151
|
Brugger W, Triller N, Blasinska-Morawiec M, Curescu S, Sakalauskas R, Manikhas GM, Mazieres J, Whittom R, Ward C, Mayne K, Trunzer K, Cappuzzo F. Prospective molecular marker analyses of EGFR and KRAS from a randomized, placebo-controlled study of erlotinib maintenance therapy in advanced non-small-cell lung cancer. J Clin Oncol 2011; 29:4113-20. [PMID: 21969500 DOI: 10.1200/jco.2010.31.8162] [Citation(s) in RCA: 238] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
PURPOSE The phase III, randomized, placebo-controlled Sequential Tarceva in Unresectable NSCLC (SATURN; BO18192) study found that erlotinib maintenance therapy extended progression-free survival (PFS) and overall survival in patients with advanced non-small-cell lung cancer (NSCLC) who had nonprogressive disease following first-line platinum-doublet chemotherapy. This study included prospective analysis of the prognostic and predictive value of several biomarkers. PATIENTS AND METHODS Mandatory diagnostic tumor specimens were collected before initiating first-line chemotherapy and were tested for epidermal growth factor receptor (EGFR) protein expression by using immunohistochemistry (IHC), EGFR gene copy number by using fluorescent in situ hybridization (FISH), and EGFR and KRAS mutations by using DNA sequencing. An EGFR CA simple sequence repeat in intron 1 (CA-SSR1) polymorphism was evaluated in blood. RESULTS All 889 randomly assigned patients provided tumor samples. EGFR IHC, EGFR FISH, KRAS mutation, and EGFR CA-SSR1 repeat length status were not predictive for erlotinib efficacy. A profound predictive effect on PFS of erlotinib relative to placebo was observed in the EGFR mutation-positive subgroup (hazard ratio [HR], 0.10; P < .001). Significant PFS benefits were also observed with erlotinib in the wild-type EGFR subgroup (HR, 0.78; P = .0185). KRAS mutation status was a significant negative prognostic factor for PFS. CONCLUSION This large prospective biomarker study found that patients with activating EGFR mutations derive the greatest PFS benefit from erlotinib maintenance therapy. No other biomarkers were predictive for outcomes with erlotinib, although the study was not powered for clinical outcomes in biomarker subgroups other than EGFR IHC-positive [corrected]. KRAS mutations were prognostic for reduced PFS. The study demonstrated the feasibility of prospective tissue collection for biomarker analyses in NSCLC.
Collapse
Affiliation(s)
- Wolfram Brugger
- Schwarzwald-Baar Klinikum, Academic Teaching Hospital, University of Freiburg, Voehrenbacher Str 23, Villingen-Schwenningen, Germany 78050.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
152
|
Mori T, Ikeda DD, Fukushima T, Takenoshita S, Kochi H. NIRF constitutes a nodal point in the cell cycle network and is a candidate tumor suppressor. Cell Cycle 2011; 10:3284-99. [PMID: 21952639 DOI: 10.4161/cc.10.19.17176] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In biological networks, a small number of "hub" proteins play critical roles in the network integrity and functions. The cell cycle network orchestrates versatile cellular functions through interactions between many signaling modules, whose defects impair diverse cellular processes, often leading to cancer. However, the network architecture and molecular basis that ensure proper coordination between distinct modules are unclear. Here, we show that the ubiquitin ligase NIRF (also known as UHRF2), which induces G1 arrest, interacts with multiple cell cycle proteins including cyclins (A2, B1, D1 and E1), p53 and pRB, and ubiquitinates cyclins D1 and E1. Consistent with its versatility, a bioinformatic network analysis demonstrated that NIRF is an intermodular hub protein that is responsible for the coordination of multiple network modules. Notably, intermodular hubs are frequently associated with oncogenesis. Indeed, we detected loss of heterozygosity of the NIRF gene in several kinds of tumors. When a cancer outlier profile analysis was applied to the Oncomine database, loss of the NIRF gene was found at statistically significant levels in diverse tumors. Importantly, a recurrent microdeletion targeting NIRF was observed in non-small cell lung carcinoma. Furthermore, NIRF is immediately adjacent to the single nucleotide polymorphism rs719725, which is reportedly associated with the risk of colorectal cancer. These observations suggest that NIRF occupies a prominent position within the cell cycle network, and is a strong candidate for a tumor suppressor whose aberration contributes to the pathogenesis of diverse malignancies.
Collapse
Affiliation(s)
- Tsutomu Mori
- Department of Human Lifesciences, Fukushima Medical University School of Nursing, Fukushima, Japan.
| | | | | | | | | |
Collapse
|
153
|
Heuckmann JM, Hölzel M, Sos ML, Heynck S, Balke-Want H, Koker M, Peifer M, Weiss J, Lovly CM, Grütter C, Rauh D, Pao W, Thomas RK. ALK mutations conferring differential resistance to structurally diverse ALK inhibitors. Clin Cancer Res 2011; 17:7394-401. [PMID: 21948233 DOI: 10.1158/1078-0432.ccr-11-1648] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE EML4-ALK fusions define a subset of lung cancers that can be effectively treated with anaplastic lymphoma kinase (ALK) inhibitors. Unfortunately, the duration of response is heterogeneous and acquired resistance limits their ultimate efficacy. Thus, a better understanding of resistance mechanisms will help to enhance tumor control in EML4-ALK-positive tumors. EXPERIMENTAL DESIGN By applying orthogonal functional mutagenesis screening approaches, we screened for mutations inducing resistance to the aminopyridine PF02341066 (crizotinib) and/or the diaminopyrimidine TAE684. RESULTS Here, we show that the resistance mutation, L1196M, as well as other crizotinib resistance mutations (F1174L and G1269S), are highly sensitive to the structurally unrelated ALK inhibitor TAE684. In addition, we identified two novel EML4-ALK resistance mutations (L1198P and D1203N), which unlike previously reported mutations, induced resistance to both ALK inhibitors. An independent resistance screen in ALK-mutant neuroblastoma cells yielded the same L1198P resistance mutation but defined two additional mutations conferring resistance to TAE684 but not to PF02341066. CONCLUSIONS Our results show that different ALK resistance mutations as well as different ALK inhibitors impact the therapeutic efficacy in the setting of EML4-ALK fusions and ALK mutations.
Collapse
Affiliation(s)
- Johannes M Heuckmann
- Max Planck Institute for Neurological Research, Klaus-Joachim-Zülch Laboratories of the Max Planck Society, Köln, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
154
|
Abstract
Ras-deregulated cells require reactive oxygen species for proliferation. They survive the resultant proteotoxic stress by maintaining sufficient levels of reduced glutathione and optimally functioning stress response machinery. In this issue of Cancer Cell, De Raedt et al. identify a novel strategy that utilizes this dependency to cause cell death.
Collapse
Affiliation(s)
- Wanping Xu
- Urologic Oncology Branch, National Cancer Institute, Center for Cancer Research, 9000 Rockville Pike, Bethesda, MD, 20892
| | - Jane Trepel
- Medical Oncology Branch, National Cancer Institute, Center for Cancer Research, 9000 Rockville Pike, Bethesda, MD, 20892
| | - Len Neckers
- Urologic Oncology Branch, National Cancer Institute, Center for Cancer Research, 9000 Rockville Pike, Bethesda, MD, 20892
| |
Collapse
|
155
|
Wang M, Morsbach F, Sander D, Gheorghiu L, Nanda A, Benes C, Kriegs M, Krause M, Dikomey E, Baumann M, Dahm-Daphi J, Settleman J, Willers H. EGF receptor inhibition radiosensitizes NSCLC cells by inducing senescence in cells sustaining DNA double-strand breaks. Cancer Res 2011; 71:6261-9. [PMID: 21852385 DOI: 10.1158/0008-5472.can-11-0213] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The mechanisms by which inhibition of the epidermal growth factor receptor (EGFR) sensitizes non-small cell lung cancer (NSCLC) cells to ionizing radiation remain poorly understood. We set out to characterize the radiosensitizing effects of the tyrosine kinase inhibitor erlotinib and the monoclonal antibody cetuximab in NSCLC cells that contain wild-type p53. Unexpectedly, EGFR inhibition led to pronounced cellular senescence but not apoptosis of irradiated cells, both in vitro and in vivo. Senescence was completely dependent on wild-type p53 and associated with a reduction in cell number as well as impaired clonogenic radiation survival. Study of ten additional NSCLC cell lines revealed that senescence is a prominent mechanism of radiosensitization in 45% of cell lines and occurs not only in cells with wild-type p53 but also in cells with mutant p53, where it is associated with an induction of p16. Interestingly, senescence and radiosensitization were linked to an increase in residual radiation-induced DNA double-strand breaks irrespective of p53/p16 status. This effect of EGFR inhibition was at least partially mediated by disruption of the MEK-ERK pathway. Thus, our data indicate a common mechanism of radiosensitization by erlotinib or cetuximab across diverse genetic backgrounds. Our findings also suggest that assays that are able to capture the initial proliferative delay that is associated with senescence should be useful for screening large cell line panels to identify genomic biomarkers of EGFR inhibitor-mediated radiosensitization.
