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Modeling K-Ras-driven lung adenocarcinoma in mice: preclinical validation of therapeutic targets. J Mol Med (Berl) 2015; 94:121-35. [DOI: 10.1007/s00109-015-1360-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 10/22/2015] [Indexed: 01/10/2023]
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Izumchenko E, Chang X, Brait M, Fertig E, Kagohara LT, Bedi A, Marchionni L, Agrawal N, Ravi R, Jones S, Hoque MO, Westra WH, Sidransky D. Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA. Nat Commun 2015; 6:8258. [PMID: 26374070 PMCID: PMC4595648 DOI: 10.1038/ncomms9258] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/03/2015] [Indexed: 01/01/2023] Open
Abstract
Lungs resected for adenocarcinomas often harbour minute discrete foci of cytologically atypical pneumocyte proliferations designated as atypical adenomatous hyperplasia (AAH). Evidence suggests that AAH represents an initial step in the progression to adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA) and fully invasive adenocarcinoma. Despite efforts to identify predictive markers of malignant transformation, alterations driving this progression are poorly understood. Here we perform targeted next-generation sequencing on multifocal AAHs and different zones of histologic progression within AISs and MIAs. Multiregion sequencing demonstrated different genetic drivers within the same tumour and reveal that clonal expansion is an early event of tumorigenesis. We find that KRAS, TP53 and EGFR mutations are indicators of malignant transition. Utilizing droplet digital PCR, we find alterations associated with early neoplasms in paired circulating DNA. This study provides insight into the heterogeneity of clonal events in the progression of early lung neoplasia and demonstrates that these events can be detected even before neoplasms have invaded and acquired malignant potential. Atypical adenomatous hyperplasia is thought to be a precursor lesion for lung adenocarcinoma. Here, using targeted deep sequencing, the authors demonstrate that hyperplastic lesions contain somatic mutations associated with malignant disease and that these can be detected in circulating tumour cells.
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Affiliation(s)
- Evgeny Izumchenko
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Xiaofei Chang
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Mariana Brait
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Elana Fertig
- Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Luciane T Kagohara
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Atul Bedi
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Luigi Marchionni
- Center for Computational Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Nishant Agrawal
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Rajani Ravi
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Sian Jones
- Personal Genome Diagnostics, Inc., 2809 Boston Street, Suite 503, Baltimore, Maryland 21224, USA
| | - Mohammad O Hoque
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - William H Westra
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, USA
| | - David Sidransky
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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Lam DC, Luo SY, Deng W, Kwan JS, Rodriguez-Canales J, Cheung AL, Cheng GH, Lin CH, Wistuba II, Sham PC, Wan TS, Tsao SW. Oncogenic mutation profiling in new lung cancer and mesothelioma cell lines. Onco Targets Ther 2015; 8:195-209. [PMID: 25653542 PMCID: PMC4303463 DOI: 10.2147/ott.s71242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Thoracic tumor, especially lung cancer, ranks as the top cancer mortality in most parts of the world. Lung adenocarcinoma is the predominant subtype and there is increasing knowledge on therapeutic molecular targets, namely EGFR, ALK, KRAS, and ROS1, among lung cancers. Lung cancer cell lines established with known clinical characteristics and molecular profiling of oncogenic targets like ALK or KRAS could be useful tools for understanding the biology of known molecular targets as well as for drug testing and screening. Materials and methods Five new cancer cell lines were established from pleural fluid or biopsy tissues obtained from Chinese patients with primary lung adenocarcinomas or malignant pleural mesothelioma. They were characterized by immunohistochemistry, growth kinetics, tests for tumorigenicity, EGFR and KRAS gene mutations, ALK gene rearrangement and OncoSeq mutation profiling. Results These newly established lung adenocarcinoma and mesothelioma cell lines were maintained for over 100 passages and demonstrated morphological and immunohistochemical features as well as growth kinetics of tumor cell lines. One of these new cell lines bears EML4-ALK rearrangement variant 2, two lung cancer cell lines bear different KRAS mutations at codon 12, and known single nucleotide polymorphism variants were identified in these cell lines. Discussion Four new lung adenocarcinoma and one mesothelioma cell lines were established from patients with different clinical characteristics and oncogenic mutation profiles. These characterized cell lines and their mutation profiles will provide resources for exploration of lung cancer and mesothelioma biology with regard to the presence of known oncogenic mutations.
