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Personalized Therapy for Lung Cancer Andre L. Moreira, MD, PhD; and Juliana Eng, MD
The past decade has seen an enormous advancement in the therapy for lung cancer, predominantly seen in adenocarcinoma, ranging from the introduction of histology-based drugs to the discovery of targetable mutations. These events have led to a personalized therapeutic approach with the delivery of drugs that target specific oncogenic pathways active in a given tumor with the intent of acquiring the best response rate. The discovery of sensitizing mutation in the epidermal growth factor receptor gene as the basis for clinical response to tyrosine kinase inhibitors led to a systematic search for other molecular targets in lung cancer. Currently, there are several molecular alterations that can be targeted by experimental drugs. These new discoveries would not be possible without a parallel technological evolution in diagnostic molecular pathology. Next-generation sequencing (NGS) is a technology that allows for the evaluation of multiple molecular alterations in the same sample using a small amount of tissue. Selective evaluation of targeted cancer genes, instead of whole-genome evaluation, is the approach that is best suited to enter clinical practice. This technology allows for the detection of most molecular alteration with a single test, thus saving tissue for future discoveries. The use of NGS is expected to increase and gain importance in clinical and experimental approaches, since it can be used as a diagnostic tool as well as for new discoveries. The technique may also help us elucidate the interplay of several genes and their alteration in the mechanism of drug response and resistance.
CHEST 2014; 146(6):1649-1657
ALK 5 anaplastic lymphoma kinase; EGFR 5 epidermal growth factor receptor; FGFR 5 fibroblast growth factor receptor; FISH 5 fluorescence in situ hybridization; MET 5 mesenchymal epithelial transition; NGS 5 next-generation sequencing; SQCC 5 squamous cell carcinoma; TKI 5 tyrosine kinase inhibitor
ABBREVIATIONS:
Personalized medicine is defined by the National Cancer Institute as a form of medicine that uses information about a person’s genes, proteins, and environment to prevent, diagnose, and treat disease. Therefore, personalized therapy in lung cancer takes into consideration specific characteristics of the tumor to prescribe the best treatment plan. In the last decade, there has been a major change from the empirical treatment
Manuscript received March 24, 2014; revision accepted July 11, 2014. AFFILIATIONS: From the Department of Pathology (Dr Moreira) and the Department of Medicine (Dr Eng), Thoracic Oncology Service, Memorial Sloan-Kettering Cancer Center, New York, NY. CORRESPONDENCE TO: Andre L. Moreira, MD, PhD, Department of Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, New York, NY 10065; e-mail: [email protected]
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in lung cancer, where one drug fits all, to a biomarker-based therapy.1,2 Personalized therapy in lung cancer starts with the histologic diagnosis. Most of the advances in lung cancer targeted therapy occurred in adenocarcinoma. Bevacizumab and pemetrexed have been shown to be an effective treatment of adenocarcinoma but not squamous cell carcinoma (SQCC)
© 2014 AMERICAN COLLEGE OF CHEST PHYSICIANS. Reproduction of this article is prohibited without written permission from the American College of Chest Physicians. See online for more details. DOI: 10.1378/chest.14-0713
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because of severe drug-associated toxicity and lack of drug activity in the latter.3,4 More importantly, targetable mutations are more commonly identified in adenocarcinomas. Currently, there are two types of molecular target therapies approved by the US Food and Drug Administration for the treatment of pulmonary adenocarcinoma. These are erlotinib/gefitinib, and more recently afatinib, for tumors that carry mutations in the tyrosine kinase domain of EGFR and crizotinib for tumors with rearrangement of ALK. Both drugs are generically called tyrosine kinase inhibitor (TKI). There has been an enormous interest in the mechanisms that lead to activation and deactivation of tyrosine kinases in tumor biology because of the importance of this pathway in regulating cell growth, signaling, and division. Receptor tyrosine kinases form a complex signaling network and can amplify the signal by a ligand through intercommunicating pathways. In the case of EGFR, the signal can be mediated through the RAS/RAF/MEK and PIK3CA/AKT/mTOR pathways,5 thereby offering multiple targets for drug interventions. All established and experimental drugs for target therapy in lung cancer are directed through these “switch on” pathways, also called oncogene addiction. There is no established targetable therapy for tumors with a mutation in a tumor suppressor gene or another distinct oncogenic mechanism.
EGFR Mutations The concept of targeted therapy in lung cancer was propelled by the discovery of activating mutations in the tyrosine kinase domain of EGFR as the basis for the observed response in patients treated with TKI.6-8 EGFR mutations are seen in approximately 20% of patients with lung adenocarcinoma. The mutation is more prevalent in nonsmokers and in the Asian population, where it has been reported as high as 60%.9 Most of mutations in EGFR are seen in exomes 18 to 21 of the kinase domain. However, not all identifiable mutations are associated with response to TKI, and indeed there are mutations associated with resistance or insensitivity to the drugs.10 The two most common EGFR mutations in pulmonary adenocarcinoma are in-frame deletions in exon 19 (E746-A750 15-base-pair deletion) and the point mutation replacing leucine with arginine at codon 858 in exon 21 (L858R). These two mutations are responsible for 90% of the EGFR mutations in lung adenocarcinoma.10 Other less-frequent mutations include in-frame deletions in exon 19 or point mutations in exon 18 and 21 (Fig 1).10 Mutations characterized by insertions in exon 20 are associated with lack of sensitivity to TKI.11,12 1650 Translating Basic Research Into Clinical Practice
Figure 1 – Simplified scheme of main mutations in the tyrosine kinase domain of EGFR. Sensitizing mutations are marked in green. Mutations associated with resistance to tyrosine kinase inhibitor (TKI) are indicated in red. The most common mutations are 15-BP deletion in exon 19 and point mutation (L858R) in exon 21. These two mutations represent almost 90% of all sensitizing mutation to TKI. Insertions in exon 20 are associated with resistance and are estimated to be the third most common mutation in the gene. BP 5 base pair; EGFR 5 epidermal growth factor receptor.
Exon 20 insertions may be the third most common mutation in the gene after exon 19 in-frame deletions and L858R.11 Computational analysis suggests that insertions in exon 20 cause structural changes in the epidermal growth factor receptor (EGFR) protein, thus preventing binding of TKI.11 T790M is a point mutation (threonime-790 to methionine) in exon 20 that is associated with acquired resistance to TKI12-14; this mutation is often seen in tumors that were rebiopsied after TKI failed.14 However, this mutation can be seen in untreated tumors, where it is associated with short-term response to TKI.12,13 Recently, a group of multidisciplinary investigators including pathologists, clinicians, and molecular pathologists published guidelines for molecular testing in lung cancer15 and emphasized that priority should be given to the molecular alterations that have approved targeted therapy, namely EGFR and anaplastic lymphoma kinase (ALK). The recommendation also suggests that a test that can identify all possible mutations in the gene should be used, thus ensuring that all possible sensitizing mutations are identified. Currently, the diagnosis of EGFR mutations and ALK rearrangement requires different techniques to identify insertions, deletions, point mutations, and, in the case of ALK, a fluorescence in situ hybridization (FISH) test. Thus, there is great need for a comprehensive technique that can accomplish all these alterations in a single test.