Collapse
Affiliation(s)
- Meng Wang
- Laboratory of Cellular & Molecular Radiation Oncology, Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
156
|
Abstract
Primary brain tumors are a leading cause of cancer-related mortality among young adults and children. The most common primary malignant brain tumor, glioma, carries a median survival of only 14 months. Two major multi-institutional programs, the Glioma Molecular Diagnostic Initiative and The Cancer Genome Atlas, have pursued a comprehensive genomic characterization of a large number of clinical glioma samples using a variety of technologies to measure gene expression, chromosomal copy number alterations, somatic and germline mutations, DNA methylation, microRNA, and proteomic changes. Classification of gliomas on the basis of gene expression has revealed six major subtypes and provided insights into the underlying biology of each subtype. Integration of genome-wide data from different technologies has been used to identify many potential protein targets in this disease, while increasing the reliability and biological interpretability of results. Mapping genomic changes onto both known and inferred cellular networks represents the next level of analysis, and has yielded proteins with key roles in tumorigenesis. Ultimately, the information gained from these approaches will be used to create customized therapeutic regimens for each patient based on the unique genomic signature of the individual tumor. In this Review, we describe efforts to characterize gliomas using genomic data, and consider how insights gained from these analyses promise to increase understanding of the biological underpinnings of the disease and lead the way to new therapeutic strategies.
Collapse
|
157
|
Hammerman PS, Sos ML, Ramos AH, Xu C, Dutt A, Zhou W, Brace LE, Woods BA, Lin W, Zhang J, Deng X, Lim SM, Heynck S, Peifer M, Simard JR, Lawrence MS, Onofrio RC, Salvesen HB, Seidel D, Zander T, Heuckmann JM, Soltermann A, Moch H, Koker M, Leenders F, Gabler F, Querings S, Ansén S, Brambilla E, Brambilla C, Lorimier P, Brustugun OT, Helland Å, Petersen I, Clement JH, Groen H, Timens W, Sietsma H, Stoelben E, Wolf J, Beer DG, Tsao MS, Hanna M, Hatton C, Eck MJ, Janne PA, Johnson BE, Winckler W, Greulich H, Bass AJ, Cho J, Rauh D, Gray NS, Wong KK, Haura EB, Thomas RK, Meyerson M. Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer. Cancer Discov 2011; 1:78-89. [PMID: 22328973 PMCID: PMC3274752 DOI: 10.1158/2159-8274.cd-11-0005] [Citation(s) in RCA: 369] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
UNLABELLED While genomically targeted therapies have improved outcomes for patients with lung adenocarcinoma, little is known about the genomic alterations which drive squamous cell lung cancer. Sanger sequencing of the tyrosine kinome identified mutations in the DDR2 kinase gene in 3.8% of squamous cell lung cancers and cell lines. Squamous lung cancer cell lines harboring DDR2 mutations were selectively killed by knock-down of DDR2 by RNAi or by treatment with the multi-targeted kinase inhibitor dasatinib. Tumors established from a DDR2 mutant cell line were sensitive to dasatinib in xenograft models. Expression of mutated DDR2 led to cellular transformation which was blocked by dasatinib. A squamous cell lung cancer patient with a response to dasatinib and erlotinib treatment harbored a DDR2 kinase domain mutation. These data suggest that gain-of-function mutations in DDR2 are important oncogenic events and are amenable to therapy with dasatinib. As dasatinib is already approved for use, these findings could be rapidly translated into clinical trials. SIGNIFICANCE DDR2 mutations are present in 4% of lung SCCs, and DDR2 mutations are associated with sensitivity to dasatinib. These findings provide a rationale for designing clinical trials with the FDA-approved drug dasatinib in patients with lung SCCs.
Collapse
Affiliation(s)
- Peter S Hammerman
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Martin L Sos
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Köln, Germany
- Department I of Internal Medicine and Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Köln – Bonn, University of Köln, Köln, Germany
| | | | - Chunxiao Xu
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Amit Dutt
- Broad Institute, Cambridge, Massachusetts, USA
| | - Wenjun Zhou
- Department of Biological Chemistry and Molecular Pharmacology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Lear E Brace
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Brittany A Woods
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Wenchu Lin
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jianming Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Xianming Deng
- Department of Biological Chemistry and Molecular Pharmacology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sang Min Lim
- Department of Biological Chemistry and Molecular Pharmacology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Stefanie Heynck
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Köln, Germany
| | - Martin Peifer
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Köln, Germany
| | - Jeffrey R Simard
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | | | | | - Helga B Salvesen
- Department of Obstetrics and Gynecology, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Danila Seidel
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Köln, Germany
| | - Thomas Zander
- Department I of Internal Medicine and Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Köln – Bonn, University of Köln, Köln, Germany
- Department I for Internal Medicine, Center for Integrated Oncology Köln-Bonn, University Hospital of Cologne, Germany
| | - Johannes M Heuckmann
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Köln, Germany
| | | | | | - Mirjam Koker
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Köln, Germany
| | - Frauke Leenders
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Köln, Germany
| | - Franziska Gabler
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Köln, Germany
| | - Silvia Querings
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Köln, Germany
| | - Sascha Ansén
- Department I for Internal Medicine, Center for Integrated Oncology Köln-Bonn, University Hospital of Cologne, Germany
| | - Elisabeth Brambilla
- Institut Albert Bonniot INSERM U823; Université Joseph Fourier Grenoble France
| | - Christian Brambilla
- Institut Albert Bonniot INSERM U823; Université Joseph Fourier Grenoble France
| | - Philippe Lorimier
- Institut Albert Bonniot INSERM U823; Université Joseph Fourier Grenoble France
| | - Odd Terje Brustugun
- Division of Surgery and Cancer, Oslo University Hospital Radiumhospitalet, Montebello 0301, Oslo, Norway
| | - Åslaug Helland
- Division of Surgery and Cancer, Oslo University Hospital Radiumhospitalet, Montebello 0301, Oslo, Norway
| | - Iver Petersen
- Jena University Hospital, Department Hematology/Oncology, Jena, Germany
| | - Joachim H Clement
- Jena University Hospital, Department Hematology/Oncology, Jena, Germany
| | - Harry Groen
- University Medical Center Groningen and University of Groningen, Pulmonology and Pathology, Groningen, Netherlands
| | - Wim Timens
- University Medical Center Groningen and University of Groningen, Pulmonology and Pathology, Groningen, Netherlands
| | - Hannie Sietsma
- University Medical Center Groningen and University of Groningen, Pulmonology and Pathology, Groningen, Netherlands
| | | | - Jürgen Wolf
- Department I of Internal Medicine and Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Köln – Bonn, University of Köln, Köln, Germany
- Department I for Internal Medicine, Center for Integrated Oncology Köln-Bonn, University Hospital of Cologne, Germany
| | - David G Beer
- Section of Thoracic Surgery, Department of Surgery, Ann Arbor, Michigan, USA
| | - Ming Sound Tsao
- Ontario Cancer Institute and Princess Margaret Hospital, Toronto, Canada
| | - Megan Hanna
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
- Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Charles Hatton
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
- Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Michael J Eck
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Pasi A Janne
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Bruce E Johnson
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Heidi Greulich
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Adam J Bass
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jeonghee Cho
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Daniel Rauh
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
- Technical University Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kwok-Kin Wong
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Eric B Haura
- Departments of Thoracic Oncology and Experimental Therapeutics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Roman K Thomas
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Köln, Germany
- Department I of Internal Medicine and Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Köln – Bonn, University of Köln, Köln, Germany
- Chemical Genomics Center of the Max Planck Society, Dortmund, Germany
| | - Matthew Meyerson
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
- Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| |
Collapse
|
158
|
Burbelo PD, Ching KH, Bren KE, Iadarola MJ. Emerging tactical strategies for fighting the war on cancer based on the genetic landscape. Am J Transl Res 2011; 3:251-258. [PMID: 21654880 PMCID: PMC3102569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 04/16/2011] [Indexed: 05/30/2023]
Abstract
Although it is well-established that cancer is driven by genetic mutations resulting in the acquisition of onco-genes and the loss of tumor suppressors, until recently many of the genomic details remained obscure. As a result of recent high-throughput DNA sequencing, basic insights into the spectrum of protein coding mutations in many cancers are now known. These findings provide an unprecedented framework of understanding and present new avenues for diagnosis, treatment, and prevention of cancer. In this article we discuss several high impact areas of global sequencing projects including developing drugs that specifically target cancer cells, creating personalized tools for better treatment and monitoring, and developing pre-symptomatic diagnostic tests. Capitalizing on these and other advances represent a new turning point in the war on cancer.