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Affiliation(s)
- David Cl Lam
- Department of Medicine, University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Susan Y Luo
- Department of Medicine, University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Wen Deng
- School of Nursing, University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Johnny Sh Kwan
- Department of Psychiatry, University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, University of Texas at Houston, Houston, TX, USA
| | - Annie Lm Cheung
- Department of Anatomy, University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Grace Hw Cheng
- Center for Genome Sciences, University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Chi-Ho Lin
- Center for Genome Sciences, University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, University of Texas at Houston, Houston, TX, USA
| | - Pak C Sham
- Center for Genome Sciences, University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Thomas Sk Wan
- Department of Pathology, University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Sai-Wah Tsao
- Department of Anatomy, University of Hong Kong, Hong Kong SAR, People's Republic of China
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Datta A, Sikdar S, Gill R. Differences in protein-protein association networks for lung adenocarcinoma: A retrospective study. Bioinformation 2014; 10:647-51. [PMID: 25489174 PMCID: PMC4248347 DOI: 10.6026/97320630010647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 10/05/2014] [Indexed: 11/23/2022] Open
Abstract
Various methods to determine the connectivity scores between groups of proteins associated with lung adenocarcinoma are examined. Proteins act together to perform a wide range of functions within biological processes. Hence, identification of key proteins and their interactions within protein networks can provide invaluable information on disease mechanisms. Differential network analysis provides a means of identifying differences in the interactions among proteins between two networks. We use connectivity scores based on the method of partial least squares to quantify the strength of the interactions between each pair of proteins. These scores are then used to perform permutation-based statistical tests. This examines if there are significant differences between the network connectivity scores for individual proteins or classes of proteins. The expression data from a study on lung adenocarcinoma is used in this study. Connectivity scores are computed for a group of 109 subjects who were in the complete remission and as well as for a group of 51 subjects whose cancer had progressed. The distributions of the connectivity scores are similar for the two networks yet subtle but statistically significant differences have been identified and their impact discussed.
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Affiliation(s)
- Anisha Datta
- Louisville Collegiate School and Department of Mathematics, University of Louisville
| | - Sinjini Sikdar
- Department of Bioinformatics and Biostatistics, University of Louisville
| | - Ryan Gill
- Department of Mathematics, University of Louisville, Louisville
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55
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Goldkorn T, Filosto S, Chung S. Lung injury and lung cancer caused by cigarette smoke-induced oxidative stress: Molecular mechanisms and therapeutic opportunities involving the ceramide-generating machinery and epidermal growth factor receptor. Antioxid Redox Signal 2014; 21:2149-74. [PMID: 24684526 PMCID: PMC4215561 DOI: 10.1089/ars.2013.5469] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) and lung cancer are frequently caused by tobacco smoking. However, these diseases present opposite phenotypes involving redox signaling at the cellular level. While COPD is characterized by excessive airway epithelial cell death and lung injury, lung cancer is caused by uncontrolled epithelial cell proliferation. Notably, epidemiological studies have demonstrated that lung cancer incidence is significantly higher in patients who have preexisting emphysema/lung injury. However, the molecular link and common cell signaling events underlying lung injury diseases and lung cancer are poorly understood. This review focuses on studies of molecular mechanism(s) underlying smoking-related lung injury (COPD) and lung cancer. Specifically, the role of the ceramide-generating machinery during cigarette smoke-induced oxidative stress leading to both apoptosis and proliferation of lung epithelial cells is emphasized. Over recent years, it has been established that ceramide is a sphingolipid playing a major role in lung epithelia structure/function leading to lung injury in chronic pulmonary diseases. However, new and unexpected findings draw attention to its potential role in lung development, cell proliferation, and tumorigenesis. To address this dichotomy in detail, evidence is presented regarding several protein targets, including Src, p38 mitogen-activated protein kinase, and neutral sphingomyelinase 2, the major sphingomyelinase that controls ceramide generation during oxidative stress. Furthermore, their roles are presented not only in apoptosis and lung injury but also in enhancing cell proliferation, lung cancer development, and resistance to epidermal growth factor receptor-targeted therapy for treating lung cancer.