ALK Rearrangement and ROS-1 Fusion In 2007, a novel driver mutation, EML4-ALK fusion gene, was identified in approximately 5%16 of patients with lung adenocarcinoma.16 This mutation is the result of an inversion of the short arm of chromosome 2 involving 2p21 and 2p23, leading to the fusion of N-terminal
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portion of the protein encoded by EML4 with the intracellular signaling portion of the receptor tyrosine kinase encoded by ALK. ALK is a receptor tyrosine kinase, and its activation leads to effects on cell proliferation, survival, migration, and alterations in cytoskeletal rearrangement. Patients with EML4-ALK fusion have some distinct clinical and pathologic features, such as younger age at the onset of disease, never or light smokers, advanced stage at presentation, and poor differentiation with solid and cribriform histology with mucin and signet ring cell features.17-20 A small subset of adenocarcinomas has a rearrangement in Ros-1 receptor tyrosine kinase gene that leads to constitute activation of the pathway. The rearrangement is more commonly seen with CD74 and SLC 34A2, but others fusion partners exist. The incidence of this rearrangement is estimated to be approximately 1% of adenocarcinomas and tends to occur in a similar age group as ALK-rearranged tumors.21 Crizotinib has been shown to be active in tumors carrying the ROS-1 fusion gene.21
Other Molecular Alterations The identification of EGFR and ALK mutations has led to a systematic study of the cancer genome to try to identify other possible targetable mutations. Many different mutations, mostly within the tyrosine kinase signaling complex, have been identified so far, leading to a fast course in drug development and testing. Examples of these identifiable mutations and incidence estimates are illustrated in Figure 2. Experimental targeted therapies and ongoing clinical trials to these mutations can be seen in Table 1. KRAS mutations can be found in approximately 30% of all pulmonary adenocarcinomas and have long been known to be associated with several cancers as well.22 In general, KRAS mutant tumors are poorly differentiated and strongly associated with smoking history.23 There is no specific therapy for KRAS mutant tumors, although this is an area of intense study. It is hoped that new developments will bring KRAS mutations into the realm of targetable mutations (Table 1).24 There has been an increased awareness of mutation in the PIK3CA/AKT/mTOR pathway. In lung cancer, these include mutations in PIK3CA, AKT, and PTEN. These mutations can be found in adenocarcinomas as well as SQCC; mutations in PIK3CA are oncogenic and the most common in this group. This mutation can coexist with other mutations in pulmonary adenocarcinoma.25 Preclinical data suggests that alterations in the PIK3CA/AKT/mTOR pathway increases sensitivity to mTOR inhibitor everolimus26,27; however, early clinical journal.publications.chestnet.org
trials have suggested only partial response to agents targeting the pathway.28 BRAF and HER2 mutations, among others, are also seen at low incidence rates.29,30 Recently, two novel alterations involving rearrangement of NTRK1 and NRG1 have been reported. NTRK1 fusion genes seem to be present in 3% of adenocarcinomas with no other mutations, whereas NRG1 rearrangements seem to be seen predominantly in invasive mucinous adenocarcinoma. Both mutations have the potential to be targeted by specific drugs.31,32 In SQCC, a few putative oncogenic drivers have been identified.33 Most alterations involve the PI3K/AKT/mTOR pathway and rat sarcoma viral oncogene (RAS). The extent to which these changes engender a state of oncogene addiction and are targetable by specific drugs remains largely unknown. Preclinical studies34 and preliminary trial data35,36 have demonstrated responses to fibroblast growth factor receptor (FGFR) inhibitors in some FGFR1-amplified SQCCs and SQCCs that carry an S768R mutation in DDR2. A small number of SQCCs with mutations or amplifications in other potential oncogenes (EGFR vIII, mesenchymal epithelial transition [MET], platelet-derived growth factor receptor A, insulin-like growth factor-1 receptor) are currently undergoing investigation with targeted inhibitors.
Next-Generation Sequencing: Its Applications and Limitations to Clinical Samples A standardized protocol for the evaluation of molecular alterations and other biomarker are necessary for the treatment of lung cancer. In view of the growing number of targetable molecular alterations, the best approach for molecular diagnosis is still a dilemma taking into consideration the important issue of tissue use, since the vast majority of patients with lung cancer that can benefit from target therapy only have small tissue biopsies.37 Currently, the molecular tests are guided toward a single gene or known alteration that can jeopardize tissue use for future discoveries in archival material. Multiplex polymerase chain reaction technologies that can evaluate several known hot spots for mutations are in use and can efficiently evaluate point mutations in several genes using clinical samples of formalin-fixed paraffin-embedded tissue. These technologies, however, cannot identify insertions and deletions, important to the characterization of EGFR mutations, which need to be evaluated in parallel tests. ALK/ROS-1 rearrangements are diagnosed by specific FISH tests. Next-generation sequencing (NGS) is a multiplex test that can detect genomewide alterations in the DNA, 1651
Figure 2 – Illustration indicating the estimated frequencies of targetable mutations in pulmonary adenocarcinoma. Mutations associated with established therapies are seen in approximately 25% of all adenocarcinomas, whereas the largest numbers of tumors do not have targetable mutation for molecular-based therapy. These included patients with KRAS mutation and tumors where no known targetable mutations are identified. Other targetable mutations are seen in smaller frequencies and are enrolled in clinical trials. ALK 5 anaplastic lymphoma kinase. See Figure 1 legend for expansion of other abbreviations.
RNA, chromatin structure, and DNA methylation patterns. There are several platforms for NGS, each with its own features and limitations, and they should be used to complement each other in the discovery phase of new molecular alterations. Platforms for genomic DNA alterations are more common in clinical practice and include whole genome/exome and targeted exome analysis. These tests are still very expensive, although the costs are coming down substantially. They generate an enormous number of data points and are therefore highly dependent on sophisticated, time consuming, and skilled statistical analysis. Validation of the findings with more specific tests is necessary to avoid false-positive or false-negative results. Whole genome/exome sequencing, whole transcriptome (RNA sequencing), and whole methylome (gene methylation pattern) analysis are not yet suitable for clinical samples but are very good tools for new discoveries.1 In addition to the limitations indicated above, these approaches are not yet validated for use with paraffin-embedded archival material but require frozen tissue, thus further limiting their use in the clinical setting. Targeted sequencing of cancer-associated genes is an approach that is more likely to succeed and is indeed being applied today to clinical samples with customized platforms that can evaluate a few to . 300 selected genes. Briefly, this technique uses hybridization capture libraries of evaluable exomes of cancer-associated genes that are more likely to have targetable alterations, followed by deep sequencing and alignment with known DNA sequences. NGS of targeted cancer genes is capable of identifying all mutations, deletions, insertions, and rearrangement using a small amount of DNA. This approach has been validated for use of paraffinembedded archival material. Therefore, this is an invalu1652 Translating Basic Research Into Clinical Practice
able tool for new discoveries of targetable genes and identification of clinically relevant mutations. Applications of this technology to clinical small biopsy samples and cytologic material have been reported.38,39 Early results are encouraging, but in many cases the amount and quality of DNA that can be extracted from small biopsy material is still limited.