Collapse
Affiliation(s)
- Peter D Burbelo
- Neurobiology and Pain Therapeutics Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, National Institutes of Health Bethesda, MD 20892, USA
| | | | | | | |
Collapse
|
159
|
Benchmarking of mutation diagnostics in clinical lung cancer specimens. PLoS One 2011; 6:e19601. [PMID: 21573178 PMCID: PMC3088700 DOI: 10.1371/journal.pone.0019601] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 04/02/2011] [Indexed: 01/04/2023] Open
Abstract
Treatment of EGFR-mutant non-small cell lung cancer patients with the tyrosine kinase inhibitors erlotinib or gefitinib results in high response rates and prolonged progression-free survival. Despite the development of sensitive mutation detection approaches, a thorough validation of these in a clinical setting has so far been lacking. We performed, in a clinical setting, a systematic validation of dideoxy ‘Sanger’ sequencing and pyrosequencing against massively parallel sequencing as one of the most sensitive mutation detection technologies available. Mutational annotation of clinical lung tumor samples revealed that of all patients with a confirmed response to EGFR inhibition, only massively parallel sequencing detected all relevant mutations. By contrast, dideoxy sequencing missed four responders and pyrosequencing missed two responders, indicating a dramatic lack of sensitivity of dideoxy sequencing, which is widely applied for this purpose. Furthermore, precise quantification of mutant alleles revealed a low correlation (r2 = 0.27) of histopathological estimates of tumor content and frequency of mutant alleles, thereby questioning the use of histopathology for stratification of specimens for individual analytical procedures. Our results suggest that enhanced analytical sensitivity is critically required to correctly identify patients responding to EGFR inhibition. More broadly, our results emphasize the need for thorough evaluation of all mutation detection approaches against massively parallel sequencing as a prerequisite for any clinical implementation.
Collapse
|
160
|
Weiss J, Sos ML, Seidel D, Peifer M, Zander T, Heuckmann JM, Ullrich RT, Menon R, Maier S, Soltermann A, Moch H, Wagener P, Fischer F, Heynck S, Koker M, Schöttle J, Leenders F, Gabler F, Dabow I, Querings S, Heukamp LC, Balke-Want H, Ansén S, Rauh D, Baessmann I, Altmüller J, Wainer Z, Conron M, Wright G, Russell P, Solomon B, Brambilla E, Brambilla C, Lorimier P, Sollberg S, Brustugun OT, Engel-Riedel W, Ludwig C, Petersen I, Sänger J, Clement J, Groen H, Timens W, Sietsma H, Thunnissen E, Smit E, Heideman D, Cappuzzo F, Ligorio C, Damiani S, Hallek M, Beroukhim R, Pao W, Klebl B, Baumann M, Buettner R, Ernestus K, Stoelben E, Wolf J, Nürnberg P, Perner S, Thomas RK. Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer. Sci Transl Med 2011; 2:62ra93. [PMID: 21160078 DOI: 10.1126/scitranslmed.3001451] [Citation(s) in RCA: 652] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Lung cancer remains one of the leading causes of cancer-related death in developed countries. Although lung adenocarcinomas with EGFR mutations or EML4-ALK fusions respond to treatment by epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) inhibition, respectively, squamous cell lung cancer currently lacks therapeutically exploitable genetic alterations. We conducted a systematic search in a set of 232 lung cancer specimens for genetic alterations that were therapeutically amenable and then performed high-resolution gene copy number analyses. We identified frequent and focal fibroblast growth factor receptor 1 (FGFR1) amplification in squamous cell lung cancer (n = 155), but not in other lung cancer subtypes, and, by fluorescence in situ hybridization, confirmed the presence of FGFR1 amplifications in an independent cohort of squamous cell lung cancer samples (22% of cases). Using cell-based screening with the FGFR inhibitor PD173074 in a large (n = 83) panel of lung cancer cell lines, we demonstrated that this compound inhibited growth and induced apoptosis specifically in those lung cancer cells carrying amplified FGFR1. We validated the FGFR1 dependence of FGFR1-amplified cell lines by FGFR1 knockdown and by ectopic expression of an FGFR1-resistant allele (FGFR1(V561M)), which rescued FGFR1-amplified cells from PD173074-mediated cytotoxicity. Finally, we showed that inhibition of FGFR1 with a small molecule led to significant tumor shrinkage in vivo. Thus, focal FGFR1 amplification is common in squamous cell lung cancer and associated with tumor growth and survival, suggesting that FGFR inhibitors may be a viable therapeutic option in this cohort of patients.
Collapse
Affiliation(s)
- Jonathan Weiss
- Max Planck Institute for Neurological Research, Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Cologne, 50931 Cologne, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
161
|
MicroRNA gene dosage alterations and drug response in lung cancer. J Biomed Biotechnol 2011; 2011:474632. [PMID: 21541180 PMCID: PMC3085440 DOI: 10.1155/2011/474632] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 01/27/2011] [Indexed: 12/26/2022] Open
Abstract
Chemotherapy resistance is a key contributor to the dismal prognoses for lung cancer patients. While the majority of studies have focused on sequence mutations and expression changes in protein-coding genes, recent reports have suggested that microRNA (miRNA) expression changes also play an influential role in chemotherapy response. However, the role of genetic alterations at miRNA loci in the context of chemotherapy response has yet to be investigated. In this study, we demonstrate the application of an integrative, multidimensional approach in order to identify miRNAs that are associated with chemotherapeutic resistance and sensitivity utilizing publicly available drug response, miRNA loci copy number, miRNA expression, and mRNA expression data from independent resources. By instigating a logical stepwise strategy, we have identified specific miRNAs that are associated with resistance to several chemotherapeutic agents and provide a proof of principle demonstration of how these various databases may be exploited to derive relevant pharmacogenomic results.
Collapse
|
162
|
Advances in the preclinical testing of cancer therapeutic hypotheses. Nat Rev Drug Discov 2011; 10:179-87. [DOI: 10.1038/nrd3385] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
163
|
Dutt A, Ramos AH, Hammerman PS, Mermel C, Cho J, Sharifnia T, Chande A, Tanaka KE, Stransky N, Greulich H, Gray NS, Meyerson M. Inhibitor-sensitive FGFR1 amplification in human non-small cell lung cancer. PLoS One 2011; 6:e20351. [PMID: 21666749 PMCID: PMC3110189 DOI: 10.1371/journal.pone.0020351] [Citation(s) in RCA: 299] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 04/30/2011] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Squamous cell lung carcinomas account for approximately 25% of new lung carcinoma cases and 40,000 deaths per year in the United States. Although there are multiple genomically targeted therapies for lung adenocarcinoma, none has yet been reported in squamous cell lung carcinoma. METHODOLOGY/PRINCIPAL FINDINGS Using SNP array analysis, we found that a region of chromosome segment 8p11-12 containing three genes-WHSC1L1, LETM2, and FGFR1-is amplified in 3% of lung adenocarcinomas and 21% of squamous cell lung carcinomas. Furthermore, we demonstrated that a non-small cell lung carcinoma cell line harboring focal amplification of FGFR1 is dependent on FGFR1 activity for cell growth, as treatment of this cell line either with FGFR1-specific shRNAs or with FGFR small molecule enzymatic inhibitors leads to cell growth inhibition. CONCLUSIONS/SIGNIFICANCE These studies show that FGFR1 amplification is common in squamous cell lung cancer, and that FGFR1 may represent a promising therapeutic target in non-small cell lung cancer.
Collapse
Affiliation(s)
- Amit Dutt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Kharghar, Navi Mumbai, India
- * E-mail: (MM); (AD)
| | - Alex H. Ramos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter S. Hammerman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Craig Mermel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeonghee Cho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Tanaz Sharifnia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - Ajit Chande
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Kharghar, Navi Mumbai, India
| | - Kumiko Elisa Tanaka
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - Nicolas Stransky
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - Heidi Greulich
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nathanael S. Gray
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (MM); (AD)
| |
Collapse
|
164
|
Su Z, Dias-Santagata D, Duke M, Hutchinson K, Lin YL, Borger DR, Chung CH, Massion PP, Vnencak-Jones CL, Iafrate AJ, Pao W. A platform for rapid detection of multiple oncogenic mutations with relevance to targeted therapy in non-small-cell lung cancer. J Mol Diagn 2011; 13:74-84. [PMID: 21227397 PMCID: PMC3070558 DOI: 10.1016/j.jmoldx.2010.11.010] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 07/17/2010] [Accepted: 08/18/2010] [Indexed: 11/19/2022] Open
Abstract
The identification of somatically acquired tumor mutations is increasingly important in the clinical management of cancer because the sensitivity of targeted drugs is related to the genetic makeup of individual tumors. Thus, mutational profiles of tumors can help prioritize anticancer therapy. We report herein the development and validation of two multiplexed assays designed to detect in DNA from FFPE tissue more than 40 recurrent mutations in nine genes relevant to existing and emerging targeted therapies in lung cancer. The platform involves two methods: a screen (SNaPshot) based on multiplex PCR, primer extension, and capillary electrophoresis that was designed to assess for 38 somatic mutations in eight genes (AKT1, BRAF, EGFR, KRAS, MEK1, NRAS, PIK3CA, and PTEN) and a PCR-based sizing assay that assesses for EGFR exon 19 deletions, EGFR exon 20 insertions, and HER2 exon 20 insertions. Both the SNaPshot and sizing assays can be performed rapidly, with minimal amounts of genetic material. Compared with direct sequencing, in which mutant DNA needs to compose 25% or more of the total DNA to easily detect a mutation, the SNaPshot and sizing assays can detect mutations in samples in which mutant DNA composes 1.56% to 12.5% and 1.56% to 6.25% of the total DNA, respectively. These robust, reliable, and relatively inexpensive assays should help accelerate adoption of a genotype-driven approach in the treatment of lung cancer.
