1
|
Wang X, Zhou T, Yang X, Cao X, Jin G, Zhang P, Guo J, Rong K, Li B, Hu Y, Liu K, Ma P, Qin A, Zhao J. DDRGK1 Enhances Osteosarcoma Chemoresistance via Inhibiting KEAP1-Mediated NRF2 Ubiquitination. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204438. [PMID: 36965071 DOI: 10.1002/advs.202204438] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 02/14/2023] [Indexed: 05/18/2023]
Abstract
Chemoresistance is the main obstacle in osteosarcoma (OS) treatment; however, the underlying mechanism remains unclear. In this study, it is discovered that DDRGK domain-containing protein 1 (DDRGK1) plays a fundamental role in chemoresistance induced in OS. Bioinformatic and tissue analyses indicate that higher expression of DDRGK1 correlates with advanced tumor stage and poor clinical prognosis of OS. Quantitative proteomic analyses suggest that DDRGK1 plays a critical role in mitochondrial oxidative phosphorylation. DDRGK1 knockout trigger the accumulation of reactive oxygen species (ROS) and attenuate the stability of nuclear factor erythroid-2-related factor 2 (NRF2), a major antioxidant response element. Furthermore, DDRGK1 inhibits ubiquitin-proteasome-mediated degradation of NRF2 via competitive binding to the Kelch-like ECH-associated protein 1 (KEAP1) protein, which recruits NRF2 to CULLIN(CUL3). DDRGK1 knockout attenuates NRF2 stability, contributing to ROS accumulation, which promotes apoptosis and enhanced chemosensitivity to doxorubicin (DOX) and etoposide in cancer cells. Indeed, DDRGK1 knockout significantly enhances osteosarcoma chemosensitivity to DOX in vivo. The combination of DDRGK1 knockdown and DOX treatment provides a promising new avenue for the effective treatment of OS.
Collapse
Affiliation(s)
- Xin Wang
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhaizaoju Road, Shanghai, 200011, P. R. China
| | - Tangjun Zhou
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhaizaoju Road, Shanghai, 200011, P. R. China
| | - Xiao Yang
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhaizaoju Road, Shanghai, 200011, P. R. China
| | - Xiankun Cao
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhaizaoju Road, Shanghai, 200011, P. R. China
| | - Gu Jin
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, P. R. China
| | - Pu Zhang
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhaizaoju Road, Shanghai, 200011, P. R. China
| | - Jiadong Guo
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhaizaoju Road, Shanghai, 200011, P. R. China
| | - Kewei Rong
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhaizaoju Road, Shanghai, 200011, P. R. China
| | - Baixing Li
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhaizaoju Road, Shanghai, 200011, P. R. China
| | - Yibin Hu
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhaizaoju Road, Shanghai, 200011, P. R. China
| | - Kexin Liu
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhaizaoju Road, Shanghai, 200011, P. R. China
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhaizaoju Road, Shanghai, 200011, P. R. China
| | - An Qin
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhaizaoju Road, Shanghai, 200011, P. R. China
| | - Jie Zhao
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhaizaoju Road, Shanghai, 200011, P. R. China
| |
Collapse
|
2
|
Gao B, Yang F, Han M, Bao H, Shen Y, Cao R, Wu X, Shao Y, Liu C, Zhang Z. Genomic landscape and evolution of arm aneuploidy in lung adenocarcinoma. Neoplasia 2021; 23:870-878. [PMID: 34303217 PMCID: PMC8322129 DOI: 10.1016/j.neo.2021.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 01/18/2023] Open
Abstract
For lung adenocarcinoma, arm aneuploidy landscape among primary and metastatic sites, and among different driver and frequently mutated gene groups have not been previously studied. We collected the largest cohort of LUAD patients (n=3533) to date and analyzed the profiles of chromosome arm aneuploidy (CAA), and its association with different metastatic sites and mutated gene groups. Our results showed distant metastasis (bone, brain, liver) were characterized by high CAA burden and biased towards arm losses compared to regional metastasis (pleura, chest) and primary tumors. Moreover, EGFR, MET, PIK3CA, PKHD1 and RB1 mutant groups were found to have high CAA burden, while those with BRAF, ERBB2 and KRAS mutations belonged to the low CAA burden group. Comparing EGFR L858R and EGFR 19del mutants, distinct CAA co-occurrences were observed. Network-based stratification with population based genomic evolution analysis revealed two distinct subtypes of LUAD with different CAA signatures and unique CAA order of acquisition. In summary, our study presented a comprehensive characterization of arm aneuploidy landscape and evolutionary trajectories in lung adenocarcinoma, which could provide basis for both biological and clinical investigations in the future.
Collapse
Affiliation(s)
- Beili Gao
- Department of Respiration, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Fujun Yang
- Department of Oncology, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, Shandong, China
| | - Ming Han
- Nanjing Geneseeq Technology Inc. Nanjing, Jiangsu, China
| | - Hua Bao
- Nanjing Geneseeq Technology Inc. Nanjing, Jiangsu, China
| | - Yi Shen
- Nanjing Geneseeq Technology Inc. Nanjing, Jiangsu, China
| | - Ran Cao
- Nanjing Geneseeq Technology Inc. Nanjing, Jiangsu, China
| | - Xue Wu
- Nanjing Geneseeq Technology Inc. Nanjing, Jiangsu, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc. Nanjing, Jiangsu, China; School of Public Health, Nanjing Medical University, Nanjing, China
| | - Changhong Liu
- Department of Thoracic Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China.
| | - Zhe Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| |
Collapse
|
3
|
SOX2 and squamous cancers. Semin Cancer Biol 2020; 67:154-167. [PMID: 32905832 DOI: 10.1016/j.semcancer.2020.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 11/10/2019] [Accepted: 05/09/2020] [Indexed: 12/20/2022]
Abstract
SOX2 is a pleiotropic nuclear transcription factor with major roles in stem cell biology and in development. Over the last 10 years SOX2 has also been implicated as a lineage-specific oncogene, notably in squamous carcinomas but also neurological tumours, particularly glioblastoma. Squamous carcinomas (SQCs) comprise a common group of malignancies for which there are no targeted therapeutic interventions. In this article we review the molecular epidemiological and laboratory evidence linking SOX2 with squamous carcinogenesis, explore in detail the multifaceted impact of SOX2 in SQC, describe areas of uncertainty and highlight areas for potential future research.