Targeted Therapy: An Evolving Process Although TKI improves life expectancy40 for targeted EGFR mutations and ALK/ROS-1 rearrangement, inevitably these patients will develop resistance to therapy within 6 to 12 months of initiation of TKI. The evaluation of resistant mechanisms to targetable drugs in lung cancer is an area of intense study. Most information on resistance mechanisms comes from evaluation of EGFR mutant tumors, in which several resistance mechanisms have been already identified.2,12-14,40-43 The most common alteration is the presence of a mutation in exon 20 denominated T790M, which is seen in approximately 50% of TKI-resistant tumors. As discussed previously, this is not a de novo mutation but favored to be a selection of resistance clones.12-14 The mechanism of T790Minduced resistance is not clear, but it is believed the mutated protein can alter the affinity of the small molecule TKI to its ligand.12 Another mechanism of resistance is the emergence of MET amplification that by signaling through ERBB3 leads to activation of the PIK3CA/AKT pathway.41 MET amplification is currently diagnosed by FISH test; it is seen in approximately 1% to 2% of all adenocarcinomas of the lung and varies between 5% to 20% in EGFR resistance tumors.41,44 Interplay with other genetic alterations in the tumor cells, such as mutation in genes downstream in the EGFR signaling pathway and HER2 amplification, has also been implicated in the resistance mechanism to TKI.42,43
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TABLE 1
] Potential Oncogenes in NSCLC Undergoing Clinical Investigation
Genomic Alteration RET
HER2
PIK3CA
ClinicalTrials.gov Identifier
Trial Title
NCT01877083
Study of the Safety and Activity of Lenvatinib (E7080) in Subjects With KIF5B-RET-Positive Adenocarcinoma of the Lung
NCT01829217
Sunitinib in Never-Smokers With Lung Adenocarcinoma
NCT00054093
A Randomized, Double-Blind, Multicenter, Phase 2 Study to Assess the Safety, Tolerability, and Efficacy of ZD6474 in Combination With Docetaxel (TAXOTERE) in Subjects With Locally Advanced or Metastatic Non-small Cell Lung Cancer (NSCLC) After Failure of Prior Platinum-Based Chemotherapy
NCT01639508
A Phase 2 Study of Cabozantinib in Patients With RET Fusion-Positive Advanced Non-small Cell Lung Cancer
NCT01823068
A Phase 2 Study of Vandetanib in Patients With Non-small Cell Lung Cancer Harboring RET Rearrangement
NCT01831726
Modular Phase 2 Study to Link Targeted Therapy to Patients With Pathway Activated Tumors: Module 2 - Dovitinib for Patients With Tumor Pathway Activations Inhibited by Dovitinib Including Tumors With Mutations or Translocations of FGFR, PDGFR, VEGF, cKIT, FLT3, CSFR1, Trk and RET
NCT00818441
A Phase 2, Open Label, Trial Of Dacomitinib (Pf-00299804) in Selected Patients With Advanced Adenocarcinoma of the Lung
NCT01827267
A Phase 2 Study of Neratinib and Neratinib Plus Temsirolimus in Patients With Non-small Cell Lung Cancer Carrying Known HER2 Activating Mutations
NCT01542437
Treatment With BIBW 2992, Irreversible Inhibitor of EGFR and HER-2 in Non Small Cell Lung Cancer in Advanced Stage, Which Have Progressed to Chemotherapy. Analysis of Mutations in EGFR, KRAS and Number of Copies of HER-2
NCT01148849
A Phase 1, Dose Escalation Study of MGAH22 in Patients With Refractory HER2 Positive Breast Cancer and Patients With Other HER2 Positive Carcinomas for Whom No Standard Therapy Is Available
NCT01465802
Archer 1042: A Phase 2 Study Of Dacomitinib in Advanced Non-small Cell Lung Cancer (Post-Chemotherapy or Select First Line Patients) to Evaluate Prophylactic Intervention on Dermatologic and Gastrointestinal Adverse Events and Patient Reported Outcomes
NCT01526473
A Phase 1 Study to Evaluate the Antitumor Activity and Safety of DUKE-002-VRP(HUHER2-ECD1TM), an Alphaviral Vector Encoding the HER2 Extracellular Domain and Transmembrane Region, in Patient With Locally Advanced or Metastatic Human Epidermal Growth Factor Receptor 2-Positive (HER21) Cancers Including Breast Cancer
NCT01723800
Phase 1 Trial of BKM120 in Combination With Carboplatin and Pemetrexed in Patients With Advanced Non-Squamous Non-small Cell Lung Cancer (NSCLC)
NCT01570296
A Phase Ib Trial of Gefitinib (EGFR Tyrosine Kinase Inhibitor, Iressa) in Combination With BKM120, an Oral Pan-Class 1 PI3K Inhibitor in Patients With Advanced Non-small Cell Lung Cancer, With Enrichment for Patients Whose Tumors Harbor Molecular Alterations of PI3K Pathway and Known to Overexpress EGFR
NCT01723800
Phase 1 Trial of BKM120 in Combination With Carboplatin and Pemetrexed in Patients With Advanced Non-Squamous Non-small Cell Lung Cancer (NSCLC)
NCT01297491
An Open Label Two-Stage Study of Orally Administered BKM120 in Patients With Metastatic Non-small Cell Lung Cancer With Activated PI3K Pathway
NCT01390818
An Open-Label, Phase Ib Dose Escalation Trial of Oral Combination Therapy With MSC1936369B (MEK inhibitor) and SAR245409 (Pi3K/mTOR inhibitor) in Subjects With Locally Advanced or Metastatic Solid Tumors
NCT01911325
A Phase Ib/II Study of Docetaxel With or Without Buparlisib as Second Line Therapy for Patients With Advanced or Metastatic Squamous Non-small Cell Lung Cancer (Continued)
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TABLE 1
] (continued)
Genomic Alteration
KRAS
BRAF
ClinicalTrials.gov Identifier
Trial Title
NCT00975182
A Phase Ib, Open-Label, Dose-Escalation Study of the Safety and Pharmacology of GDC-0941 in Combination With Erlotinib in Patients With Advanced Solid Tumors
NCT01487265
Phase 2 Trial of Erlotinib and BKM120 in Patients With Advanced Non Small Cell Lung Cancer Previously Sensitive to Erlotinib
NCT01363232
A Phase Ib, Open-Label, Multi-center, Dose-Escalation and Expansion Study of an Orally Administered Combination of BKM120 Plus MEK162 in Adult Patients With Selected Advanced Solid Tumors
NCT01294306
Phase 2 Trial of the Akt Inhibitor MK-2206 Plus Erlotinib (OSI-774) in Patients With Advanced Non-small Cell Lung Cancer Who Have Progressed After Previous Response (Including Stable Disease) With Erlotinib Therapy
NCT01859026
A Phase 1/IB Trial of MEK162 in Combination With Erlotinib in Non-small Cell Lung Cancer (NSCLC) Harboring KRAS or EGFR Mutation
NCT01229150
Randomized Phase 2 Study of AZD6244 MEK-Inhibitor With Erlotinib in KRAS Wild Type and KRAS Mutant Advanced Non-small Cell Lung Cancer
NCT00890825
A Phase 2, Double-Blind, Randomized, Placebo-Controlled Study to Assess the Efficacy of AZD6244 (Hyd-Sulfate) in Combination With Docetaxel, Compared With Docetaxel Alone, in Second Line Patients With KRAS Mutation Positive Locally Advanced Metastatic Non Small Cell Lung Cancer (Stage IIIB- IV)
NCT01833143
A Phase 2 Trial of Bortezomib in KRAS-Mutant Non-small Cell Lung Cancer in Never Smokers or Those With KRAS G12D
NCT01951690
Phase 2 Study of VS-6063, a Focal Adhesion Kinase (FAK) Inhibitor, in Patients With KRAS Mutant Non-small Cell Lung Cancer
NCT01859026
A Phase 1/IB Trial of MEK162 in Combination With Erlotinib in Non-small Cell Lung Cancer (NSCLC) Harboring KRAS or EGFR Mutation
NCT01933932
A Phase 3, Double-Blind, Randomized, Placebo-Controlled Study to Assess the Efficacy and Safety of Selumetinib (AZD6244; ARRY-142886) (Hyd-Sulfate) in Combination With Docetaxel, in Patients Receiving Second Line Treatment of KRAS Mutation-Positive Locally Advanced or Metastatic Non Small Cell Lung Cancer (Stage IIIB - IV) (SELECT 1)
NCT02022982
Phase 1/II Study of the CDK4/6 Inhibitor Palbociclib (PD-0332991) in Combination With the MEK Inhibitor PD-0325901 for Patients With KRAS Mutant Non-small Cell Lung Cancer and Other Solid Tumors
NCT02079740
An Open Label, Two-Part, Phase Ib/II Study to Investigate the Safety, Pharmacokinetics, Pharmacodynamics, and Clinical Activity of the MEK Inhibitor Trametinib and the BCL2-Family Inhibitor Navitoclax (ABT-263) in Combination in Subjects With KRAS Mutation-Positive Advanced Solid Tumors
NCT02039336
Phase 1/II Study With the Combination of Dacomitinib and PD-0325901 in Advanced KRAS Mutation Positive Colorectal, Non-small Cell Lung and Pancreatic Cancer
NCT01336634
A Phase 2 Study of the BRAF Inhibitor Dabrafenib as a Single Agent and in Combination With the MEK Inhibitor Trametinib in Subjects With BRAF V600E Mutation Positive Metastatic (Stage IV) Non-small Cell Lung Cancer
NCT02109653
A Phase 2, Single Arm, Open-label, Multicenter, Study of Oral LGX818 in Patients With BRAF V600 Mutant, Advanced Non-small Cell Lung Cancer (NSCLC) That Have Progressed During or After at Least One Prior Chemotherapy
NCT01362296
A Phase 2, Open-label, Multicenter, Randomized Study to Assess the Efficacy and Safety of GSK1120212 Compared With Docetaxel in Second Line Subjects With Targeted Mutations (KRAS, NRAS, BRAF, MEK1) in Locally Advanced or Metastatic Non-small Cell Lung Cancer (NSCLC Stage IV) (Continued)
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TABLE 1
] (continued)
Genomic Alteration
ClinicalTrials.gov Identifier
MET
Trial Title
NCT02012231
A Phase 1/IIa Study to Assess the Safety, Pharmacokinetics, and Pharmacodynamics of PLX8394 in Patients With Advanced, Unresectable Solid Tumors
NCT00888134
Phase 2 Clinical Trial of the MEK 1/2 Inhibitor AZD6244 in Cancers With BRAF Mutations Identified by Prospective Genotypic Analysis
NCT01514864
Phase 2 Trial of Dasatinib in Subjects With Advanced Cancers Harboring DDR2 Mutation or Inactivating B-RAF Mutation
NCT01395758
A Phase 2 Randomized Open-label Study of Erlotinib Plus Tivantinib (ARQ 197) Vs Single Agent Chemotherapy in Previously Treated KRAS Mutation Positive Subjects With Locally Advanced or Metastatic Non-small Cell Lung Cancer
NCT01610336
A Phase IB/II, Open Label, Multicenter Study of INC280 Administered Orally in Combination With Gefitinib in Adult Patients With EGFR Mutated, c-MET-Amplified Non-small Cell Lung Cancer Who Have Progressed After EGFR Inhibitor Treatment
NCT01441128
A Phase 1, Open-Label, Dose Escalation Study to Evaluate Safety, Pharmacokinetics and Pharmacodynamics of Combined Oral C-Met/ALK Inhibitor (PF-02341066) and Pan-Her Inhibitor (PF-0299804) in Patients With Advanced Non-small Cell Lung Cancer
Data from clinicaltrials.gov.