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Affiliation(s)
- Tzipora Goldkorn
- Center for Comparative Respiratory Biology and Medicine, Genome and Biomedical Sciences Facility, University of California School of Medicine , Davis, California
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Fakhruddin N, Mahfouz R, Farhat F, Tfayli A, Abdelkhalik R, Jabbour M, Yehia L, Mahfoud Z, Zaatari G. Epidermal growth factor receptor and KRAS mutations in lung adenocarcinoma: a retrospective study of the Lebanese population. Oncol Rep 2014; 32:2223-9. [PMID: 25120214 DOI: 10.3892/or.2014.3406] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 07/02/2014] [Indexed: 11/06/2022] Open
Abstract
Molecular genetic analysis of epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma viral oncogene (KRAS) mutations in lung adenocarcinoma has become an integral part of lung cancer diagnosis and treatment; however, their prevalence varies with ethnicity. Little is know concerning their prevalence in Arab populations. In the present study, mutational analysis for EGFR and KRAS was performed on two cohorts of the Lebanese population. Lung adenocarcinoma cases (106) underwent mutational analysis for KRAS in exon 2, codon 12 and 13 and exon 3 codon 61 by reverse hybridization using the KRAS 12/13/61 StripAssay®. Subsequently, cases with no KRAS mutations underwent EGFR mutational analysis using the EGFR RGQ polymerase chain reaction (PCR) kits for real‑time PCR on the Rotor‑Gene Q 5-plex HRM. KRAS mutations were detected in 37.7% of 106 lung adenocarcinomas; 85% had a G>T substitution in codon 12 and 13 of exon 2, and 8.5% had EGFR mutations with exon 19 deletions (88.9%) and one case with L858R substitution in exon 21. EGFR mutations were significantly correlated with females, non-smokers and well differentiation of the tumor. This is the first study in an Arab population that reports the prevalence of both EGFR and KRAS gene mutations in lung adenocarcinoma using very sensitive mutational analysis techniques. Therefore, EGFR reflex testing should be implemented in the management of lung adenocarcinomas, while KRAS testing must await the identification of effective targeted therapy.
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Affiliation(s)
- Najla Fakhruddin
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rami Mahfouz
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Fadi Farhat
- Department of Hematology-Oncology, Hammoud Hospital University Medical Center, Sidon, Lebanon
| | - Arafat Tfayli
- Department of Hematology-Oncology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rabab Abdelkhalik
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Mark Jabbour
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Lamis Yehia
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ziyad Mahfoud
- Department of Public Health, Weill Cornell Medical College, Doha, Qatar
| | - Ghazi Zaatari
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
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Fisher KE, Pillai RN, Kudchadkar RR, Rossi MR. Section IV: non-small cell lung cancer and malignant melanoma. Curr Probl Cancer 2014; 38:180-98. [PMID: 25281457 DOI: 10.1016/j.currproblcancer.2014.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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58
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Zhang J, Wu LY, Zhang XS, Zhang S. Discovery of co-occurring driver pathways in cancer. BMC Bioinformatics 2014; 15:271. [PMID: 25106096 PMCID: PMC4133618 DOI: 10.1186/1471-2105-15-271] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 08/01/2014] [Indexed: 01/08/2023] Open
Abstract