Collapse
|
4
|
Suster DI, Mino-Kenudson M. Molecular Pathology of Primary Non-small Cell Lung Cancer. Arch Med Res 2020; 51:784-798. [PMID: 32873398 DOI: 10.1016/j.arcmed.2020.08.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023]
Abstract
Lung carcinoma is one of the most common human cancers and is estimated to have an incidence of approximately 2 million new cases per year worldwide with a 20% mortality rate. Lung cancer represents one of the leading causes of cancer related death in the world. Of all cancer types to affect the pulmonary system, non-small cell lung carcinoma comprises approximately 80-85% of all tumors. In the past few decades cytogenetic and advanced molecular techniques have helped define the genomic landscape of lung cancer, and in the process, revolutionized the clinical management and treatment of patients with advanced non-small cell lung cancer. The discovery of specific, recurrent genetic abnormalities has led to the development of targeted therapies that have extended the life expectancy of patients who develop carcinoma of the lungs. Patients are now routinely treated with targeted therapies based on identifiable molecular alterations or other predictive biomarkers which has led to a revolution in the field of pulmonary pathology and oncology. Numerous different testing modalities, with various strengths and limitations now exist which complicate diagnostic algorithms, however recently emerging consensus guidelines and recommendations have begun to standardize the way to approach diagnostic testing of lung carcinoma. Herein we provide an overview of the molecular genetic landscape of non-small cell lung carcinoma, with attention to those clinically relevant alterations which drive management, as well as review current recommendations for molecular testing.
Collapse
Affiliation(s)
- David Ilan Suster
- Department of Pathology, Rutgers University, New Jersey Medical School, Newark, NJ, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
5
|
Kachouie NN, Shutaywi M, Christiani DC. Discriminant Analysis of Lung Cancer Using Nonlinear Clustering of Copy Numbers. Cancer Invest 2020; 38:102-112. [PMID: 31977287 PMCID: PMC10283398 DOI: 10.1080/07357907.2020.1719501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/18/2020] [Indexed: 01/14/2023]
Abstract
Background: Patient survival is not optimal for non-small cell lung cancer (NSCLC) patients, recurrence rate is high, and hence, early detection is crucial to increase the patient's survival. Gene-cancer mapping intends to discover associated genes with cancers and due to advances in high-throughput genotyping, screening for disease loci on a genome-wide scale is now possible. DNA copy numbers can potentially be used to identify cancer from normal cells in early detection of cancer.Methods: We use a nonlinear clustering method, so-called kernel K-means to separate cancer from normal samples. Kernel K-means is applied to the copy numbers obtained for each chromosome to cluster 63 paired cancer-blood samples (total of 126 samples) into two groups. Clustering performance is evaluated using true and false-positive rates, true and false-negative rates, and a nonlinear criterion, normalized mutual information (NMI).Results: Copy numbers of paired cancer-blood samples for 63 NSCLC patients are used in this study. Kernel K-means was applied to cluster 126 samples in two groups using copy numbers on each chromosome separately. The clustering results for 22 chromosomes are evaluated and discriminant power of them in identifying cancer is computed. We identified the top five and bottom five chromosomes based on their discriminant power.Conclusions: The results reveal high discriminant power of chromosomes 8, 5, 1, 3, and 19 for identifying cancer with the highest sensitivity of 75% yielded by chromosome 5. Bottom 5 chromosomes 9, 6, 4, 13, and 21 show low discriminant power with the accuracy of below 54% where true cancer and normal samples are grouped into substantially overlapping groups using copy numbers. This indicates the similarities of copy numbers obtained for cancer and normal samples on these chromosomes.