Resistance to TKI from tumor transformation into small cell carcinoma in never smokers has also been reported. In these cases, the small cell carcinoma component carries the same EGFR mutation as the original adenocarcinoma.45,46 Secondary mutations in ALK have been implicated in resistance to crizotinib therapy. New compounds have shown promising results in crizotinib-resistant tumors in preclinical tests and clinical trials.47,48 Development of resistance has also been identified in other mutations.2
Role of NGS in a Comprehensive Understanding of Tumor Genome Studies of the cancer genome atlas using NGS showed that TP53, a tumor suppressor gene, is the most common mutation seen in all tumors. In lung cancer, it has been reported that in EGFR mutant adenocarcinomas, a commutation in TP53 leads to a worse prognosis and shorter response to TKI therapy.49 In fact, NGS frequently identifies mutations in tumor suppressor genes as well as mutations in chromatin remodeling genes, which are associated with epigenetic regulations of the genome. The interplay of coexisting mutations such as chromatin remodeling genes and tumor suppressor genes with targetable mutations needs to be further exploited. This is an area of future developments in
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targetable therapy as more data from NGS become available. Interestingly, not all molecular alterations can be explained by modification in the genomic DNA. DNA methylation is a mechanism implicated in silencing of gene expression. In lung carcinomas, silencing the PTEN gene by methylation is seen in approximately 50% of NSCLC,2,50 whereas mutations in the gene are rare. PTEN methylation leads to loss of protein expression and results in activation of the PIK3CA/AKT/mTOR pathway.2,28 In the future, a comprehensive approach that can evaluate DNA, RNA, and protein expression must be performed to determine the best therapeutic target for individual patients. Systematic evaluation of other histologic types of lung cancer, such as SQCC and endocrine tumors, especially small cell carcinomas, must be carried out to expand therapeutic options for these patients. NGS and proteomic studies are necessary for the identification of potential therapeutic targets and biomarkers, and generation of knowledge of the complex interplay of gene expression and signaling pathways, thus allowing for maximization of resource for therapeutic intervention in this devastating disease.
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Acknowledgments Financial/nonfinancial disclosures: The authors have reported to CHEST that no potential conflicts of interest exist with any companies/organizations whose products or services may be discussed in this article.
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20.
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screening of EML4-ALK-positive lung adenocarcinoma. J Clin Pathol. 2010;63(12):1066-1070. Rodig SJ, Mino-Kenudson M, Dacic S, et al. Unique clinicopathologic features characterize ALK-rearranged lung adenocarcinoma in the western population. Clin Cancer Res. 2009;15(16):5216-5223. Shaw AT, Yeap BY, Mino-Kenudson M, et al. Clinical features and outcome of patients with non-small-cell lung cancer who harbor EML4-ALK. J Clin Oncol. 2009;27(26):4247-4253. Bergethon K, Shaw AT, Ou SH, et al. ROS1 rearrangements define a unique molecular class of lung cancers. J Clin Oncol. 2012;30(8): 863-870. Malumbres M, Barbacid M. RAS oncogenes: the first 30 years. Nat Rev Cancer. 2003;3(6):459-465. Rekhtman N, Ang DC, Riely GJ, Ladanyi M, Moreira AL. KRAS mutations are associated with solid growth pattern and tumorinfiltrating leukocytes in lung adenocarcinoma. Mod Pathol. 2013;26(10):1307-1319. Liu SV, Subramaniam D, Cyriac GC, Abdul-Khalek FJ, Giaccone G. Emerging protein kinase inhibitors for non-small cell lung cancer. Expert Opin Emerg Drugs. 2014;19(1):51-65. Chaft JE, Arcila ME, Paik PK, et al. Coexistence of PIK3CA and other oncogene mutations in lung adenocarcinoma-rationale for comprehensive mutation profiling. Mol Cancer Ther. 2012;11(2): 485-491. Di Nicolantonio F, Arena S, Tabernero J, et al. Deregulation of the PI3K and KRAS signaling pathways in human cancer cells determines their response to everolimus. J Clin Invest. 2010;120(8): 2858-2866. Engelman JA, Chen L, Tan X, et al. Effective use of PI3K and MEK inhibitors to treat mutant Kras G12D and PIK3CA H1047R murine lung cancers. Nat Med. 2008;14(12):1351-1356. Janku F, Hong DS, Fu S, et al. Assessing PIK3CA and PTEN in early-phase trials with PI3K/AKT/mTOR inhibitors. Cell Rep 2014; 6(2):377-387. Arcila ME, Chaft JE, Nafa K, et al. Prevalence, clinicopathologic associations, and molecular spectrum of ERBB2 (HER2) tyrosine kinase mutations in lung adenocarcinomas. Clin Cancer Res. 2012;18(18):4910-4918. Brustugun OT, Khattak AM, Trømborg AK, et al. BRAF-mutations in non-small cell lung cancer. Lung Cancer. 2014;84(1):36-38. Fernandez-Cuesta L, Plenker D, Osada H, et al. CD74-NRG1 fusions in lung adenocarcinoma. Cancer Discov 2014;4(4):415-422. Vaishnavi A, Capelletti M, Le AT, et al. Oncogenic and drug-sensitive NTRK1 rearrangements in lung cancer. Nat Med. 2013;19(11): 1469-1472. Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012; 489(7417):519-525. Dutt A, Ramos AH, Hammerman PS, et al. Inhibitor-sensitive FGFR1 amplification in human non-small cell lung cancer. PLoS ONE. 2011;6(6):e20351. Dienstmann R, Bahleda R, Adamo B, et al. First in human study of JNJ-42756493, a potent pan fibroblast growth factor receptor (FGFR) inhibitor in patients with advanced solid tumors. In: Proceedings from the American Association for Cancer Research; April 5-9, 2014; San Diego, CA. Abstract CT325. Sequist LV, Cassier P, Varga A, et al. Phase 1 study of BGJ398, a selective pan-EGFR inhibitor in genetically preselected advanced solid tumors. In: Proceedings from the American Association for Cancer Research; April 5-9, 2014; San Diego, CA. Abstract CT326. Moreira AL, Thornton RH. Personalized medicine for nonsmall-cell lung cancer: implications of recent advances in tissue acquisition for molecular and histologic testing. Clin Lung Cancer. 2012;13(5):334-339. Wagle N, Berger MF, Davis MJ, et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov 2012;2(1):82-93. Young G, Wang K, He J, et al. Clinical next-generation sequencing successfully applied to fine-needle aspirations of pulmonary and pancreatic neoplasms. Cancer Cytopathol 2013;121(12): 688-694.