Collapse
Affiliation(s)
- Zengliu Su
- Vanderbilt-Ingram Cancer Center, the Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Dora Dias-Santagata
- Translational Research Laboratory, Massachusetts General Hospital, Boston, Massachusetts
| | - MarKeesa Duke
- Vanderbilt-Ingram Cancer Center, the Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Katherine Hutchinson
- Vanderbilt-Ingram Cancer Center, the Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Ya-Lun Lin
- Vanderbilt-Ingram Cancer Center, the Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Darrell R. Borger
- Translational Research Laboratory, Massachusetts General Hospital, Boston, Massachusetts
| | - Christine H. Chung
- Vanderbilt-Ingram Cancer Center, the Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Pierre P. Massion
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Cindy L. Vnencak-Jones
- Departments of Pathology and Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - A. John Iafrate
- Translational Research Laboratory, Massachusetts General Hospital, Boston, Massachusetts
| | - William Pao
- Vanderbilt-Ingram Cancer Center, the Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee
| |
Collapse
|
165
|
[Oncology and palliative medicine]. Internist (Berl) 2010; 52:15-6, 18-9. [PMID: 21181108 DOI: 10.1007/s00108-010-2689-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Approximately one half of patients who receive the diagnosis of cancer still die as the result of their disease. To be able to adequately meet the patients and their families needs, it is essential that oncologists and palliative care physicians cooperate closely. How the recommendations of international institutions are concerning the cooperation between the fields of oncology and palliative care medicine can be approached is exemplified by the concepts developed in the Center for Integrated Oncology (CIO Cologne/Bonn) at the University Hospital in Cologne and discussed critically.
Collapse
|
166
|
Mayer EL, Krop IE. Advances in targeting SRC in the treatment of breast cancer and other solid malignancies. Clin Cancer Res 2010; 16:3526-32. [PMID: 20634194 DOI: 10.1158/1078-0432.ccr-09-1834] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Src, a membrane-associated nonreceptor tyrosine kinase, plays a crucial role in the coordination and facilitation of cell-signaling pathways controlling a wide range of cellular functions, including growth, survival, invasion, adhesion, and migration. Deregulation and increased activity of Src has been observed in multiple human malignancies, prompting the development of specific inhibitors of Src. In preclinical studies, Src inhibitors show antitumor effects in multiple solid tumor types. Recently completed early-phase trials using the inhibitors dasatinib and bosutinib have suggested modest activity as monotherapy in breast and prostate cancer, with potentially greater activity in combination regimens. Given the interaction between Src and the estrogen receptor, ongoing trials are exploring combinations with endocrine therapy. The relationship between Src and the vascular endothelial growth factor receptor also justifies investigation of combinations with angiogenesis inhibitors. Future trials will continue to explore the contribution of Src inhibition with both chemotherapy and targeted agents.
Collapse
Affiliation(s)
- Erica L Mayer
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.
| | | |
Collapse
|
167
|
Etemadmoghadam D, George J, Cowin PA, Cullinane C, Kansara M, Gorringe KL, Smyth GK, Bowtell DDL. Amplicon-dependent CCNE1 expression is critical for clonogenic survival after cisplatin treatment and is correlated with 20q11 gain in ovarian cancer. PLoS One 2010; 5:e15498. [PMID: 21103391 PMCID: PMC2980490 DOI: 10.1371/journal.pone.0015498] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 10/17/2010] [Indexed: 01/02/2023] Open
Abstract
Genomic amplification of 19q12 occurs in several cancer types including ovarian cancer where it is associated with primary treatment failure. We systematically attenuated expression of genes within the minimally defined 19q12 region in ovarian cell lines using short-interfering RNAs (siRNA) to identify driver oncogene(s) within the amplicon. Knockdown of CCNE1 resulted in G1/S phase arrest, reduced cell viability and apoptosis only in amplification-carrying cells. Although CCNE1 knockdown increased cisplatin resistance in short-term assays, clonogenic survival was inhibited after treatment. Gain of 20q11 was highly correlated with 19q12 amplification and spanned a 2.5 Mb region including TPX2, a centromeric protein required for mitotic spindle function. Expression of TPX2 was highly correlated with gene amplification and with CCNE1 expression in primary tumors. siRNA inhibition of TPX2 reduced cell viability but this effect was not amplicon-dependent. These findings demonstrate that CCNE1 is a key driver in the 19q12 amplicon required for survival and clonogenicity in cells with locus amplification. Co-amplification at 19q12 and 20q11 implies the presence of a cooperative mutational network. These observations have implications for the application of targeted therapies in CCNE1 dependent ovarian cancers.
Collapse
Affiliation(s)
| | - Joshy George
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
- Department of Biochemistry, University of Melbourne, Parkville, Australia
| | - Prue A. Cowin
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | - Carleen Cullinane
- Translational Research Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | - Maya Kansara
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | | | - Kylie L. Gorringe
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
- Department of Pathology, University of Melbourne, Parkville, Australia
| | - Gordon K. Smyth
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - David D. L. Bowtell
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
- Department of Biochemistry, University of Melbourne, Parkville, Australia
- * E-mail:
| |
Collapse
|
168
|
Rode HB, Sos ML, Grütter C, Heynck S, Simard JR, Rauh D. Synthesis and biological evaluation of 7-substituted-1-(3-bromophenylamino)isoquinoline-4-carbonitriles as inhibitors of myosin light chain kinase and epidermal growth factor receptor. Bioorg Med Chem 2010; 19:429-39. [PMID: 21130659 DOI: 10.1016/j.bmc.2010.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 11/02/2010] [Accepted: 11/04/2010] [Indexed: 12/22/2022]
Abstract
Here we present the synthesis and biological activity of a series of 7-substituted-1-(3-bromophenylamino)isoquinoline-4-carbonitriles as inhibitors of myosin light chain kinase (MLCK) and the epidermal growth factor receptor kinase (EGFR). The inhibitory effect of these molecules was found to be dependent on the nature of the substituents at the 7-position of the isoquinoline scaffold.
Collapse
Affiliation(s)
- Haridas B Rode
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany
| | | | | | | | | | | |
Collapse
|
169
|
Rothschild SI, Gautschi O, Haura EB, Johnson FM. Src inhibitors in lung cancer: current status and future directions. Clin Lung Cancer 2010; 11:238-42. [PMID: 20630825 DOI: 10.3816/clc.2010.n.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Src tyrosine kinases regulate multiple genetic and signaling pathways involved in the proliferation, survival, angiogenesis, invasion, and migration of various types of cancer cells They are frequently expressed and activated in many cancer types, including lung cancer. Several Src inhibitors, including dasatinib, saracatinib, bosutinib, and KX2-391, are currently being investigated in clinical trials. Preliminary results of the use of single-agent Src inhibitors in unselected patients with lung cancer show that these inhibitors have a favorable safety profile and anticancer activity. Their combination with cytotoxic chemotherapy, other targeted therapy, and radiation therapy is currently being explored. In this review, we summarize the rationale for and the current status of Src inhibitor development and discuss future directions based on emerging preclinical data.
Collapse
Affiliation(s)
- Sacha I Rothschild
- Department of Medical Oncology, University and University Hospital of Bern, Switzerland.
| | | | | | | |
Collapse
|
170
|
Abstract
We outline the near 50-year history of leukemia-lymphoma (LL) cell lines - a key model system in biomedicine. Due to the detailed documentation of their oncogenomic and transcriptional alterations via recent advances in molecular medicine, LL cell lines may be fitted to parent tumors with a degree of precision unattainable in other cancers. We have surveyed the corpus of published LL cell lines and found 637 examples that meet minimum standards of authentication and characterization. Alarmingly, the rate of establishment of new LL cell lines has plummeted over the last decade. Although the main hematopoietic developmental cell types are represented by cell lines, some LL categories stubbornly resist establishment in vitro. The advent of engineering techniques for immortalizing primary human cells that maintain differentiation means the time is ripe for renewed search for in vitro models from un(der)represented hematologic entities. Given their manifold applications in biomedicine, there is little doubt that LL-derived cell lines will continue to play a vital part well into the next half-century as well.