Collapse
Affiliation(s)
| | - Meshal Shutaywi
- Department of Mathematical Sciences, Florida Institute of Technology
| | - David C. Christiani
- Department of Environmental Health, Harvard School of Public Health
- Department of Epidemiology, Harvard School of Public Health
| |
Collapse
|
6
|
Larsen TV, Hussmann D, Nielsen AL. PD-L1 and PD-L2 expression correlated genes in non-small-cell lung cancer. Cancer Commun (Lond) 2019; 39:30. [PMID: 31159869 PMCID: PMC6545701 DOI: 10.1186/s40880-019-0376-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/23/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Programmed cell death ligand-1 (PD-L1) and ligand-2 (PD-L2) interaction with programmed cell death protein-1 (PD-1) represent an immune-inhibiting checkpoint mediating immune evasion and is, accordingly, an important target for blockade-based immunotherapy in cancer. In non-small-cell lung cancer (NSCLC), improved understanding of PD-1 checkpoint blockade-responsive biology and identification of biomarkers for prediction of a clinical response to immunotherapy is warranted. Thus, in the present study, we systematically described PD-L1 and PD-L2 expression correlated genes in NSCLC. METHODS We performed comparative retrospective analyses to identify PD-L1 and PD-L2 mRNA expression correlated genes in NSCLC. For this, we examined available datasets from the cancer cell line encyclopedia (CCLE) project lung non-small-cell (Lung_NSC) and the cancer genome atlas (TCGA) projects lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC). RESULTS Analysis of the CCLE dataset Lung_NSC identified expression correlation between PD-L1 and PD-L2. Moreover, we identified expression correlation between 489 genes and PD-L1, 191 genes and PD-L2, and 111 genes for both. PD-L1 and PD-L2 also expression correlated in TCGA datasets LUAD and LUSC. In LUAD, we identified expression correlation between 257 genes and PD-L1, 914 genes and PD-L2, and 211 genes for both. In LUSC, we identified expression correlation between 26 genes and PD-L1, 326 genes and PD-L2, and 13 genes for both. Only a few genes expression correlated with PD-L1 and PD-L2 across the CCLE and TCGA datasets. Expression of Interferon signaling-involved genes converged in particular with the expression correlated genes for PD-L1 in Lung_NSC, for PD-L2 in LUSC, and for both PD-L1 and PD-L2 in LUAD. In LUSC, PD-L1, and to a lesser extent PD-L2, expression correlated with chromosome 9p24 localized genes, indicating a chromosome 9p24 topologically associated domain as an important driver of in particular LUSC PD-L1 expression. Expression correlation analyses of the PD-L1 and PD-L2 receptors programmed cell death protein-1 (PD-1), Cluster of differentiation 80 (CD80), and Repulsive guidance molecule B (RGMB) showed that PD-1 and CD80 expression correlated with both PD-L1 and PD-L2 in LUAD. CD80 expression correlated with PD-L2 in LUSC. CONCLUSIONS We present gene signatures associated with PD-L1 and PD-L2 mRNA expression in NSCLC which could possess importance in relation to understand PD-1 checkpoint blockade-responsive biology and development of gene signature based biomarkers for predicting clinical responses to immunotherapy.
Collapse
Affiliation(s)
| | - Dianna Hussmann
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | | |
Collapse
|
7
|
Qiu ZW, Bi JH, Gazdar AF, Song K. Genome-wide copy number variation pattern analysis and a classification signature for non-small cell lung cancer. Genes Chromosomes Cancer 2017; 56:559-569. [PMID: 28379620 DOI: 10.1002/gcc.22460] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/25/2017] [Accepted: 03/26/2017] [Indexed: 02/06/2023] Open
Abstract
The accurate classification of non-small cell lung carcinoma (NSCLC) into lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) is essential for both clinical practice and lung cancer research. Although the standard WHO diagnosis of NSCLC on biopsy material is rapid and economic, more than 13% of NSCLC tumors in the USA are not further classified. The purpose of this study was to analyze the genome-wide pattern differences in copy number variations (CNVs) and to develop a CNV signature as an adjunct test for the routine histopathologic classification of NSCLCs. We investigated the genome-wide CNV differences between these two tumor types using three independent patient datasets. Approximately half of the genes examined exhibited significant differences between LUAD and LUSC tumors and the corresponding non-malignant tissues. A new classifier was developed to identify signature genes out of 20 000 genes. Thirty-three genes were identified as a CNV signature of NSCLC. Using only their CNV values, the classification model separated the LUADs from the LUSCs with an accuracy of 0.88 and 0.84, respectively, in the training and validation datasets. The same signature also classified NSCLC tumors from their corresponding non-malignant samples with an accuracy of 0.96 and 0.98, respectively. We also compared the CNV patterns of NSCLC tumors with those of histologically similar tumors arising at other sites, such as the breast, head, and neck, and four additional tumors. Of greater importance, the significant differences between these tumors may offer the possibility of identifying the origin of tumors whose origin is unknown.
Collapse
Affiliation(s)
- Zhe-Wei Qiu
- School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China
| | - Jia-Hao Bi
- School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China
| | - Adi F Gazdar
- Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA.,Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Kai Song
- School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China.,Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| |
Collapse
|
8
|
He LR, Ma NF, Chen JW, Li BK, Guan XY, Liu MZ, Xie D. Overexpression of CHD1L is positively associated with metastasis of lung adenocarcinoma and predicts patients poor survival. Oncotarget 2016; 6:31181-90. [PMID: 26360781 PMCID: PMC4741596 DOI: 10.18632/oncotarget.5070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 08/14/2015] [Indexed: 12/13/2022] Open
Abstract
CHD1L (chromodomain helicase/ATPase DNA binding protein 1-like gene) has been demonstrated as an oncogene in hepatocellular carcinoma (HCC), however, the role of CHD1L in non-small-cell lung cancer (NSCLC) tumorigenesis hasn't been elucidated. In this study, the expression and amplification status of CHD1L were examined by immunohistochemistry and fluorescence in situ hybridization respectively in 248 surgically resected NSCLCs. The associations between CHD1L expression and clinicopathologic features and the prognostic value of CHD1L were analyzed. Overexpression and amplification of CHD1L was found in 42.1% and 17.7% of NSCLCs, respectively. The frequency of CHD1L overexpression (53.2% vs. 28.1%, P = 0.002) and amplification (25.2% vs. 8.2%, P = 0.020) in adenocarcinoma (ADC), was much higher than that in squamous cell carcinoma (SCC). CHD1L overexpression was associated closely with ascending pN status (P < 0.001), advanced clinical stage (P = 0.001) and tumor distant metastasis (P = 0.001) in ADCs, but not in SCCs. For the whole cohort and ADC patients, univariate survival analysis demonstrated a significant association of CHD1L overexpression with shortened survival; and in multivariate analysis, CHD1L overexpression was evaluated as a independent predictor for overall survival and distant metastasis free survival. These results suggested that overexpression of CHD1L is positively associated with tumor metastasis of lung ADC, and might serve as a novel prognostic biomarker and potential therapeutic target for lung ADC patients.