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40. Lee CK, Brown C, Gralla RJ, et al. Impact of EGFR inhibitor in non-small cell lung cancer on progression-free and overall survival: a meta-analysis. J Natl Cancer Inst. 2013;105(9):595-605. 41. Engelman JA, Zejnullahu K, Mitsudomi T, et al. MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. Science. 2007;316(5827):1039-1043. 42. Jeannot V, Busser B, Brambilla E, et al. The PI3K/AKT pathway promotes gefitinib resistance in mutant KRAS lung adenocarcinoma by a deacetylase-dependent mechanism. Int J Cancer. 2014;134(11):2560-2571. 43. Takezawa K, Pirazzoli V, Arcila ME, et al. HER2 amplification: a potential mechanism of acquired resistance to EGFR inhibition in EGFR-mutant lung cancers that lack the second-site EGFRT790M mutation. Cancer Discov 2012;2(10):922-933. 44. Sequist LV, Waltman BA, Dias-Santagata D, et al. Genotypic and histological evolution of lung cancers acquiring resistance to EGFR inhibitors. Sci Transl Med. 2011;3(75):75ra26. 45. Zakowski MF, Ladanyi M, Kris MG; Memorial Sloan-Kettering Cancer Center Lung Cancer OncoGenome Group. EGFR mutations
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46.
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in small-cell lung cancers in patients who have never smoked. N Engl J Med. 2006;355(2):213-215. Watanabe S, Sone T, Matsui T, et al. Transformation to smallcell lung cancer following treatment with EGFR tyrosine kinase inhibitors in a patient with lung adenocarcinoma. Lung Cancer. 2013;82(2):370-372. Perez CA, Velez M, Raez LE, Santos ES. Overcoming the resistance to crizotinib in patients with non-small cell lung cancer harboring EML4/ALK translocation. Lung Cancer. 2014;84(2): 110-115. Shaw AT, Kim DW, Mehra R, et al. Ceritinib in ALK-rearranged non-small-cell lung cancer. N Engl J Med. 2014;370(13):1189-1197. Clinical Lung Cancer Genome Project (CLCGP), Network Genomic Medicine (NGM). A genomics-based classification of human lung tumors. Sci Transl Med. 2013;5(209):209ra153. Marsit CJ, Zheng S, Aldape K, et al. PTEN expression in nonsmall-cell lung cancer: evaluating its relation to tumor characteristics, allelic loss, and epigenetic alteration. Hum Pathol. 2005;36(7): 768-776.
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Personalized Therapy for Lung Cancer Andre L. Moreira, MD, PhD; and Juliana Eng, MD
The past decade has seen an enormous advancement in the therapy for lung cancer, predominantly seen in adenocarcinoma, ranging from the introduction of histology-based drugs to the discovery of targetable mutations. These events have led to a personalized therapeutic approach with the delivery of drugs that target specific oncogenic pathways active in a given tumor with the intent of acquiring the best response rate. The discovery of sensitizing mutation in the epidermal growth factor receptor gene as the basis for clinical response to tyrosine kinase inhibitors led to a systematic search for other molecular targets in lung cancer. Currently, there are several molecular alterations that can be targeted by experimental drugs. These new discoveries would not be possible without a parallel technological evolution in diagnostic molecular pathology. Next-generation sequencing (NGS) is a technology that allows for the evaluation of multiple molecular alterations in the same sample using a small amount of tissue. Selective evaluation of targeted cancer genes, instead of whole-genome evaluation, is the approach that is best suited to enter clinical practice. This technology allows for the detection of most molecular alteration with a single test, thus saving tissue for future discoveries. The use of NGS is expected to increase and gain importance in clinical and experimental approaches, since it can be used as a diagnostic tool as well as for new discoveries. The technique may also help us elucidate the interplay of several genes and their alteration in the mechanism of drug response and resistance.
CHEST 2014; 146(6):1649-1657
ALK 5 anaplastic lymphoma kinase; EGFR 5 epidermal growth factor receptor; FGFR 5 fibroblast growth factor receptor; FISH 5 fluorescence in situ hybridization; MET 5 mesenchymal epithelial transition; NGS 5 next-generation sequencing; SQCC 5 squamous cell carcinoma; TKI 5 tyrosine kinase inhibitor
ABBREVIATIONS:
Personalized medicine is defined by the National Cancer Institute as a form of medicine that uses information about a person’s genes, proteins, and environment to prevent, diagnose, and treat disease. Therefore, personalized therapy in lung cancer takes into consideration specific characteristics of the tumor to prescribe the best treatment plan. In the last decade, there has been a major change from the empirical treatment
Manuscript received March 24, 2014; revision accepted July 11, 2014. AFFILIATIONS: From the Department of Pathology (Dr Moreira) and the Department of Medicine (Dr Eng), Thoracic Oncology Service, Memorial Sloan-Kettering Cancer Center, New York, NY. CORRESPONDENCE TO: Andre L. Moreira, MD, PhD, Department of Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, New York, NY 10065; e-mail: [email protected]
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in lung cancer, where one drug fits all, to a biomarker-based therapy.1,2 Personalized therapy in lung cancer starts with the histologic diagnosis. Most of the advances in lung cancer targeted therapy occurred in adenocarcinoma. Bevacizumab and pemetrexed have been shown to be an effective treatment of adenocarcinoma but not squamous cell carcinoma (SQCC)
© 2014 AMERICAN COLLEGE OF CHEST PHYSICIANS. Reproduction of this article is prohibited without written permission from the American College of Chest Physicians. See online for more details. DOI: 10.1378/chest.14-0713
1649
because of severe drug-associated toxicity and lack of drug activity in the latter.3,4 More importantly, targetable mutations are more commonly identified in adenocarcinomas. Currently, there are two types of molecular target therapies approved by the US Food and Drug Administration for the treatment of pulmonary adenocarcinoma. These are erlotinib/gefitinib, and more recently afatinib, for tumors that carry mutations in the tyrosine kinase domain of EGFR and crizotinib for tumors with rearrangement of ALK. Both drugs are generically called tyrosine kinase inhibitor (TKI). There has been an enormous interest in the mechanisms that lead to activation and deactivation of tyrosine kinases in tumor biology because of the importance of this pathway in regulating cell growth, signaling, and division. Receptor tyrosine kinases form a complex signaling network and can amplify the signal by a ligand through intercommunicating pathways. In the case of EGFR, the signal can be mediated through the RAS/RAF/MEK and PIK3CA/AKT/mTOR pathways,5 thereby offering multiple targets for drug interventions. All established and experimental drugs for target therapy in lung cancer are directed through these “switch on” pathways, also called oncogene addiction. There is no established targetable therapy for tumors with a mutation in a tumor suppressor gene or another distinct oncogenic mechanism.