Background It has been widely realized that pathways rather than individual genes govern the course of carcinogenesis. Therefore, discovering driver pathways is becoming an important step to understand the molecular mechanisms underlying cancer and design efficient treatments for cancer patients. Previous studies have focused mainly on observation of the alterations in cancer genomes at the individual gene or single pathway level. However, a great deal of evidence has indicated that multiple pathways often function cooperatively in carcinogenesis and other key biological processes. Results In this study, an exact mathematical programming method was proposed to de novo identify co-occurring mutated driver pathways (CoMDP) in carcinogenesis without any prior information beyond mutation profiles. Two possible properties of mutations that occurred in cooperative pathways were exploited to achieve this: (1) each individual pathway has high coverage and high exclusivity; and (2) the mutations between the pair of pathways showed statistically significant co-occurrence. The efficiency of CoMDP was validated first by testing on simulated data and comparing it with a previous method. Then CoMDP was applied to several real biological data including glioblastoma, lung adenocarcinoma, and ovarian carcinoma datasets. The discovered co-occurring driver pathways were here found to be involved in several key biological processes, such as cell survival and protein synthesis. Moreover, CoMDP was modified to (1) identify an extra pathway co-occurring with a known pathway and (2) detect multiple significant co-occurring driver pathways for carcinogenesis. Conclusions The present method can be used to identify gene sets with more biological relevance than the ones currently used for the discovery of single driver pathways. Electronic supplementary material The online version of this article (doi:10.1186/1471-2105-15-271) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junhua Zhang
- National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.
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59
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Imielinski M, Hammerman PS, Thomas R, Meyerson M. Somatic Genome Alterations in Human Lung Cancers. Lung Cancer 2014. [DOI: 10.1002/9781118468791.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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60
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Ross JS, Wang K, Al-Rohil RN, Nazeer T, Sheehan CE, Otto GA, He J, Palmer G, Yelensky R, Lipson D, Ali S, Balasubramanian S, Curran JA, Garcia L, Mahoney K, Downing SR, Hawryluk M, Miller VA, Stephens PJ. Advanced urothelial carcinoma: next-generation sequencing reveals diverse genomic alterations and targets of therapy. Mod Pathol 2014; 27:271-80. [PMID: 23887298 DOI: 10.1038/modpathol.2013.135] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/07/2013] [Accepted: 06/11/2013] [Indexed: 11/09/2022]
Abstract
Although urothelial carcinoma (UC) of the urinary bladder generally portends a favorable prognosis, metastatic tumors often follow an aggressive clinical course. DNA was extracted from 40 μm of formalin-fixed, paraffin-embedded (FFPE) sections from 35 stage IV UCs that had relapsed and progressed after primary surgery and conventional chemotherapy. Next-generation sequencing (NGS) was performed on hybridization-captured, adaptor ligation-based libraries for 3320 exons of 182 cancer-related genes plus 37 introns from 14 genes frequently rearranged in cancer to at an average sequencing depth of 1164 × and evaluated for all classes of genomic alterations (GAs). Actionable GAs were defined as those impacting the selection of targeted anticancer therapies on the market or in registered clinical trials. A total of 139 GAs were identified, with an average of 4.0 GAs per tumor (range 0-10), of which 78 (56%) were considered actionable, with an average of 2.2 per tumor (range 0-7). Twenty-nine (83%) cases harbored at least one actionable GA including: PIK3CA (9 cases; 26%); CDKN2A/B (8 cases; 23%); CCND1 (5 cases; 14%); FGFR1 (5 cases; 14%); CCND3 (4 cases; 11%); FGFR3 (4 cases; 11%); MCL1 (4 cases; 11%); MDM2 (4 cases; 11%); EGFR (2 cases, 6%); ERBB2 (HER2/neu) (2 cases, 6%); NF1 (2 cases, 6%) and TSC1 (2 cases, 6%). Notable additional alterations included TP53 (19 cases, 54%) and RB1 (6 cases; 17%). Genes involved in chromatin modification were altered by nonsense mutation, splice site mutation or frameshift indel in a mutually exclusive manner in nearly half of all cases including KDM6A (10 cases; 29%) and ARID1A (7 cases; 20%). Comprehensive NGS of 35 UCs of the bladder revealed a diverse spectrum of actionable GAs in 83% of cases, which has the potential to inform treatment decisions for patients with relapsed and metastatic disease.