Collapse
Affiliation(s)
- Li-Ru He
- The State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Ning-Fang Ma
- Department of Histology and Embryology, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Jie-Wei Chen
- The State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Bin-Kui Li
- The State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xin-Yuan Guan
- The State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Departments of Clinical Oncology, The University of Hong Kong, Hong Kong, China
| | - Meng-Zhong Liu
- The State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Dan Xie
- The State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| |
Collapse
|
9
|
Saber A, van der Wekken AJ, Kok K, Terpstra MM, Bosman LJ, Mastik MF, Timens W, Schuuring E, Hiltermann TJN, Groen HJM, van den Berg A. Genomic Aberrations in Crizotinib Resistant Lung Adenocarcinoma Samples Identified by Transcriptome Sequencing. PLoS One 2016; 11:e0153065. [PMID: 27045755 PMCID: PMC4821611 DOI: 10.1371/journal.pone.0153065] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/23/2016] [Indexed: 12/18/2022] Open
Abstract
ALK-break positive non-small cell lung cancer (NSCLC) patients initially respond to crizotinib, but resistance occurs inevitably. In this study we aimed to identify fusion genes in crizotinib resistant tumor samples. Re-biopsies of three patients were subjected to paired-end RNA sequencing to identify fusion genes using deFuse and EricScript. The IGV browser was used to determine presence of known resistance-associated mutations. Sanger sequencing was used to validate fusion genes and digital droplet PCR to validate mutations. ALK fusion genes were detected in all three patients with EML4 being the fusion partner. One patient had no additional fusion genes. Another patient had one additional fusion gene, but without a predicted open reading frame (ORF). The third patient had three additional fusion genes, of which two were derived from the same chromosomal region as the EML4-ALK. A predicted ORF was identified only in the CLIP4-VSNL1 fusion product. The fusion genes validated in the post-treatment sample were also present in the biopsy before crizotinib. ALK mutations (p.C1156Y and p.G1269A) detected in the re-biopsies of two patients, were not detected in pre-treatment biopsies. In conclusion, fusion genes identified in our study are unlikely to be involved in crizotinib resistance based on presence in pre-treatment biopsies. The detection of ALK mutations in post-treatment tumor samples of two patients underlines their role in crizotinib resistance.
Collapse
Affiliation(s)
- Ali Saber
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Anthonie J. van der Wekken
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - M. Martijn Terpstra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Lisette J. Bosman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Mirjam F. Mastik
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - T. Jeroen N. Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Harry J. M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- * E-mail:
| |
Collapse
|
10
|
MYC and human telomerase gene (TERC) copy number gain in early-stage non-small cell lung cancer. Am J Clin Oncol 2015; 38:152-8. [PMID: 25806711 DOI: 10.1097/coc.0000000000000012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
OBJECTIVES We investigated the frequency of MYC and TERC increased gene copy number (GCN) in early-stage non-small cell lung cancer (NSCLC) and evaluated the correlation of these genomic imbalances with clinicopathologic parameters and outcome. MATERIALS AND METHODS Tumor tissues were obtained from 113 resected NSCLCs. MYC and TERC GCNs were tested by fluorescence in situ hybridization (FISH) according to the University of Colorado Cancer Center (UCCC) criteria and based on the receiver operating characteristic (ROC) classification. RESULTS When UCCC criteria were applied, 41 (36%) cases for MYC and 41 (36%) cases for TERC were considered FISH-positive. MYC and TERC concurrent FISH-positive was observed in 12 cases (11%): 2 (17%) cases with gene amplification and 10 (83%) with high polysomy. By using the ROC analysis, high MYC (mean ≥ 2.83 copies/cell) and TERC (mean ≥ 2.65 copies/cell) GCNs were observed in 60 (53.1%) cases and 58 (51.3%) cases, respectively. High TERC GCN was associated with squamous cell carcinoma (SCC) histology (P=0.001). In univariate analysis, increased MYC GCN was associated with shorter overall survival (P=0.032 [UCCC criteria] or P=0.02 [ROC classification]), whereas high TERC GCN showed no association. In multivariate analysis including stage and age, high MYC GCN remained significantly associated with worse overall survival using both the UCCC criteria (P=0.02) and the ROC classification (P=0.008). CONCLUSIONS Our results confirm MYC as frequently amplified in early-stage NSCLC and increased MYC GCN as a strong predictor of worse survival. Increased TERC GCN does not have prognostic impact but has strong association with squamous histology.