EGFR Mutations The concept of targeted therapy in lung cancer was propelled by the discovery of activating mutations in the tyrosine kinase domain of EGFR as the basis for the observed response in patients treated with TKI.6-8 EGFR mutations are seen in approximately 20% of patients with lung adenocarcinoma. The mutation is more prevalent in nonsmokers and in the Asian population, where it has been reported as high as 60%.9 Most of mutations in EGFR are seen in exomes 18 to 21 of the kinase domain. However, not all identifiable mutations are associated with response to TKI, and indeed there are mutations associated with resistance or insensitivity to the drugs.10 The two most common EGFR mutations in pulmonary adenocarcinoma are in-frame deletions in exon 19 (E746-A750 15-base-pair deletion) and the point mutation replacing leucine with arginine at codon 858 in exon 21 (L858R). These two mutations are responsible for 90% of the EGFR mutations in lung adenocarcinoma.10 Other less-frequent mutations include in-frame deletions in exon 19 or point mutations in exon 18 and 21 (Fig 1).10 Mutations characterized by insertions in exon 20 are associated with lack of sensitivity to TKI.11,12 1650 Translating Basic Research Into Clinical Practice
Figure 1 – Simplified scheme of main mutations in the tyrosine kinase domain of EGFR. Sensitizing mutations are marked in green. Mutations associated with resistance to tyrosine kinase inhibitor (TKI) are indicated in red. The most common mutations are 15-BP deletion in exon 19 and point mutation (L858R) in exon 21. These two mutations represent almost 90% of all sensitizing mutation to TKI. Insertions in exon 20 are associated with resistance and are estimated to be the third most common mutation in the gene. BP 5 base pair; EGFR 5 epidermal growth factor receptor.
Exon 20 insertions may be the third most common mutation in the gene after exon 19 in-frame deletions and L858R.11 Computational analysis suggests that insertions in exon 20 cause structural changes in the epidermal growth factor receptor (EGFR) protein, thus preventing binding of TKI.11 T790M is a point mutation (threonime-790 to methionine) in exon 20 that is associated with acquired resistance to TKI12-14; this mutation is often seen in tumors that were rebiopsied after TKI failed.14 However, this mutation can be seen in untreated tumors, where it is associated with short-term response to TKI.12,13 Recently, a group of multidisciplinary investigators including pathologists, clinicians, and molecular pathologists published guidelines for molecular testing in lung cancer15 and emphasized that priority should be given to the molecular alterations that have approved targeted therapy, namely EGFR and anaplastic lymphoma kinase (ALK). The recommendation also suggests that a test that can identify all possible mutations in the gene should be used, thus ensuring that all possible sensitizing mutations are identified. Currently, the diagnosis of EGFR mutations and ALK rearrangement requires different techniques to identify insertions, deletions, point mutations, and, in the case of ALK, a fluorescence in situ hybridization (FISH) test. Thus, there is great need for a comprehensive technique that can accomplish all these alterations in a single test.
ALK Rearrangement and ROS-1 Fusion In 2007, a novel driver mutation, EML4-ALK fusion gene, was identified in approximately 5%16 of patients with lung adenocarcinoma.16 This mutation is the result of an inversion of the short arm of chromosome 2 involving 2p21 and 2p23, leading to the fusion of N-terminal
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portion of the protein encoded by EML4 with the intracellular signaling portion of the receptor tyrosine kinase encoded by ALK. ALK is a receptor tyrosine kinase, and its activation leads to effects on cell proliferation, survival, migration, and alterations in cytoskeletal rearrangement. Patients with EML4-ALK fusion have some distinct clinical and pathologic features, such as younger age at the onset of disease, never or light smokers, advanced stage at presentation, and poor differentiation with solid and cribriform histology with mucin and signet ring cell features.17-20 A small subset of adenocarcinomas has a rearrangement in Ros-1 receptor tyrosine kinase gene that leads to constitute activation of the pathway. The rearrangement is more commonly seen with CD74 and SLC 34A2, but others fusion partners exist. The incidence of this rearrangement is estimated to be approximately 1% of adenocarcinomas and tends to occur in a similar age group as ALK-rearranged tumors.21 Crizotinib has been shown to be active in tumors carrying the ROS-1 fusion gene.21
Other Molecular Alterations The identification of EGFR and ALK mutations has led to a systematic study of the cancer genome to try to identify other possible targetable mutations. Many different mutations, mostly within the tyrosine kinase signaling complex, have been identified so far, leading to a fast course in drug development and testing. Examples of these identifiable mutations and incidence estimates are illustrated in Figure 2. Experimental targeted therapies and ongoing clinical trials to these mutations can be seen in Table 1. KRAS mutations can be found in approximately 30% of all pulmonary adenocarcinomas and have long been known to be associated with several cancers as well.22 In general, KRAS mutant tumors are poorly differentiated and strongly associated with smoking history.23 There is no specific therapy for KRAS mutant tumors, although this is an area of intense study. It is hoped that new developments will bring KRAS mutations into the realm of targetable mutations (Table 1).24 There has been an increased awareness of mutation in the PIK3CA/AKT/mTOR pathway. In lung cancer, these include mutations in PIK3CA, AKT, and PTEN. These mutations can be found in adenocarcinomas as well as SQCC; mutations in PIK3CA are oncogenic and the most common in this group. This mutation can coexist with other mutations in pulmonary adenocarcinoma.25 Preclinical data suggests that alterations in the PIK3CA/AKT/mTOR pathway increases sensitivity to mTOR inhibitor everolimus26,27; however, early clinical journal.publications.chestnet.org
trials have suggested only partial response to agents targeting the pathway.28 BRAF and HER2 mutations, among others, are also seen at low incidence rates.29,30 Recently, two novel alterations involving rearrangement of NTRK1 and NRG1 have been reported. NTRK1 fusion genes seem to be present in 3% of adenocarcinomas with no other mutations, whereas NRG1 rearrangements seem to be seen predominantly in invasive mucinous adenocarcinoma. Both mutations have the potential to be targeted by specific drugs.31,32 In SQCC, a few putative oncogenic drivers have been identified.33 Most alterations involve the PI3K/AKT/mTOR pathway and rat sarcoma viral oncogene (RAS). The extent to which these changes engender a state of oncogene addiction and are targetable by specific drugs remains largely unknown. Preclinical studies34 and preliminary trial data35,36 have demonstrated responses to fibroblast growth factor receptor (FGFR) inhibitors in some FGFR1-amplified SQCCs and SQCCs that carry an S768R mutation in DDR2. A small number of SQCCs with mutations or amplifications in other potential oncogenes (EGFR vIII, mesenchymal epithelial transition [MET], platelet-derived growth factor receptor A, insulin-like growth factor-1 receptor) are currently undergoing investigation with targeted inhibitors.
Next-Generation Sequencing: Its Applications and Limitations to Clinical Samples A standardized protocol for the evaluation of molecular alterations and other biomarker are necessary for the treatment of lung cancer. In view of the growing number of targetable molecular alterations, the best approach for molecular diagnosis is still a dilemma taking into consideration the important issue of tissue use, since the vast majority of patients with lung cancer that can benefit from target therapy only have small tissue biopsies.37 Currently, the molecular tests are guided toward a single gene or known alteration that can jeopardize tissue use for future discoveries in archival material. Multiplex polymerase chain reaction technologies that can evaluate several known hot spots for mutations are in use and can efficiently evaluate point mutations in several genes using clinical samples of formalin-fixed paraffin-embedded tissue. These technologies, however, cannot identify insertions and deletions, important to the characterization of EGFR mutations, which need to be evaluated in parallel tests. ALK/ROS-1 rearrangements are diagnosed by specific FISH tests. Next-generation sequencing (NGS) is a multiplex test that can detect genomewide alterations in the DNA, 1651
Figure 2 – Illustration indicating the estimated frequencies of targetable mutations in pulmonary adenocarcinoma. Mutations associated with established therapies are seen in approximately 25% of all adenocarcinomas, whereas the largest numbers of tumors do not have targetable mutation for molecular-based therapy. These included patients with KRAS mutation and tumors where no known targetable mutations are identified. Other targetable mutations are seen in smaller frequencies and are enrolled in clinical trials. ALK 5 anaplastic lymphoma kinase. See Figure 1 legend for expansion of other abbreviations.