Collapse
Affiliation(s)
- Hans G Drexler
- DSMZ-German Collection of Microorganisms & Cell Cultures, Department of Human and Animal Cell Cultures, Braunschweig, Germany.
| | | |
Collapse
|
171
|
Nagji AS, Cho SH, Liu Y, Lee JK, Jones DR. Multigene expression-based predictors for sensitivity to Vorinostat and Velcade in non-small cell lung cancer. Mol Cancer Ther 2010; 9:2834-43. [PMID: 20713531 PMCID: PMC2953585 DOI: 10.1158/1535-7163.mct-10-0327] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The ability to predict the efficacy of molecularly targeted therapies for non-small cell lung cancer (NSCLC) for an individual patient remains problematic. The purpose of this study was to identify, using a refined "coexpression extrapolation (COXEN)" algorithm with a continuous spectrum of drug activity, tumor biomarkers that predict drug sensitivity and therapeutic efficacy in NSCLC to Vorinostat, a histone deacetylase inhibitor, and Velcade, a proteasome inhibitor. Using our refined COXEN algorithm, biomarker prediction models were discovered and trained for Vorinostat and Velcade based on the in vitro drug activity profiles of nine NSCLC cell lines (NCI-9). Independently, a panel of 40 NSCLC cell lines (UVA-40) were treated with Vorinostat or Velcade to obtain 50% growth inhibition values. Genome-wide expression profiles for both the NCI-9 and UVA-40 cell lines were determined using the Affymetrix HG-U133A platform. Modeling generated multigene expression signatures for Vorinostat (45-gene; P = 0.002) and Velcade (15-gene; P = 0.0002), with one overlapping gene (CFLAR). Examination of Vorinostat gene ontogeny revealed a predilection for cellular replication and death, whereas that of Velcade suggested involvement in cellular development and carcinogenesis. Multivariate regression modeling of the refined COXEN scores significantly predicted the activity of combination therapy in NSCLC cells (P = 0.007). Through the refinement of the COXEN algorithm, we provide an in silico method to generate biomarkers that predict tumor sensitivity to molecularly targeted therapies. Use of this refined COXEN method has significant implications for the a priori examination of targeted therapies to more effectively streamline subsequent clinical trial design and cost.
Collapse
Affiliation(s)
- Alykhan S. Nagji
- Department of Surgery, University of Virginia, Charlottesville, Virginia
| | - Sang-Hoon Cho
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Yuan Liu
- Department of Surgery, University of Virginia, Charlottesville, Virginia
| | - Jae K. Lee
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
- Department of Statistics, University of Virginia, Charlottesville, Virginia
| | - David R. Jones
- Department of Surgery, University of Virginia, Charlottesville, Virginia
| |
Collapse
|
172
|
Johnson FM, Bekele BN, Feng L, Wistuba I, Tang XM, Tran HT, Erasmus JJ, Hwang LL, Takebe N, Blumenschein GR, Lippman SM, Stewart DJ. Phase II study of dasatinib in patients with advanced non-small-cell lung cancer. J Clin Oncol 2010; 28:4609-15. [PMID: 20855820 DOI: 10.1200/jco.2010.30.5474] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Src family kinases (SFKs) promote cancer progression and are commonly expressed in non-small-cell lung cancer (NSCLC), but the clinical effects of SFK inhibition in NSCLC are unknown. We conducted a phase II trial of the SFK inhibitor dasatinib for advanced NSCLC. We tested the hypotheses that the activation of epidermal growth factor receptor (EGFR) or SFK or modulation of serum cytokines may predict a response to dasatinib. PATIENTS AND METHODS Patients received dasatinib as first-line therapy. Response was measured by tumor size on computed tomography scans and by metabolic activity on positron emission tomography scans. Tissue samples taken before patients received dasatinib were tested for EGFR and Kras mutation and phosphorylated SFK expression. RESULTS Thirty-four patients were enrolled. The overall disease control rate (partial responses plus stable disease) for dasatinib was 43%. One patient had a partial response to therapy. Eleven patients (32%) had a metabolic response to dasatinib. SFK activation and EGFR and Kras mutations in tumor tissue did not predict response to dasatinib. Significant toxicities included fatigue and dyspnea. The presence of a pleural effusion before dasatanib therapy predicted the development of a clinically significant effusion during therapy. CONCLUSION Dasatinib as a single agent had modest clinical activity that was lower than that generally observed in patients with NSCLC who receive chemotherapy. Pleural effusion was an expected and problematic toxicity that was successfully treated with steroids, diuretics, and dose interruptions. Marked activity in one patient and prolonged stable disease in four others suggested a potential subpopulation of patients with dasatinib-sensitive NSCLC.
Collapse
Affiliation(s)
- Faye M Johnson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030-4009, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
173
|
Schreiber SL, Shamji AF, Clemons PA, Hon C, Koehler AN, Munoz B, Palmer M, Stern AM, Wagner BK, Powers S, Lowe SW, Guo X, Krasnitz A, Sawey ET, Sordella R, Stein L, Trotman LC, Califano A, Dalla-Favera R, Ferrando A, Iavarone A, Pasqualucci L, Silva J, Stockwell BR, Hahn WC, Chin L, DePinho RA, Boehm JS, Gopal S, Huang A, Root DE, Weir BA, Gerhard DS, Zenklusen JC, Roth MG, White MA, Minna JD, MacMillan JB, Posner BA. Towards patient-based cancer therapeutics. Nat Biotechnol 2010; 28:904-6. [PMID: 20829823 PMCID: PMC2939009 DOI: 10.1038/nbt0910-904] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A new approach to the discovery of cancer therapeutics is emerging that begins with the cancer patient. Genomic analysis of primary tumors is providing an unprecedented molecular characterization of the disease. The next step requires relating the genetic features of cancers to acquired gene and pathway dependencies and identifying small-molecule therapeutics that target them.
Collapse
|
174
|
Dias-Santagata D, Akhavanfard S, David SS, Vernovsky K, Kuhlmann G, Boisvert SL, Stubbs H, McDermott U, Settleman J, Kwak EL, Clark JW, Isakoff SJ, Sequist LV, Engelman JA, Lynch TJ, Haber DA, Louis DN, Ellisen LW, Borger DR, Iafrate AJ. Rapid targeted mutational analysis of human tumours: a clinical platform to guide personalized cancer medicine. EMBO Mol Med 2010; 2:146-58. [PMID: 20432502 PMCID: PMC3377316 DOI: 10.1002/emmm.201000070] [Citation(s) in RCA: 326] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Targeted cancer therapy requires the rapid and accurate identification of genetic abnormalities predictive of therapeutic response. We sought to develop a high-throughput genotyping platform that would allow prospective patient selection to the best available therapies, and that could readily and inexpensively be adopted by most clinical laboratories. We developed a highly sensitive multiplexed clinical assay that performs very well with nucleic acid derived from formalin fixation and paraffin embedding (FFPE) tissue, and tests for 120 previously described mutations in 13 cancer genes. Genetic profiling of 250 primary tumours was consistent with the documented oncogene mutational spectrum and identified rare events in some cancer types. The assay is currently being used for clinical testing of tumour samples and contributing to cancer patient management. This work therefore establishes a platform for real-time targeted genotyping that can be widely adopted. We expect that efforts like this one will play an increasingly important role in cancer management.
Collapse
Affiliation(s)
- Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
175
|
Gazdar AF, Girard L, Lockwood WW, Lam WL, Minna JD. Lung cancer cell lines as tools for biomedical discovery and research. J Natl Cancer Inst 2010; 102:1310-21. [PMID: 20679594 DOI: 10.1093/jnci/djq279] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Lung cancer cell lines have made a substantial contribution to lung cancer translational research and biomedical discovery. A systematic approach to initiating and characterizing cell lines from small cell and non-small cell lung carcinomas has led to the current collection of more than 200 lung cancer cell lines, a number that exceeds those for other common epithelial cancers combined. The ready availability and widespread dissemination of the lines to investigators worldwide have resulted in more than 9000 citations, including multiple examples of important biomedical discoveries. The high (but not perfect) genomic similarities between lung cancer cell lines and the lung tumor type from which they were derived provide evidence of the relevance of their use. However, major problems including misidentification or cell line contamination remain. Ongoing studies and new approaches are expected to reveal the full potential of the lung cancer cell line panel.
Collapse
Affiliation(s)
- Adi F Gazdar
- University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390-8593, USA.
| | | | | | | | | |
Collapse
|
176
|
Robubi A, Waldmann H, Rauh D. RAF Kinase Inhibitors in Cancer Treatment: Like a Bull in a China Shop? Chembiochem 2010; 11:1645-8. [DOI: 10.1002/cbic.201000348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
177
|
Array comparative genomic hybridization-based characterization of genetic alterations in pulmonary neuroendocrine tumors. Proc Natl Acad Sci U S A 2010; 107:13040-5. [PMID: 20615970 DOI: 10.1073/pnas.1008132107] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The goal of this study was to characterize and classify pulmonary neuroendocrine tumors based on array comparative genomic hybridization (aCGH). Using aCGH, we performed karyotype analysis of 33 small cell lung cancer (SCLC) tumors, 13 SCLC cell lines, 19 bronchial carcinoids, and 9 gastrointestinal carcinoids. In contrast to the relatively conserved karyotypes of carcinoid tumors, the karyotypes of SCLC tumors and cell lines were highly aberrant. High copy number (CN) gains were detected in SCLC tumors and cell lines in cytogenetic bands encoding JAK2, FGFR1, and MYC family members. In some of those samples, the CN of these genes exceeded 100, suggesting that they could represent driver alterations and potential drug targets in subgroups of SCLC patients. In SCLC tumors, as well as bronchial carcinoids and carcinoids of gastrointestinal origin, recurrent CN alterations were observed in 203 genes, including the RB1 gene and 59 microRNAs of which 51 locate in the DLK1-DIO3 domain. These findings suggest the existence of partially shared CN alterations in these tumor types. In contrast, CN alterations of the TP53 gene and the MYC family members were predominantly observed in SCLC. Furthermore, we demonstrated that the aCGH profile of SCLC cell lines highly resembles that of clinical SCLC specimens. Finally, by analyzing potential drug targets, we provide a genomics-based rationale for targeting the AKT-mTOR and apoptosis pathways in SCLC.