Collapse
|
11
|
Jiang J, Sun X, Zhu J, Ma J, Luan J, Liu S. [Genetic characteristics and research progress of targeted therapy in squamous cell carcinoma]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2015; 18:172-8. [PMID: 25800575 PMCID: PMC6000005 DOI: 10.3779/j.issn.1009-3419.2015.03.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jing Jiang
- Department of Oncology, Harbin Medical University Cancer Hospital , Harbin 150000, China
| | - Xiuwei Sun
- Department of Oncology, Harbin Medical University Cancer Hospital , Harbin 150000, China
| | - Jinhong Zhu
- Department of Oncology, Harbin Medical University Cancer Hospital , Harbin 150000, China
| | - Jianqun Ma
- Department of Oncology, Harbin Medical University Cancer Hospital , Harbin 150000, China
| | - Jinwei Luan
- Department of Oncology, Harbin Medical University Cancer Hospital , Harbin 150000, China
| | - Shanshan Liu
- Department of Oncology, Harbin Medical University Cancer Hospital , Harbin 150000, China
| |
Collapse
|
12
|
Loss of 4q21.23-22.1 is a prognostic marker for disease free and overall survival in non-small cell lung cancer. PLoS One 2014; 9:e113315. [PMID: 25501003 PMCID: PMC4263470 DOI: 10.1371/journal.pone.0113315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 10/26/2014] [Indexed: 01/21/2023] Open
Abstract
This study was performed to assess the prognostic relevance of genomic aberrations at chromosome 4q in NSCLC patients. We have previously identified copy number changes at 4q12-q32 to be significantly associated with the early hematogenous dissemination of non-small cell lung cancer (NSCLC), and now aim to narrow down potential hot-spots within this 107 Mb spanning region. Using eight microsatellite markers at position 4q12-35, allelic imbalance (AI) analyses were performed on a preliminary study cohort (n = 86). Positions indicating clinicopathological and prognostic associations in AI analyses were further validated in a larger study cohort using fluorescence in situ hybridization (FISH) in 209 NSCLC patients. Losses at positions 4q21.23 and 4q22.1 were shown to be associated with advanced clinicopathological characteristics as well as with shortened disease free (DFS) and overall survival (OS) (DFS: P = 0.019; OS: P = 0.002). Multivariate analyses identified the losses of 4q21.23-22.1 to be an independent prognostic marker for both DFS and OS in NSCLC (HR 1.64–2.20, all P<0.04), and especially in squamous cell lung cancer (P<0.05). A case report study of a lung cancer patient further revealed a loss of 4q21.23 in disseminated tumor cells (DTCs). Neither gains at the latter positions, nor genomic aberrations at 4q12, 4q31.2 and 4q35.1, indicated a prognostic relevance. In conclusion, our data indicate that loss at 4q21.23-22.1 in NSCLC is of prognostic relevance in NSCLC patients and thus, includes potential new tumor suppressor genes with clinical relevance.
Collapse
|
13
|
Ávila-Moreno F, Armas-López L, Álvarez-Moran AM, López-Bujanda Z, Ortiz-Quintero B, Hidalgo-Miranda A, Urrea-Ramírez F, Rivera-Rosales RM, Vázquez-Manríquez E, Peña-Mirabal E, Morales-Gómez J, Vázquez-Minero JC, Téllez-Becerra JL, Ramírez-Mendoza R, Ávalos-Bracho A, de Alba EG, Vázquez-Santillán K, Maldonado-Lagunas V, Santillán-Doherty P, Piña-Sánchez P, Zúñiga-Ramos J. Overexpression of MEOX2 and TWIST1 is associated with H3K27me3 levels and determines lung cancer chemoresistance and prognosis. PLoS One 2014; 9:e114104. [PMID: 25460568 PMCID: PMC4252097 DOI: 10.1371/journal.pone.0114104] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/29/2014] [Indexed: 12/26/2022] Open
Abstract
Lung cancer is the leading cause of death from malignant diseases worldwide, with the non-small cell (NSCLC) subtype accounting for the majority of cases. NSCLC is characterized by frequent genomic imbalances and copy number variations (CNVs), but the epigenetic aberrations that are associated with clinical prognosis and therapeutic failure remain not completely identify. In the present study, a total of 55 lung cancer patients were included and we conducted genomic and genetic expression analyses, immunohistochemical protein detection, DNA methylation and chromatin immunoprecipitation assays to obtain genetic and epigenetic profiles associated to prognosis and chemoresponse of NSCLC patients. Finally, siRNA transfection-mediated genetic silencing and cisplatinum cellular cytotoxicity assays in NSCLC cell lines A-427 and INER-37 were assessed to describe chemoresistance mechanisms involved. Our results identified high frequencies of CNVs (66–51% of cases) in the 7p22.3–p21.1 and 7p15.3–p15.2 cytogenetic regions. However, overexpression of genes, such as MEOX2, HDAC9, TWIST1 and AhR, at 7p21.2–p21.1 locus occurred despite the absence of CNVs and little changes in DNA methylation. In contrast, the promoter sequences of MEOX2 and TWIST1 displayed significantly lower/decrease in the repressive histone mark H3K27me3 and increased in the active histone mark H3K4me3 levels. Finally these results correlate with poor survival in NSCLC patients and cellular chemoresistance to oncologic drugs in NSCLC cell lines in a MEOX2 and TWIST1 overexpression dependent-manner. In conclusion, we report for the first time that MEOX2 participates in chemoresistance irrespective of high CNV, but it is significantly dependent upon H3K27me3 enrichment probably associated with aggressiveness and chemotherapy failure in NSCLC patients, however additional clinical studies must be performed to confirm our findings as new probable clinical markers in NSCLC patients.