RNA, chromatin structure, and DNA methylation patterns. There are several platforms for NGS, each with its own features and limitations, and they should be used to complement each other in the discovery phase of new molecular alterations. Platforms for genomic DNA alterations are more common in clinical practice and include whole genome/exome and targeted exome analysis. These tests are still very expensive, although the costs are coming down substantially. They generate an enormous number of data points and are therefore highly dependent on sophisticated, time consuming, and skilled statistical analysis. Validation of the findings with more specific tests is necessary to avoid false-positive or false-negative results. Whole genome/exome sequencing, whole transcriptome (RNA sequencing), and whole methylome (gene methylation pattern) analysis are not yet suitable for clinical samples but are very good tools for new discoveries.1 In addition to the limitations indicated above, these approaches are not yet validated for use with paraffin-embedded archival material but require frozen tissue, thus further limiting their use in the clinical setting. Targeted sequencing of cancer-associated genes is an approach that is more likely to succeed and is indeed being applied today to clinical samples with customized platforms that can evaluate a few to . 300 selected genes. Briefly, this technique uses hybridization capture libraries of evaluable exomes of cancer-associated genes that are more likely to have targetable alterations, followed by deep sequencing and alignment with known DNA sequences. NGS of targeted cancer genes is capable of identifying all mutations, deletions, insertions, and rearrangement using a small amount of DNA. This approach has been validated for use of paraffinembedded archival material. Therefore, this is an invalu1652 Translating Basic Research Into Clinical Practice
able tool for new discoveries of targetable genes and identification of clinically relevant mutations. Applications of this technology to clinical small biopsy samples and cytologic material have been reported.38,39 Early results are encouraging, but in many cases the amount and quality of DNA that can be extracted from small biopsy material is still limited.
Targeted Therapy: An Evolving Process Although TKI improves life expectancy40 for targeted EGFR mutations and ALK/ROS-1 rearrangement, inevitably these patients will develop resistance to therapy within 6 to 12 months of initiation of TKI. The evaluation of resistant mechanisms to targetable drugs in lung cancer is an area of intense study. Most information on resistance mechanisms comes from evaluation of EGFR mutant tumors, in which several resistance mechanisms have been already identified.2,12-14,40-43 The most common alteration is the presence of a mutation in exon 20 denominated T790M, which is seen in approximately 50% of TKI-resistant tumors. As discussed previously, this is not a de novo mutation but favored to be a selection of resistance clones.12-14 The mechanism of T790Minduced resistance is not clear, but it is believed the mutated protein can alter the affinity of the small molecule TKI to its ligand.12 Another mechanism of resistance is the emergence of MET amplification that by signaling through ERBB3 leads to activation of the PIK3CA/AKT pathway.41 MET amplification is currently diagnosed by FISH test; it is seen in approximately 1% to 2% of all adenocarcinomas of the lung and varies between 5% to 20% in EGFR resistance tumors.41,44 Interplay with other genetic alterations in the tumor cells, such as mutation in genes downstream in the EGFR signaling pathway and HER2 amplification, has also been implicated in the resistance mechanism to TKI.42,43
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TABLE 1
] Potential Oncogenes in NSCLC Undergoing Clinical Investigation
Genomic Alteration RET
HER2
PIK3CA
ClinicalTrials.gov Identifier
Trial Title
NCT01877083
Study of the Safety and Activity of Lenvatinib (E7080) in Subjects With KIF5B-RET-Positive Adenocarcinoma of the Lung
NCT01829217
Sunitinib in Never-Smokers With Lung Adenocarcinoma
NCT00054093
A Randomized, Double-Blind, Multicenter, Phase 2 Study to Assess the Safety, Tolerability, and Efficacy of ZD6474 in Combination With Docetaxel (TAXOTERE) in Subjects With Locally Advanced or Metastatic Non-small Cell Lung Cancer (NSCLC) After Failure of Prior Platinum-Based Chemotherapy
NCT01639508
A Phase 2 Study of Cabozantinib in Patients With RET Fusion-Positive Advanced Non-small Cell Lung Cancer
NCT01823068
A Phase 2 Study of Vandetanib in Patients With Non-small Cell Lung Cancer Harboring RET Rearrangement
NCT01831726
Modular Phase 2 Study to Link Targeted Therapy to Patients With Pathway Activated Tumors: Module 2 - Dovitinib for Patients With Tumor Pathway Activations Inhibited by Dovitinib Including Tumors With Mutations or Translocations of FGFR, PDGFR, VEGF, cKIT, FLT3, CSFR1, Trk and RET
NCT00818441
A Phase 2, Open Label, Trial Of Dacomitinib (Pf-00299804) in Selected Patients With Advanced Adenocarcinoma of the Lung
NCT01827267
A Phase 2 Study of Neratinib and Neratinib Plus Temsirolimus in Patients With Non-small Cell Lung Cancer Carrying Known HER2 Activating Mutations
NCT01542437
Treatment With BIBW 2992, Irreversible Inhibitor of EGFR and HER-2 in Non Small Cell Lung Cancer in Advanced Stage, Which Have Progressed to Chemotherapy. Analysis of Mutations in EGFR, KRAS and Number of Copies of HER-2
NCT01148849
A Phase 1, Dose Escalation Study of MGAH22 in Patients With Refractory HER2 Positive Breast Cancer and Patients With Other HER2 Positive Carcinomas for Whom No Standard Therapy Is Available
NCT01465802
Archer 1042: A Phase 2 Study Of Dacomitinib in Advanced Non-small Cell Lung Cancer (Post-Chemotherapy or Select First Line Patients) to Evaluate Prophylactic Intervention on Dermatologic and Gastrointestinal Adverse Events and Patient Reported Outcomes
NCT01526473
A Phase 1 Study to Evaluate the Antitumor Activity and Safety of DUKE-002-VRP(HUHER2-ECD1TM), an Alphaviral Vector Encoding the HER2 Extracellular Domain and Transmembrane Region, in Patient With Locally Advanced or Metastatic Human Epidermal Growth Factor Receptor 2-Positive (HER21) Cancers Including Breast Cancer
NCT01723800
Phase 1 Trial of BKM120 in Combination With Carboplatin and Pemetrexed in Patients With Advanced Non-Squamous Non-small Cell Lung Cancer (NSCLC)
NCT01570296
A Phase Ib Trial of Gefitinib (EGFR Tyrosine Kinase Inhibitor, Iressa) in Combination With BKM120, an Oral Pan-Class 1 PI3K Inhibitor in Patients With Advanced Non-small Cell Lung Cancer, With Enrichment for Patients Whose Tumors Harbor Molecular Alterations of PI3K Pathway and Known to Overexpress EGFR
NCT01723800
Phase 1 Trial of BKM120 in Combination With Carboplatin and Pemetrexed in Patients With Advanced Non-Squamous Non-small Cell Lung Cancer (NSCLC)
NCT01297491
An Open Label Two-Stage Study of Orally Administered BKM120 in Patients With Metastatic Non-small Cell Lung Cancer With Activated PI3K Pathway
NCT01390818
An Open-Label, Phase Ib Dose Escalation Trial of Oral Combination Therapy With MSC1936369B (MEK inhibitor) and SAR245409 (Pi3K/mTOR inhibitor) in Subjects With Locally Advanced or Metastatic Solid Tumors
NCT01911325
A Phase Ib/II Study of Docetaxel With or Without Buparlisib as Second Line Therapy for Patients With Advanced or Metastatic Squamous Non-small Cell Lung Cancer (Continued)
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TABLE 1
] (continued)
Genomic Alteration
KRAS
BRAF
ClinicalTrials.gov Identifier
Trial Title
NCT00975182