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Affiliation(s)
- Jeffrey S Ross
- 1] Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, USA [2] Foundation Medicine, Cambridge, MA, USA
| | - Kai Wang
- Foundation Medicine, Cambridge, MA, USA
| | - Rami N Al-Rohil
- Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, USA
| | - Tipu Nazeer
- Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, USA
| | - Christine E Sheehan
- Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, USA
| | | | - Jie He
- Foundation Medicine, Cambridge, MA, USA
| | | | | | | | - Siraj Ali
- Foundation Medicine, Cambridge, MA, USA
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61
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Ross JS, Wang K, Gay LM, Al-Rohil RN, Nazeer T, Sheehan CE, Jennings TA, Otto GA, Donahue A, He J, Palmer G, Ali S, Nahas M, Young G, LaBrecque E, Frampton G, Erlich R, Curran JA, Brennan K, Downing SR, Yelensky R, Lipson D, Hawryluk M, Miller VA, Stephens PJ. A High Frequency of Activating Extracellular Domain ERBB2 (HER2) Mutation in Micropapillary Urothelial Carcinoma. Clin Cancer Res 2013; 20:68-75. [DOI: 10.1158/1078-0432.ccr-13-1992] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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KANG JIUN. Characterization of amplification patterns and target genes on the short arm of chromosome 7 in early-stage lung adenocarcinoma. Mol Med Rep 2013; 8:1373-8. [DOI: 10.3892/mmr.2013.1686] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 09/09/2013] [Indexed: 11/05/2022] Open
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63
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Dearden S, Stevens J, Wu YL, Blowers D. Mutation incidence and coincidence in non small-cell lung cancer: meta-analyses by ethnicity and histology (mutMap). Ann Oncol 2013; 24:2371-6. [PMID: 23723294 PMCID: PMC3755331 DOI: 10.1093/annonc/mdt205] [Citation(s) in RCA: 455] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 04/18/2013] [Accepted: 04/22/2013] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Meta-analyses were conducted to characterize patterns of mutation incidence in non small-cell lung cancer (NSCLC). DESIGN Nine genes with the most complete published mutation coincidence data were evaluated. One meta-analysis generated a 'mutMap' to visually represent mutation coincidence by ethnicity (Western/Asian) and histology (adenocarcinoma [ADC] or squamous cell carcinoma). Another meta-analysis evaluated incidence of individual mutations. Extended analyses explored incidence of EGFR and KRAS mutations by ethnicity, histology, and smoking status. RESULTS Genes evaluated were TP53, EGFR, KRAS, LKB1, EML4-ALK, PTEN, BRAF, PIK3CA, and ErbB2. The mutMap highlighted mutation coincidences occurring in ≥5% of patients, including TP53 with KRAS or EGFR mutations in patients with ADC, and TP53 with LKB1 mutation in Western patients. TP53 was the most frequently mutated gene overall. Frequencies of TP53, EGFR, KRAS, LKB1, PTEN, and BRAF mutations were influenced by histology and/or ethnicity. Although EGFR mutations were most frequent in patients with ADC and never/light smokers from Asia, and KRAS mutations were most frequent in patients with ADC and ever/heavy smokers from Western countries, both were detected outside these subgroups. CONCLUSIONS Potential molecular pathology segments of NSCLC were identified. Further studies of mutations in NSCLC are warranted to facilitate more specific diagnoses and guide treatment.
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Affiliation(s)
- S Dearden
- R&D Genetics, Personalised Healthcare & Biomarkers, AstraZeneca, Macclesfield, UK.