Collapse
|
178
|
Suda K, Tomizawa K, Mitsudomi T. Biological and clinical significance of KRAS mutations in lung cancer: an oncogenic driver that contrasts with EGFR mutation. Cancer Metastasis Rev 2010; 29:49-60. [PMID: 20108024 DOI: 10.1007/s10555-010-9209-4] [Citation(s) in RCA: 162] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
KRAS and epidermal growth factor receptor (EGFR) are the two most frequently mutated proto-oncogenes in adenocarcinoma of the lung. The occurrence of these two oncogenic mutations is mutually exclusive, and they exhibit many contrasting characteristics such as clinical background, pathological features of patients harboring each mutation, and prognostic or predictive implications. Lung cancers harboring the EGFR mutations are remarkably sensitive to EGFR tyrosine kinase inhibitors such as gefitinib or erlotinib. This discovery has dramatically changed the clinical treatment of lung cancer in that it almost doubled the duration of survival for lung cancer patients with an EGFR mutation. In this review, we describe the features of KRAS mutations in lung cancer and contrast these with the features of EGFR mutations. Recent strategies to combat lung cancer harboring KRAS mutations are also reviewed.
Collapse
Affiliation(s)
- Kenichi Suda
- Department of Thoracic Surgery, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, 464-8681, Japan
| | | | | |
Collapse
|
179
|
|
180
|
Sharma SV, Haber DA, Settleman J. Cell line-based platforms to evaluate the therapeutic efficacy of candidate anticancer agents. Nat Rev Cancer 2010; 10:241-53. [PMID: 20300105 DOI: 10.1038/nrc2820] [Citation(s) in RCA: 407] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Efforts to discover new cancer drugs and predict their clinical activity are limited by the fact that laboratory models to test drug efficacy do not faithfully recapitulate this complex disease. One important model system for evaluating candidate anticancer agents is human tumour-derived cell lines. Although cultured cancer cells can exhibit distinct properties compared with their naturally growing counterparts, recent technologies that facilitate the parallel analysis of large panels of such lines, together with genomic technologies that define their genetic constitution, have revitalized efforts to use cancer cell lines to assess the clinical utility of new investigational cancer drugs and to discover predictive biomarkers.
Collapse
Affiliation(s)
- Sreenath V Sharma
- Center for Molecular Therapeutics, Massachusetts General Hospital Cancer Center and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA
| | | | | |
Collapse
|
181
|
Keller U, von Bubnoff N, Peschel C, Duyster J. Oncologist's/haematologist's view on the roles of pathologists for molecular targeted cancer therapy. J Cell Mol Med 2010; 14:805-17. [PMID: 20158573 PMCID: PMC3823113 DOI: 10.1111/j.1582-4934.2010.01032.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In the past two decades there has been a tremendous increase in the understanding of the molecular basis of human malignancies. In a variety of neoplasms, specific molecular markers became part of disease classifications and are now routinely used to define specific entities. Molecular analyses discriminate prognostic groups, guide differential treatment strategies and identify targets for molecular defined cancer therapy. A battery of new drugs has been developed to specifically inhibit oncogenic pathways. For an increasing number of solid and haematological malignancies, the availability of molecular targeted drugs has fundamentally changed treatment algorithms. However, the diagnostic, prognostic and therapeutic impact of selected molecular markers is still limited in many cases. After all, the success of a molecular targeted therapy is clearly determined by the significance of the targeted structure for the biology of cancer and the ability of the malignant cell to evade specific inhibition.
Collapse
Affiliation(s)
- Ulrich Keller
- III. Medical Department, Technische Universität München, Munich, Germany.
| | | | | | | |
Collapse
|
182
|
Current world literature. Curr Opin Oncol 2010; 22:155-61. [PMID: 20147786 DOI: 10.1097/cco.0b013e32833681df] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
183
|
Haura EB, Tanvetyanon T, Chiappori A, Williams C, Simon G, Antonia S, Gray J, Litschauer S, Tetteh L, Neuger A, Song L, Rawal B, Schell MJ, Bepler G. Phase I/II study of the Src inhibitor dasatinib in combination with erlotinib in advanced non-small-cell lung cancer. J Clin Oncol 2010; 28:1387-94. [PMID: 20142592 DOI: 10.1200/jco.2009.25.4029] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Src family kinase (SFK) proteins are frequently activated in cancer and can coordinate tumor cell growth, survival, invasion, and angiogenesis. Given the importance of SFK signaling in cancer, known cooperation between SFK and epidermal growth factor receptor (EGFR) signaling, and efficacy of EGFR inhibitors, we performed a phase I trial combining dasatinib, an SFK and multikinase inhibitor, with erlotinib, an EGFR inhibitor, in patients with advanced non-small-cell lung cancer. PATIENTS AND METHODS Patients received erlotinib for 1 week before addition of dasatinib; pharmacokinetics were performed after weeks 1 and 2. Four cohorts were examined, including twice-daily and daily dasatinib dosing. Responses were assessed after 8 weeks. Plasma levels of angiogenic markers (vascular endothelial growth factor [VEGF], interleukin-8, and basic fibroblast growth factor [bFGF]) were determined before and during treatment. RESULTS Thirty-four patients were enrolled. The average duration of treatment was 73 days. The main adverse events include GI (diarrhea, anorexia, and nausea), skin rash, cytopenias, pleural effusions, and fatigue. No effect of escalating doses of dasatinib was observed on erlotinib pharmacokinetics. Two partial responses and one bone response were observed, and the disease control rate was 63%. Reductions in plasma VEGF and bFGF were observed, and reductions in VEGF correlated with disease control. CONCLUSION The combination of erlotinib and dasatinib is tolerable, with adverse effects consistent with the two agents. Disease control and inhibition of plasma angiogenesis markers were observed. Personalized strategies for deployment of SFK should receive further attention.
Collapse
Affiliation(s)
- Eric B Haura
- Department of Thoracic Oncology and Biostatistics, Clinical Trials and Clinical Pharmacology Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612-9497, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
184
|
Peifer M, Weiss J, Sos ML, Koker M, Heynck S, Netzer C, Fischer S, Rode H, Rauh D, Rahnenführer J, Thomas RK. Analysis of compound synergy in high-throughput cellular screens by population-based lifetime modeling. PLoS One 2010; 5:e8919. [PMID: 20111714 PMCID: PMC2811738 DOI: 10.1371/journal.pone.0008919] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Accepted: 01/08/2010] [Indexed: 12/12/2022] Open
Abstract
Despite the successful introduction of potent anti-cancer therapeutics, most of these drugs lead to only modest tumor-shrinkage or transient responses, followed by re-growth of tumors. Combining different compounds has resulted in enhanced tumor control and prolonged survival. However, methods querying the efficacy of such combinations have been hampered by limited scalability, analytical resolution, statistical feasibility, or a combination thereof. We have developed a theoretical framework modeling cellular viability as a stochastic lifetime process to determine synergistic compound combinations from high-throughput cellular screens. We apply our method to data derived from chemical perturbations of 65 cancer cell lines with two inhibitors. Our analysis revealed synergy for the combination of both compounds in subsets of cell lines. By contrast, in cell lines in which inhibition of one of both targets was sufficient to induce cell death, no synergy was detected, compatible with the topology of the oncogenically activated signaling network. In summary, we provide a tool for the measurement of synergy strength for combination perturbation experiments that might help define pathway topologies and direct clinical trials.
Collapse
Affiliation(s)
- Martin Peifer
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Max Planck Society, Köln, Germany
- * E-mail: (MP); (RT)
| | - Jonathan Weiss
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Max Planck Society, Köln, Germany
| | - Martin L. Sos
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Max Planck Society, Köln, Germany
| | - Mirjam Koker
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Max Planck Society, Köln, Germany
| | - Stefanie Heynck
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Max Planck Society, Köln, Germany
| | - Christian Netzer
- Department of Statistics, Technical University of Dortmund, Dortmund, Germany
| | - Stefanie Fischer
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Max Planck Society, Köln, Germany
| | - Haridas Rode
- Chemical Genomics Center of the Max Planck Society, Max Planck Society, Dortmund, Germany
| | - Daniel Rauh
- Chemical Genomics Center of the Max Planck Society, Max Planck Society, Dortmund, Germany
| | - Jörg Rahnenführer
- Department of Statistics, Technical University of Dortmund, Dortmund, Germany
| | - Roman K. Thomas
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max Planck Society and the Medical Faculty of the University of Köln, Max Planck Society, Köln, Germany
- Department I of Internal Medicine and Center of Integrated Oncology Köln – Bonn, University of Köln, Köln, Germany
- Chemical Genomics Center of the Max Planck Society, Max Planck Society, Dortmund, Germany
- * E-mail: (MP); (RT)
| |
Collapse
|
185
|
Sos ML, Rode HB, Heynck S, Peifer M, Fischer F, Klüter S, Pawar VG, Reuter C, Heuckmann JM, Weiss J, Ruddigkeit L, Rabiller M, Koker M, Simard JR, Getlik M, Yuza Y, Chen TH, Greulich H, Thomas RK, Rauh D. Chemogenomic Profiling Provides Insights into the Limited Activity of Irreversible EGFR Inhibitors in Tumor Cells Expressing the T790M EGFR Resistance Mutation. Cancer Res 2010; 70:868-74. [DOI: 10.1158/0008-5472.can-09-3106] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
186
|
Abstract
Guidance molecules were first described in the nervous system to control axon outgrowth direction. They are also widely expressed outside the nervous system where they control cell migration, tissue development and establishment of the vascular network. In addition, they are involved in cancer development, tumor angiogenesis and metastasis. This review is primarily focused on their functions in lung cancer and their involvement in lung development is also presented. Five guidance molecule families and their corresponding receptors are described, including the semaphorins/neuropilins/plexins, ephrins and Eph receptors, netrin/DCC/UNC5, Slit/Robo and Notch/Delta. In addition, the possibility to target these molecules as a therapeutic approach in cancer is discussed.