Collapse
Affiliation(s)
- Federico Ávila-Moreno
- Universidad Nacional Autónoma de México (UNAM), Facultad de Estudios Superiores (FES)-Iztacala, Biomedicine Research Unit (UBIMED), Cancer Epigenomics Laboratory 12, Tlalnepantla, Mexico State, Mexico; Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City, Mexico
| | - Leonel Armas-López
- Universidad Nacional Autónoma de México (UNAM), Facultad de Estudios Superiores (FES)-Iztacala, Biomedicine Research Unit (UBIMED), Cancer Epigenomics Laboratory 12, Tlalnepantla, Mexico State, Mexico
| | | | - Zoila López-Bujanda
- Universidad Nacional Autónoma de México (UNAM), Facultad de Estudios Superiores (FES)-Iztacala, Biomedicine Research Unit (UBIMED), Cancer Epigenomics Laboratory 12, Tlalnepantla, Mexico State, Mexico; Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City, Mexico; Johns Hopkins University, Medical Institutions, Maryland, Baltimore, United States of America
| | | | | | | | | | | | - Erika Peña-Mirabal
- Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City, Mexico
| | - José Morales-Gómez
- Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City, Mexico
| | | | | | - Roberto Ramírez-Mendoza
- Universidad Nacional Autónoma de México (UNAM), Facultad de Estudios Superiores (FES)-Iztacala, Biomedicine Research Unit (UBIMED), Cancer Epigenomics Laboratory 12, Tlalnepantla, Mexico State, Mexico
| | | | | | | | | | | | - Patricia Piña-Sánchez
- Unidad de Investigación Médica en Enfermedades Oncológicas (UIMEO), Instituto Mexicano del Seguro Social (IMSS), Centro Médico Nacional (CMN), Siglo XXI, México City, México
| | | |
Collapse
|
14
|
Combined analysis with copy number variation identifies risk loci in lung cancer. BIOMED RESEARCH INTERNATIONAL 2014; 2014:469103. [PMID: 25093167 PMCID: PMC4100386 DOI: 10.1155/2014/469103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 06/11/2014] [Accepted: 06/11/2014] [Indexed: 12/26/2022]
Abstract
Background. Lung cancer is the most important cause of cancer mortality worldwide, but the underlying mechanisms of this disease are not fully understood. Copy number variations (CNVs) are promising genetic variations to study because of their potential effects on cancer.
Methodology/Principal Findings. Here we conducted a pilot study in which we systematically analyzed the association of CNVs in two lung cancer datasets: the Environment And Genetics in Lung cancer Etiology (EAGLE) and the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial datasets. We used a preestablished association method to test the datasets separately and conducted a combined analysis to test the association accordance between the two datasets. Finally, we identified 167 risk SNP loci and 22 CNVs associated with lung cancer and linked them with recombination hotspots. Functional annotation and biological relevance analyses implied that some of our predicted risk loci were supported by other studies and might be potential candidate loci for lung cancer studies. Conclusions/Significance. Our results further emphasized the importance of copy number variations in cancer and might be a valuable complement to current genome-wide association studies on cancer.
Collapse
|
15
|
Li BQ, You J, Huang T, Cai YD. Classification of non-small cell lung cancer based on copy number alterations. PLoS One 2014; 9:e88300. [PMID: 24505469 PMCID: PMC3914971 DOI: 10.1371/journal.pone.0088300] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 01/06/2014] [Indexed: 01/13/2023] Open
Abstract
Lung cancer is one of the leading causes of cancer mortality worldwide and non–small cell lung cancer (NSCLC) accounts for the most part. NSCLC can be further divided into adenocarcinoma (ACA) and squamous cell carcinoma (SCC). It is of great value to distinguish these two subgroups clinically. In this study, we compared the genome-wide copy number alterations (CNAs) patterns of 208 early stage ACA and 93 early stage SCC tumor samples. As a result, 266 CNA probes stood out for better discrimination of ACA and SCC. It was revealed that the genes corresponding to these 266 probes were enriched in lung cancer related pathways and enriched in the chromosome regions where CNA usually occur in lung cancer. This study sheds lights on the CNA study of NSCLC and provides some insights on the epigenetic of NSCLC.
Collapse
Affiliation(s)
- Bi-Qing Li
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Jin You
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Tao Huang
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York City, New York, United States of America
- * E-mail: (TH); (Y-DC)
| | - Yu-Dong Cai
- Institute of Systems Biology, Shanghai University, Shanghai, P.R. China
- * E-mail: (TH); (Y-DC)
| |
Collapse
|
16
|
Genetic alterations defining NSCLC subtypes and their therapeutic implications. Lung Cancer 2013; 82:179-89. [PMID: 24011633 DOI: 10.1016/j.lungcan.2013.07.025] [Citation(s) in RCA: 245] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/20/2013] [Accepted: 07/29/2013] [Indexed: 01/03/2023]
Abstract
Lung cancer is the leading cause of cancer death worldwide, accounting for more deaths than breast, prostate and colon cancer combined. While treatment decisions are determined primarily by stage, therapeutically non small cell lung cancer (NSCLC) has traditionally been treated as a single disease. However, recent findings have led to the recognition of histology and molecular subtypes as important determinants in treatment selection. Identifying the genetic differences that define these molecular and histological subtypes has the potential to impact treatment and as such is currently the focus of much research. Microarray and genomic sequencing efforts have provided unparalleled insight into the genomes of lung cancer subtypes, specifically adenocarcinoma (AC) and squamous cell carcinoma (SqCC), revealing subtype specific genomic alterations and molecular subtypes as well as differences in cell signaling pathways. In this review, we discuss the recurrent genomic alterations characteristic of AC and SqCC (including molecular subtypes), their therapeutic implications and emerging clinical practices aimed at tailoring treatments based on a tumor's molecular alterations with the hope of improving patient response and survival.