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Sato T, Arai E, Kohno T, Tsuta K, Watanabe SI, Soejima K, Betsuyaku T, Kanai Y. DNA methylation profiles at precancerous stages associated with recurrence of lung adenocarcinoma. PLoS One 2013; 8:e59444. [PMID: 23544068 PMCID: PMC3609833 DOI: 10.1371/journal.pone.0059444] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 02/14/2013] [Indexed: 12/19/2022] Open
Abstract
The aim of this study was to clarify the significance of DNA methylation alterations at precancerous stages of lung adenocarcinoma. Using single-CpG resolution Infinium array, genome-wide DNA methylation analysis was performed in 36 samples of normal lung tissue obtained from patients without any primary lung tumor, 145 samples of non-cancerous lung tissue (N) obtained from patients with lung adenocarcinomas, and 145 samples of tumorous tissue (T). Stepwise progression of DNA methylation alterations from normal lung tissue to non-cancerous lung tissue obtained from patients with lung adenocarcinomas, and then tumorous tissue samples, was observed at 3,270 CpG sites, suggesting that non-cancerous lung tissue obtained from patients with lung adenocarcinomas was at precancerous stages with DNA methylation alterations. At CpG sites of 2,083 genes, DNA methylation status in samples of non-cancerous lung tissue obtained from patients with lung adenocarcinomas was significantly correlated with recurrence after establishment of lung adenocarcinomas. Among such recurrence-related genes, 28 genes are normally unmethylated (average β-values based on Infinium assay in normal lung tissue samples was less than 0.2) and their DNA hypermethylation at precancerous stages was strengthened during progression to lung adenocarcinomas (Δβ(T-N)>0.1). Among these 28 genes, we focused on 6 for which implications in transcription regulation, apoptosis or cell adhesion had been reported. DNA hypermethylation of the ADCY5, EVX1, GFRA1, PDE9A, and TBX20 genes resulted in reduced mRNA expression in tumorous tissue samples. 5-Aza-2'-deoxycytidine treatment of lung cancer cell lines restored the mRNA expression levels of these 5 genes. Reduced mRNA expression in tumorous tissue samples was significantly correlated with tumor aggressiveness. These data suggest that DNA methylation alterations at precancerous stages determine tumor aggressiveness and outcome through silencing of specific genes.
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Affiliation(s)
- Takashi Sato
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Eri Arai
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
- * E-mail:
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Koji Tsuta
- Department of Pathology and Clinical Laboratories, Pathology Division, National Cancer Center Hospital, Tokyo, Japan
| | - Shun-ichi Watanabe
- Department of Thoracic Oncology, Thoracic Surgery Division, National Cancer Center Hospital, Tokyo, Japan
| | - Kenzo Soejima
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Tomoko Betsuyaku
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yae Kanai
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
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Lin C, Song H, Huang C, Yao E, Gacayan R, Xu SM, Chuang PT. Alveolar type II cells possess the capability of initiating lung tumor development. PLoS One 2012; 7:e53817. [PMID: 23285300 PMCID: PMC3527621 DOI: 10.1371/journal.pone.0053817] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 12/03/2012] [Indexed: 01/19/2023] Open
Abstract
Identifying cells of tumor origin is a fundamental question in tumor biology. Answers to this central question will not only advance our understanding of tumor initiation and progression but also have important therapeutic implications. In this study, we aimed to uncover the cells of origin of lung adenocarcinoma, a major subtype of non-small cell lung cancer. To this end, we developed new mouse models of lung adenocarcinoma that enabled selective manipulation of gene activity in surfactant associated protein C (SPC)-expressing cells, including alveolar type II cells and bronchioalveolar stem cells (BASCs) that reside at the bronchioalveolar duct junction (BADJ). Our findings showed that activation of oncogenic Kras alone or in combination with the removal of the tumor suppressor p53 in SPC+ cells resulted in development of alveolar tumors. Similarly, sustained EGF signaling in SPC+ cells led to alveolar tumors. By contrast, BASCs failed to proliferate or produce tumors under these conditions. Importantly, in a mouse strain in which Kras/p53 activity was selectively altered in type II cells but not BASCs, alveolar tumors developed while BADJs retained normal architecture. These results confirm and extend previous findings and support a model in which lung adenocarcinoma can initiate in alveolar type II cells. Our results establish the foundation for elucidating the molecular mechanisms by which lung cancer initiates and progresses in a specific lung cell type.