A Phase Ib, Open-Label, Dose-Escalation Study of the Safety and Pharmacology of GDC-0941 in Combination With Erlotinib in Patients With Advanced Solid Tumors
NCT01487265
Phase 2 Trial of Erlotinib and BKM120 in Patients With Advanced Non Small Cell Lung Cancer Previously Sensitive to Erlotinib
NCT01363232
A Phase Ib, Open-Label, Multi-center, Dose-Escalation and Expansion Study of an Orally Administered Combination of BKM120 Plus MEK162 in Adult Patients With Selected Advanced Solid Tumors
NCT01294306
Phase 2 Trial of the Akt Inhibitor MK-2206 Plus Erlotinib (OSI-774) in Patients With Advanced Non-small Cell Lung Cancer Who Have Progressed After Previous Response (Including Stable Disease) With Erlotinib Therapy
NCT01859026
A Phase 1/IB Trial of MEK162 in Combination With Erlotinib in Non-small Cell Lung Cancer (NSCLC) Harboring KRAS or EGFR Mutation
NCT01229150
Randomized Phase 2 Study of AZD6244 MEK-Inhibitor With Erlotinib in KRAS Wild Type and KRAS Mutant Advanced Non-small Cell Lung Cancer
NCT00890825
A Phase 2, Double-Blind, Randomized, Placebo-Controlled Study to Assess the Efficacy of AZD6244 (Hyd-Sulfate) in Combination With Docetaxel, Compared With Docetaxel Alone, in Second Line Patients With KRAS Mutation Positive Locally Advanced Metastatic Non Small Cell Lung Cancer (Stage IIIB- IV)
NCT01833143
A Phase 2 Trial of Bortezomib in KRAS-Mutant Non-small Cell Lung Cancer in Never Smokers or Those With KRAS G12D
NCT01951690
Phase 2 Study of VS-6063, a Focal Adhesion Kinase (FAK) Inhibitor, in Patients With KRAS Mutant Non-small Cell Lung Cancer
NCT01859026
A Phase 1/IB Trial of MEK162 in Combination With Erlotinib in Non-small Cell Lung Cancer (NSCLC) Harboring KRAS or EGFR Mutation
NCT01933932
A Phase 3, Double-Blind, Randomized, Placebo-Controlled Study to Assess the Efficacy and Safety of Selumetinib (AZD6244; ARRY-142886) (Hyd-Sulfate) in Combination With Docetaxel, in Patients Receiving Second Line Treatment of KRAS Mutation-Positive Locally Advanced or Metastatic Non Small Cell Lung Cancer (Stage IIIB - IV) (SELECT 1)
NCT02022982
Phase 1/II Study of the CDK4/6 Inhibitor Palbociclib (PD-0332991) in Combination With the MEK Inhibitor PD-0325901 for Patients With KRAS Mutant Non-small Cell Lung Cancer and Other Solid Tumors
NCT02079740
An Open Label, Two-Part, Phase Ib/II Study to Investigate the Safety, Pharmacokinetics, Pharmacodynamics, and Clinical Activity of the MEK Inhibitor Trametinib and the BCL2-Family Inhibitor Navitoclax (ABT-263) in Combination in Subjects With KRAS Mutation-Positive Advanced Solid Tumors
NCT02039336
Phase 1/II Study With the Combination of Dacomitinib and PD-0325901 in Advanced KRAS Mutation Positive Colorectal, Non-small Cell Lung and Pancreatic Cancer
NCT01336634
A Phase 2 Study of the BRAF Inhibitor Dabrafenib as a Single Agent and in Combination With the MEK Inhibitor Trametinib in Subjects With BRAF V600E Mutation Positive Metastatic (Stage IV) Non-small Cell Lung Cancer
NCT02109653
A Phase 2, Single Arm, Open-label, Multicenter, Study of Oral LGX818 in Patients With BRAF V600 Mutant, Advanced Non-small Cell Lung Cancer (NSCLC) That Have Progressed During or After at Least One Prior Chemotherapy
NCT01362296
A Phase 2, Open-label, Multicenter, Randomized Study to Assess the Efficacy and Safety of GSK1120212 Compared With Docetaxel in Second Line Subjects With Targeted Mutations (KRAS, NRAS, BRAF, MEK1) in Locally Advanced or Metastatic Non-small Cell Lung Cancer (NSCLC Stage IV) (Continued)
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TABLE 1
] (continued)
Genomic Alteration
ClinicalTrials.gov Identifier
MET
Trial Title
NCT02012231
A Phase 1/IIa Study to Assess the Safety, Pharmacokinetics, and Pharmacodynamics of PLX8394 in Patients With Advanced, Unresectable Solid Tumors
NCT00888134
Phase 2 Clinical Trial of the MEK 1/2 Inhibitor AZD6244 in Cancers With BRAF Mutations Identified by Prospective Genotypic Analysis
NCT01514864
Phase 2 Trial of Dasatinib in Subjects With Advanced Cancers Harboring DDR2 Mutation or Inactivating B-RAF Mutation
NCT01395758
A Phase 2 Randomized Open-label Study of Erlotinib Plus Tivantinib (ARQ 197) Vs Single Agent Chemotherapy in Previously Treated KRAS Mutation Positive Subjects With Locally Advanced or Metastatic Non-small Cell Lung Cancer
NCT01610336
A Phase IB/II, Open Label, Multicenter Study of INC280 Administered Orally in Combination With Gefitinib in Adult Patients With EGFR Mutated, c-MET-Amplified Non-small Cell Lung Cancer Who Have Progressed After EGFR Inhibitor Treatment
NCT01441128
A Phase 1, Open-Label, Dose Escalation Study to Evaluate Safety, Pharmacokinetics and Pharmacodynamics of Combined Oral C-Met/ALK Inhibitor (PF-02341066) and Pan-Her Inhibitor (PF-0299804) in Patients With Advanced Non-small Cell Lung Cancer
Data from clinicaltrials.gov.
Resistance to TKI from tumor transformation into small cell carcinoma in never smokers has also been reported. In these cases, the small cell carcinoma component carries the same EGFR mutation as the original adenocarcinoma.45,46 Secondary mutations in ALK have been implicated in resistance to crizotinib therapy. New compounds have shown promising results in crizotinib-resistant tumors in preclinical tests and clinical trials.47,48 Development of resistance has also been identified in other mutations.2
Role of NGS in a Comprehensive Understanding of Tumor Genome Studies of the cancer genome atlas using NGS showed that TP53, a tumor suppressor gene, is the most common mutation seen in all tumors. In lung cancer, it has been reported that in EGFR mutant adenocarcinomas, a commutation in TP53 leads to a worse prognosis and shorter response to TKI therapy.49 In fact, NGS frequently identifies mutations in tumor suppressor genes as well as mutations in chromatin remodeling genes, which are associated with epigenetic regulations of the genome. The interplay of coexisting mutations such as chromatin remodeling genes and tumor suppressor genes with targetable mutations needs to be further exploited. This is an area of future developments in
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targetable therapy as more data from NGS become available. Interestingly, not all molecular alterations can be explained by modification in the genomic DNA. DNA methylation is a mechanism implicated in silencing of gene expression. In lung carcinomas, silencing the PTEN gene by methylation is seen in approximately 50% of NSCLC,2,50 whereas mutations in the gene are rare. PTEN methylation leads to loss of protein expression and results in activation of the PIK3CA/AKT/mTOR pathway.2,28 In the future, a comprehensive approach that can evaluate DNA, RNA, and protein expression must be performed to determine the best therapeutic target for individual patients. Systematic evaluation of other histologic types of lung cancer, such as SQCC and endocrine tumors, especially small cell carcinomas, must be carried out to expand therapeutic options for these patients. NGS and proteomic studies are necessary for the identification of potential therapeutic targets and biomarkers, and generation of knowledge of the complex interplay of gene expression and signaling pathways, thus allowing for maximization of resource for therapeutic intervention in this devastating disease.
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Acknowledgments Financial/nonfinancial disclosures: The authors have reported to CHEST that no potential conflicts of interest exist with any companies/organizations whose products or services may be discussed in this article.
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