Collapse
Affiliation(s)
- Patrick Nasarre
- Medical University of South Carolina, Division of Hematology/Oncology, Charleston, SC, USA
| | | | | | | |
Collapse
|
187
|
Benes C, Settleman J. Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug? BMC Med 2009; 7:78. [PMID: 20003409 PMCID: PMC2799438 DOI: 10.1186/1741-7015-7-78] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 12/14/2009] [Indexed: 12/18/2022] Open
Abstract
It is becoming increasingly apparent that cancer drug therapies can only reach their full potential through appropriate patient selection. Matching drugs and cancer patients has proven to be a complex challenge, due in large part to the substantial molecular heterogeneity inherent to human cancers. This is not only a major hurdle to the improvement of the use of current treatments but also for the development of novel therapies and the ability to steer them to the relevant clinical indications. In this commentary we discuss recent studies from Kuo et al., published this month in BMC Medicine, in which they used a panel of cancer cell lines as a model for capturing patient heterogeneity at the genomic and proteomic level in order to identify potential biomarkers for predicting the clinical activity of a novel candidate chemotherapeutic across a patient population. The findings highlight the ability of a 'systems approach' to develop a better understanding of the properties of novel candidate therapeutics and to guide clinical testing and application.See the associated research paper by Kuo et al: http://www.biomedcentral.com/1741-7015/7/77.
Collapse
Affiliation(s)
- Cyril Benes
- Center for Molecular Therapeutics, Massachusetts General Hospital Cancer Center and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.
| | | |
Collapse
|
188
|
Ramos AH, Dutt A, Mermel C, Perner S, Cho J, Lafargue CJ, Johnson LA, Stiedl AC, Tanaka KE, Bass AJ, Barretina J, Weir BA, Beroukhim R, Thomas RK, Minna JD, Chirieac LR, Lindeman NI, Giordano T, Beer DG, Wagner P, Wistuba II, Rubin MA, Meyerson M. Amplification of chromosomal segment 4q12 in non-small cell lung cancer. Cancer Biol Ther 2009; 8:2042-50. [PMID: 19755855 PMCID: PMC2833355 DOI: 10.4161/cbt.8.21.9764] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In cancer, proto-oncogenes are often altered by genomic amplification. Here we report recurrent focal amplifications of chromosomal segment 4q12 overlapping the proto-oncogenes PDGFRA and KIT in non-small cell lung cancer (NSCLC). Single nucleotide polymorphism (SNP) array and fluorescent in situ hybridization (FISH) analysis indicate that 4q12 is amplified in 3-7% of lung adenocarcinomas and 8-10% of lung squamous cell carcinomas. In addition, we demonstrate that the NSCLC cell line NCI-H1703 exhibits focal amplification of PDGFRA and is dependent on PDGFRalpha activity for cell growth. Treatment of NCI-H1703 cells with PDGFRA-specific shRNAs or with the PDGFRalpha/KIT small molecule inhibitors imatinib or sunitinib leads to cell growth inhibition. However, these observations do not extend to NSCLC cell lines with lower-amplitude and broader gains of chromosome 4q. Together these observations implicate PDGFRA and KIT as potential oncogenes in NSCLC, but further study is needed to define the specific characteristics of those tumors that could respond to PDGFRalpha/KIT inhibitors.
Collapse
Affiliation(s)
- Alex H. Ramos
- Department of Medical Oncology and Center for Cancer Genome Discovery; Dana-Farber Cancer Institute; Boston, MA USA
- Cancer Program; Broad Institute of Harvard and MIT; Cambridge, MA USA
- Department of Pathology; Harvard Medical School; Boston, MA USA
| | - Amit Dutt
- Department of Medical Oncology and Center for Cancer Genome Discovery; Dana-Farber Cancer Institute; Boston, MA USA
- Cancer Program; Broad Institute of Harvard and MIT; Cambridge, MA USA
| | - Craig Mermel
- Department of Medical Oncology and Center for Cancer Genome Discovery; Dana-Farber Cancer Institute; Boston, MA USA
- Cancer Program; Broad Institute of Harvard and MIT; Cambridge, MA USA
- Department of Pathology; Harvard Medical School; Boston, MA USA
| | - Sven Perner
- Department of Pathology; University Hospital of Tübingen; Tübingen, Germany
| | - Jeonghee Cho
- Department of Medical Oncology and Center for Cancer Genome Discovery; Dana-Farber Cancer Institute; Boston, MA USA
| | | | - Laura A. Johnson
- Department of Medical Oncology and Center for Cancer Genome Discovery; Dana-Farber Cancer Institute; Boston, MA USA
- Cancer Program; Broad Institute of Harvard and MIT; Cambridge, MA USA
| | - Ann-Cathrin Stiedl
- Department of Pathology; University Hospital of Tübingen; Tübingen, Germany
| | - Kumiko E. Tanaka
- Department of Medical Oncology and Center for Cancer Genome Discovery; Dana-Farber Cancer Institute; Boston, MA USA
- Cancer Program; Broad Institute of Harvard and MIT; Cambridge, MA USA
| | - Adam J. Bass
- Department of Medical Oncology and Center for Cancer Genome Discovery; Dana-Farber Cancer Institute; Boston, MA USA
- Cancer Program; Broad Institute of Harvard and MIT; Cambridge, MA USA
| | - Jordi Barretina
- Department of Medical Oncology and Center for Cancer Genome Discovery; Dana-Farber Cancer Institute; Boston, MA USA
- Cancer Program; Broad Institute of Harvard and MIT; Cambridge, MA USA
| | - Barbara A. Weir
- Department of Medical Oncology and Center for Cancer Genome Discovery; Dana-Farber Cancer Institute; Boston, MA USA
- Cancer Program; Broad Institute of Harvard and MIT; Cambridge, MA USA
| | - Rameen Beroukhim
- Department of Medical Oncology and Center for Cancer Genome Discovery; Dana-Farber Cancer Institute; Boston, MA USA
- Cancer Program; Broad Institute of Harvard and MIT; Cambridge, MA USA
| | - Roman K. Thomas
- Max Planck Institute for Neurological Research with Klaus-Joachim-Zülch Laboratories of the Max-Planck Society and the Medical Faculty of the University of Cologne; Cologne, Germany
- Center for Integrated Oncology and Department for Internal Medicine; University of Cologne; Cologne, Germany
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research-Simmons Cancer Center; and Department of University of Texas Southwestern Medical Center; Dallas, TX USA
- Department of Internal Medicine; University of Texas Southwestern Medical Center; Dallas, TX USA
- Department of Pharmacology; University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Lucian R. Chirieac
- Department of Pathology; Harvard Medical School; Boston, MA USA
- Department of Pathology; Brigham and Women’s Hospital; Boston, MA USA
| | - Neal I. Lindeman
- Department of Pathology; Harvard Medical School; Boston, MA USA
- Department of Pathology; Brigham and Women’s Hospital; Boston, MA USA
| | - Thomas Giordano
- Department of Pathology; University of Michigan; Ann Arbor, MI USA
| | - David G. Beer
- Section of Thoracic Surgery; Department of Surgery; University of Michigan; Ann Arbor, MI USA
| | - Patrick Wagner
- Department of Pathology; Weill Medical College of Cornell University; New York, NY USA
| | - Ignacio I. Wistuba
- Department of Epidemiology; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
- Department of Pathology; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Mark A. Rubin
- Department of Pathology; Weill Medical College of Cornell University; New York, NY USA
| | - Matthew Meyerson
- Department of Medical Oncology and Center for Cancer Genome Discovery; Dana-Farber Cancer Institute; Boston, MA USA
- Cancer Program; Broad Institute of Harvard and MIT; Cambridge, MA USA
- Department of Pathology; Harvard Medical School; Boston, MA USA
- Correspondence to: Matthew Meyerson;
| |
Collapse
|
189
|
Ceppi P, Papotti M, Monica V, Lo Iacono M, Saviozzi S, Pautasso M, Novello S, Mussino S, Bracco E, Volante M, Scagliotti GV. Effects of Src kinase inhibition induced by dasatinib in non-small cell lung cancer cell lines treated with cisplatin. Mol Cancer Ther 2009; 8:3066-74. [PMID: 19861409 DOI: 10.1158/1535-7163.mct-09-0151] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
c-Src is a tyrosine kinase involved in tumor proliferation, migration, and angiogenesis and has been shown to modulate the cytotoxicity following cisplatin-induced DNA damages. c-Src is frequently activated in non-small cell lung cancer (NSCLC) tissues and cell lines, but no preclinical data regarding the effects of the novel potent Src inhibitor, dasatinib (BMS-354825), in the modulation of cisplatin resistance are currently available. The present study reports that treatment with dasatinib completely abrogated Src phosphorylation in the majority of the NSCLC cell lines tested (n = 7), with modest effects on cell proliferation and survival. In five cell lines, a higher cytotoxicity was observed delivering cisplatin in combination with dasatinib: the most evident effects were found in the squamous H520 cells due to the effective block of cisplatin-induced Src phosphorylation. Moreover, dasatinib treatment significantly blocked cisplatin-induced transcription of a panel of DNA repair and synthesis genes. In addition, a real-time PCR analysis done on tumor and matched normal lung specimens from 44 surgically resected NSCLC patients showed that Src transcripts are significantly upregulated in 23% of cases. In conclusion, Src-directed therapeutic strategies could interfere with cisplatin resistance, possibly allowing to reduce cisplatin doses, thus improving its efficacy. The data of this study support further clinical studies aimed to evaluate the efficacy of Src-inhibiting agents in combination with cisplatin in the treatment of NSCLC.