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Affiliation(s)
- Chuwen Lin
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Hai Song
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Cecilia Huang
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Erica Yao
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Rhodora Gacayan
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Shan-Mei Xu
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Pao-Tien Chuang
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2. Proc Natl Acad Sci U S A 2012; 109:14476-81. [PMID: 22908275 DOI: 10.1073/pnas.1203201109] [Citation(s) in RCA: 222] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We assessed somatic alleles of six receptor tyrosine kinase genes mutated in lung adenocarcinoma for oncogenic activity. Five of these genes failed to score in transformation assays; however, novel recurring extracellular domain mutations of the receptor tyrosine kinase gene ERBB2 were potently oncogenic. These ERBB2 extracellular domain mutants were activated by two distinct mechanisms, characterized by elevated C-terminal tail phosphorylation or by covalent dimerization mediated by intermolecular disulfide bond formation. These distinct mechanisms of receptor activation converged upon tyrosine phosphorylation of cellular proteins, impacting cell motility. Survival of Ba/F3 cells transformed to IL-3 independence by the ERBB2 extracellular domain mutants was abrogated by treatment with small-molecule inhibitors of ERBB2, raising the possibility that patients harboring such mutations could benefit from ERBB2-directed therapy.
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Abstract
Lung cancer, of which non-small-cell lung cancer comprises the majority, is the leading cause of cancer-related deaths in the United States and worldwide. Lung adenocarcinomas are a major subtype of non-small-cell lung cancers, are increasing in incidence globally in both males and females and in smokers and non-smokers, and are the cause for almost 50% of deaths attributable to lung cancer. Lung adenocarcinoma is a tumour with complex biology that we have recently started to understand with the advent of various histological, transcriptomic, genomic and proteomic technologies. However, the histological and molecular pathogenesis of this malignancy is still largely unknown. This review will describe advances in the molecular pathology of lung adenocarcinoma with emphasis on genomics and DNA alterations of this disease. Moreover, the review will discuss recognized lung adenocarcinoma preneoplastic lesions and current concepts of the early pathogenesis and progression of the disease. We will also portray the field cancerization phenomenon and lineage-specific oncogene expression pattern in lung cancer and how both remerging concepts can be exploited to increase our understanding of lung adenocarcinoma pathogenesis for subsequent development of biomarkers for early detection of adenocarcinomas and possibly personalized prevention.
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Affiliation(s)
- Humam Kadara
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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Leslie NR, Dixon MJ, Schenning M, Gray A, Batty IH. Distinct inactivation of PI3K signalling by PTEN and 5-phosphatases. Adv Biol Regul 2012; 52:205-213. [PMID: 21930147 DOI: 10.1016/j.advenzreg.2011.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 09/06/2011] [Indexed: 05/31/2023]
Affiliation(s)
- Nick R Leslie
- Division of Cell Signalling and Immunology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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Mestan KK, Ilkhanoff L, Mouli S, Lin S. Genomic sequencing in clinical trials. J Transl Med 2011; 9:222. [PMID: 22206293 PMCID: PMC3269395 DOI: 10.1186/1479-5876-9-222] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 12/30/2011] [Indexed: 12/02/2022] Open
Abstract
Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to find its way into clinical trials both nationally and worldwide. We highlight the currently available types of genomic sequencing platforms, outline the advantages and disadvantages of each, and compare first- and next-generation techniques with respect to capabilities, quality, and cost. We describe the current geographical distributions and types of disease conditions in which these technologies are used, and how next-generation sequencing is strategically being incorporated into new and existing studies. Lastly, recent major breakthroughs and the ongoing challenges of using genomic sequencing in clinical research are discussed.
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Affiliation(s)
- Karen K Mestan
- Department of Pediatrics, Division of Neonatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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