Collapse
|
17
|
True 3q chromosomal amplification in squamous cell lung carcinoma by FISH and aCGH molecular analysis: impact on targeted drugs. PLoS One 2012; 7:e49689. [PMID: 23236352 PMCID: PMC3516520 DOI: 10.1371/journal.pone.0049689] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 10/11/2012] [Indexed: 01/15/2023] Open
Abstract
Squamous lung carcinoma lacks specific “ad hoc” therapies. Amplification of chromosome 3q is the most common genomic aberration and this region harbours genes having role as novel targets for therapeutics. There is no standard definition on how to score and report 3q amplification. False versus true 3q chromosomal amplification in squamous cell lung carcinoma may have tremendous impact on trials involving drugs which target DNA zones mapping on 3q. Forty squamous lung carcinomas were analyzed by FISH to assess chromosome 3q amplification. aCGH was performed as gold-standard to avoid false positive amplifications. Three clustered patterns of fluorescent signals were observed. Eight cases out of 40 (20%) showed ≥8 3q signals. Twenty out of 40 (50%) showed from 3 to 7 signals. The remaining showed two fluorescent signals (30%). When corrected by whole chromosome 3 signals, only cases with ≥8 signals maintained a LSI 3q/CEP3 ratio >2. Only the cases showing 3q amplification by aCGH (+3q25.3−3q27.3) showed ≥8 fluorescent signals at FISH evidencing a 3q/3 ratio >2. The remaining cases showed flat genomic portrait at aCGH on chromosome 3. We concluded that: 1) absolute copy number of 3q chromosomal region may harbour false positive interpretation of 3q amplification in squamous cell carcinoma; 2) a case results truly “amplified for chromosome 3q” when showing ≥8 fluorescent 3q signals; 3) trials involving drugs targeting loci on chromosome 3q in squamous lung carcinoma therapy have to consider false versus true 3q chromosomal amplification.
Collapse
|
18
|
Staaf J, Isaksson S, Karlsson A, Jönsson M, Johansson L, Jönsson P, Botling J, Micke P, Baldetorp B, Planck M. Landscape of somatic allelic imbalances and copy number alterations in human lung carcinoma. Int J Cancer 2012; 132:2020-31. [PMID: 23023297 DOI: 10.1002/ijc.27879] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/13/2012] [Indexed: 12/27/2022]
Abstract
Lung cancer is the worldwide leading cause of death from cancer and has been shown to be a heterogeneous disease at the genomic level. To delineate the genomic landscape of copy number alterations, amplifications, loss-of-heterozygosity (LOH), tumor ploidy and copy-neutral allelic imbalance in lung cancer, microarray-based genomic profiles from 2,141 tumors and cell lines including adenocarcinomas (AC, n = 1,206), squamous cell carcinomas (SqCC, n = 467), large cell carcinomas (n = 37) and small cell lung carcinomas (SCLC, n = 88) were assembled from different repositories. Copy number alteration differences between lung cancer histologies were confirmed in 285 unrelated tumors analyzed by BAC array comparative genomic hybridization. Tumor ploidy patterns were validated by DNA flow cytometry analysis of 129 unrelated cases. Eighty-nine recurrent copy number alterations (55 gains, 34 losses) were identified harboring genes with gene expression putatively driven by gene dosage through integration with gene expression data for 496 cases. Thirteen and 26 of identified regions discriminated AC/SqCC and AC/SqCC/SCLC, respectively, while 48 regions harbored recurrent (n > 15) high-level amplifications comprising established and putative oncogenes, differing in frequency and coamplification patterns between histologies. Lung cancer histologies displayed differences in patterns/frequency of copy number alterations, genomic architecture, LOH, copy-neutral allelic imbalance and tumor ploidy, with AC generally displaying less copy number alterations and allelic imbalance. Moreover, a strong association was demonstrated between different types of copy number alterations and allelic imbalances with tumor aneuploidy. In summary, these analyses provide a comprehensive overview of the landscape of genomic alterations in lung cancer, highlighting differences but also similarities between subgroups of the disease.
Collapse
Affiliation(s)
- Johan Staaf
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, Lund, Sweden.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Abstract
Identifying specific somatic mutations that drive tumor growth has transformed the treatment of lung cancer. For example, cancers with sensitizing epidermal growth factor receptor mutations and echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase translocations can have remarkable responses to epidermal growth factor receptor and ALK inhibitors respectively, leading to significant clinical benefit. However, effective molecularly targeted therapies have disproportionately impacted adenocarcinomas compared to squamous cell carcinomas, and never or light smokers compared to heavy smokers. Further progress in non-small-cell lung cancer will require the identification and effective targeting of molecular alterations in all subtypes of lung cancer. Here, we review the current knowledge about the molecular alterations found in squamous cell carcinoma of the lung. First, we will discuss the ongoing efforts to comprehensively assess the squamous cell carcinoma genome. We will then discuss the evidence supporting the role of specific genes in driving squamous cell carcinomas. By describing the landscape of somatic targets in squamous cell lung cancer, we hope to crystallize the current understanding of potential targets, spur development of therapies that can have clinical impact, and underscore the importance of new discoveries in this field.
Collapse
|
20
|
Smida M, Nijman SMB. Functional drug-gene interactions in lung cancer. Expert Rev Mol Diagn 2012; 12:291-302. [PMID: 22468819 DOI: 10.1586/erm.12.16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite the dawn of the genomic information era, the challenges of cancer treatment remain formidable. Particularly for the most prevalent cancer types, including lung cancer, successful treatment of metastatic disease is rare and escalating costs for modern targeted drugs place an increasing strain on healthcare systems. Although powerful diagnostic tools to characterize individual tumor samples in great molecular detail are becoming rapidly available, the transformation of this information into therapy provides a major challenge. A fundamental difficulty is the molecular complexity of cancer cells that often causes drug resistance, but can also render tumors exquisitely sensitive to targeted agents. By using lung cancer as an example, we outline the principles that govern drug sensitivity and resistance from a genetic perspective and discuss how in vitro chemical-genetic screens can impact on patient stratification in the clinic.
