development, molecular phenotyping is used in patient diagnosis such that the appropriate targeted therapy can be assigned to the patient. Finally, once the treatment regimen is employed, molecular phenotyping is used to assess drug sensitivity and potency in an attempt to monitor prognosis (1). This advanced approach to therapy has improved the treatment not only of lung cancer patients, but patients with a variety of cancers.