Collapse
Affiliation(s)
- Paolo Ceppi
- University of Turin, Department of Clinical and Biological Sciences, San Luigi Hospital, Regione Gonzole 10, Orbassano, Italy.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
190
|
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature 2009; 462:108-12. [PMID: 19847166 PMCID: PMC2783335 DOI: 10.1038/nature08460] [Citation(s) in RCA: 2363] [Impact Index Per Article: 157.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 08/27/2009] [Indexed: 12/15/2022]
Abstract
The proto-oncogene KRAS is mutated in a wide array of human cancers, most of which are aggressive and respond poorly to standard therapies. Although the identification of specific oncogenes has led to the development of clinically effective, molecularly targeted therapies in some cases, KRAS has remained refractory to this approach. A complementary strategy for targeting KRAS is to identify gene products that, when inhibited, result in cell death only in the presence of an oncogenic allele1,2. Here we have used systematic RNA interference (RNAi) to detect synthetic lethal partners of oncogenic KRAS and found that the non-canonical IκB kinase, TBK1, was selectively essential in cells that harbor mutant KRAS. Suppression of TBK1 induced apoptosis specifically in human cancer cell lines that depend on oncogenic KRAS expression. In these cells, TBK1 activated NF-κB anti-apoptotic signals involving cREL and BCL-XL that were essential for survival, providing mechanistic insights into this synthetic lethal interaction. These observations identify TBK1 and NF-κB signaling as essential in KRAS mutant tumors and establish a general approach for the rational identification of co-dependent pathways in cancer.
Collapse
|
191
|
Gong Y, Yao E, Shen R, Goel A, Arcila M, Teruya-Feldstein J, Zakowski MF, Frankel S, Peifer M, Thomas RK, Ladanyi M, Pao W. High expression levels of total IGF-1R and sensitivity of NSCLC cells in vitro to an anti-IGF-1R antibody (R1507). PLoS One 2009; 4:e7273. [PMID: 19806209 PMCID: PMC2752171 DOI: 10.1371/journal.pone.0007273] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 09/05/2009] [Indexed: 01/05/2023] Open
Abstract
Background The IGF receptor type 1 (IGF-1R) pathway is frequently deregulated in human tumors and has become a target of interest for anti-cancer therapy. Methodology/Principal Findings We used a panel of 22 non-small cell lung cancer (NSCLC) cell lines to investigate predictive biomarkers of response to R1507, a fully-humanized anti-IGF-1R monoclonal antibody (Ab; Roche). 5 lines were moderately sensitive (25–50% growth inhibition) to R1507 alone. While levels of phospho-IGF-1R did not correlate with drug sensitivity, 4 out of 5 sensitive lines displayed high levels of total IGF-1R versus 1 out of 17 resistant lines (p = 0.003, Fisher's Exact). Sensitive lines also harbored higher copy numbers of IGF-1R as assessed by independent SNP array analysis. Addition of erlotinib or paclitaxel to R1507 led to further growth inhibition in sensitive but not resistant lines. In one EGFR mutant lung adenocarcinoma cell line (11–18), R1507 and erlotinib co-treatment induced apoptosis, whereas treatment with either drug alone induced only cell cycle arrest. Apoptosis was mediated, in part, by the survival-related AKT pathway. Additionally, immunohistochemical (IHC) staining of total IGF-1R with an anti-total IGF-1R Ab (G11;Ventana) was performed on tissue microarrays (TMAs) containing 270 independent NSCLC tumor samples. Staining intensity was scored on a scale of 0 to 3+. 39.3% of tumors showed medium to high IGF-1R IHC staining (scores of 2+ or 3+, respectively), while 16.7% had scores of 3+. Conclusions/Significance In NSCLC cell lines, high levels of total IGF-1R are associated with moderate sensitivity to R1507. These results suggest a possible enrichment strategy for clinical trials with anti-IGF-1R therapy.
Collapse
Affiliation(s)
- Yixuan Gong
- Pao Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Evelyn Yao
- Pao Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Aviva Goel
- Pao Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Maria Arcila
- Ladanyi Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Julie Teruya-Feldstein
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Maureen F. Zakowski
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Stanley Frankel
- Medical Sciences, Oncology, Hoffmann-La Roche Inc., Nutley, New Jersey, United States of America
| | - Martin Peifer
- Max Planck Institute for Neurological Research with Klaus-Joachim Zülch Laboratories of the Max-Planck-Society and the Medical Faculty of the University of Köln, Köln, Germany
| | - Roman K. Thomas
- Max Planck Institute for Neurological Research with Klaus-Joachim Zülch Laboratories of the Max-Planck-Society and the Medical Faculty of the University of Köln, Köln, Germany
- Department I of Internal Medicine and Center of Integrated Oncology, University of Köln, Köln, Germany
- Chemical Genomics Center of the Max-Planck-Society, Dortmund, Germany
| | - Marc Ladanyi
- Ladanyi Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - William Pao
- Pao Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
192
|
Identifying genotype-dependent efficacy of single and combined PI3K- and MAPK-pathway inhibition in cancer. Proc Natl Acad Sci U S A 2009; 106:18351-6. [PMID: 19805051 DOI: 10.1073/pnas.0907325106] [Citation(s) in RCA: 219] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In cancer, genetically activated proto-oncogenes often induce "upstream" dependency on the activity of the mutant oncoprotein. Therapeutic inhibition of these activated oncoproteins can induce massive apoptosis of tumor cells, leading to sometimes dramatic tumor regressions in patients. The PI3K and MAPK signaling pathways are central regulators of oncogenic transformation and tumor maintenance. We hypothesized that upstream dependency engages either one of these pathways preferentially to induce "downstream" dependency. Therefore, we analyzed whether downstream pathway dependency segregates by genetic aberrations upstream in lung cancer cell lines. Here, we show by systematically linking drug response to genomic aberrations in non-small-cell lung cancer, as well as in cell lines of other tumor types and in a series of in vivo cancer models, that tumors with genetically activated receptor tyrosine kinases depend on PI3K signaling, whereas tumors with mutations in the RAS/RAF axis depend on MAPK signaling. However, efficacy of downstream pathway inhibition was limited by release of negative feedback loops on the reciprocal pathway. By contrast, combined blockade of both pathways was able to overcome the reciprocal pathway activation induced by inhibitor-mediated release of negative feedback loops and resulted in a significant increase in apoptosis and tumor shrinkage. Thus, by using a systematic chemo-genomics approach, we identify genetic lesions connected to PI3K and MAPK pathway activation and provide a rationale for combined inhibition of both pathways. Our findings may have implications for patient stratification in clinical trials.
Collapse
|
193
|
Frommolt P, Thomas RK. Standardized high-throughput evaluation of cell-based compound screens. BMC Bioinformatics 2008; 9:475. [PMID: 19014471 PMCID: PMC2639430 DOI: 10.1186/1471-2105-9-475] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 11/12/2008] [Indexed: 12/02/2022] Open
Abstract
Background High-throughput screening of pharmaceutical compound activity in tissue culture experiments requires time-consuming repeated analysis of the large amounts of data generated. Automation of the evaluation procedure and assessment of measurement accuracy can save time and improve the comparability of results. Results We present a tool for simultaneous evaluation of an arbitrary number of compound screens including a standardized statistical validation. It is provided as a novel R package with a Tcl/Tk-based GUI for convenient use in the lab and runs on usual platforms like Linux, Windows and Mac OS. In a compound screen of lung cancer cells, the tool was successfully and efficiently applied for data analysis. Conclusion The package provides an efficient and intuitive platform for automatic evaluation of compound screens, improving the performance and standardization of data analysis.
Collapse
Affiliation(s)
- Peter Frommolt
- Institute of Medical Statistics, Informatics and Epidemiology, University of Köln, Köln, Germany.
| | | |
Collapse
|