Collapse
Affiliation(s)
- Michal Smida
- CeMM Research Center for Molecular Medicine of Austrian Academy of Sciences, Vienna, Austria
| | | |
Collapse
|
21
|
Lockwood WW, Wilson IM, Coe BP, Chari R, Pikor LA, Thu KL, Solis LM, Nunez MI, Behrens C, Yee J, English J, Murray N, Tsao MS, Minna JD, Gazdar AF, Wistuba II, MacAulay CE, Lam S, Lam WL. Divergent genomic and epigenomic landscapes of lung cancer subtypes underscore the selection of different oncogenic pathways during tumor development. PLoS One 2012; 7:e37775. [PMID: 22629454 PMCID: PMC3357406 DOI: 10.1371/journal.pone.0037775] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 04/27/2012] [Indexed: 01/12/2023] Open
Abstract
For therapeutic purposes, non-small cell lung cancer (NSCLC) has traditionally been regarded as a single disease. However, recent evidence suggest that the two major subtypes of NSCLC, adenocarcinoma (AC) and squamous cell carcinoma (SqCC) respond differently to both molecular targeted and new generation chemotherapies. Therefore, identifying the molecular differences between these tumor types may impact novel treatment strategy. We performed the first large-scale analysis of 261 primary NSCLC tumors (169 AC and 92 SqCC), integrating genome-wide DNA copy number, methylation and gene expression profiles to identify subtype-specific molecular alterations relevant to new agent design and choice of therapy. Comparison of AC and SqCC genomic and epigenomic landscapes revealed 778 altered genes with corresponding expression changes that are selected during tumor development in a subtype-specific manner. Analysis of >200 additional NSCLCs confirmed that these genes are responsible for driving the differential development and resulting phenotypes of AC and SqCC. Importantly, we identified key oncogenic pathways disrupted in each subtype that likely serve as the basis for their differential tumor biology and clinical outcomes. Downregulation of HNF4α target genes was the most common pathway specific to AC, while SqCC demonstrated disruption of numerous histone modifying enzymes as well as the transcription factor E2F1. In silico screening of candidate therapeutic compounds using subtype-specific pathway components identified HDAC and PI3K inhibitors as potential treatments tailored to lung SqCC. Together, our findings suggest that AC and SqCC develop through distinct pathogenetic pathways that have significant implication in our approach to the clinical management of NSCLC.
Collapse
Affiliation(s)
- William W Lockwood
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
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.
Collapse
Affiliation(s)
- Humam Kadara
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| | | | | |
Collapse
|
23
|
Sriram KB, Larsen JE, Savarimuthu Francis SM, Wright CM, Clarke BE, Duhig EE, Brown KM, Hayward NK, Yang IA, Bowman RV, Fong KM. Array-comparative genomic hybridization reveals loss of SOCS6 is associated with poor prognosis in primary lung squamous cell carcinoma. PLoS One 2012; 7:e30398. [PMID: 22363434 PMCID: PMC3281847 DOI: 10.1371/journal.pone.0030398] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 12/15/2011] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Primary tumor recurrence commonly occurs after surgical resection of lung squamous cell carcinoma (SCC). Little is known about the genes driving SCC recurrence. METHODS We used array comparative genomic hybridization (aCGH) to identify genes affected by copy number alterations that may be involved in SCC recurrence. Training and test sets of resected primary lung SCC were assembled. aCGH was used to determine genomic copy number in a training set of 62 primary lung SCCs (28 with recurrence and 34 with no evidence of recurrence) and the altered copy number of candidate genes was confirmed by quantitative PCR (qPCR). An independent test set of 72 primary lung SCCs (20 with recurrence and 52 with no evidence of recurrence) was used for biological validation. mRNA expression of candidate genes was studied using qRT-PCR. Candidate gene promoter methylation was evaluated using methylation microarrays and Sequenom EpiTYPER analysis. RESULTS 18q22.3 loss was identified by aCGH as being significantly associated with recurrence (p = 0.038). Seven genes within 18q22.3 had aCGH copy number loss associated with recurrence but only SOCS6 copy number was both technically replicated by qPCR and biologically validated in the test set. SOCS6 copy number loss correlated with reduced mRNA expression in the study samples and in the samples with copy number loss, there was a trend for increased methylation, albeit non-significant. Overall survival was significantly poorer in patients with SOCS6 loss compared to patients without SOCS6 loss in both the training (30 vs. 43 months, p = 0.023) and test set (27 vs. 43 months, p = 0.010). CONCLUSION Reduced copy number and mRNA expression of SOCS6 are associated with disease recurrence in primary lung SCC and may be useful prognostic biomarkers.
Collapse
MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/surgery
- Chromosomes, Human/genetics
- Chromosomes, Human, Pair 18/genetics
- Comparative Genomic Hybridization
- DNA Copy Number Variations/genetics
- DNA Methylation/genetics
- Female
- Follow-Up Studies
- Gene Dosage/genetics
- Gene Expression Regulation, Neoplastic
- Genes, Neoplasm/genetics
- Genetic Association Studies
- Genome, Human/genetics
- Humans
- Kaplan-Meier Estimate
- Lung Neoplasms/genetics
- Lung Neoplasms/surgery
- Male
- Middle Aged
- Phenotype
- Polymerase Chain Reaction
- Prognosis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recurrence
- Reproducibility of Results
- Suppressor of Cytokine Signaling Proteins/genetics
- Tumor Cells, Cultured
Collapse
Affiliation(s)
- Krishna B Sriram
- School of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Scrima M, De Marco C, De Vita F, Fabiani F, Franco R, Pirozzi G, Rocco G, Malanga D, Viglietto G. The nonreceptor-type tyrosine phosphatase PTPN13 is a tumor suppressor gene in non-small cell lung cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 180:1202-1214. [PMID: 22245727 DOI: 10.1016/j.ajpath.2011.11.038] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/13/2011] [Accepted: 11/17/2011] [Indexed: 01/31/2023]
Abstract
The aim of the present work was to identify protein tyrosine phosphatases (PTPs) as novel, candidate tumor suppressor genes in lung cancer. Among the 38 PTPs in the human genome that show specificity for phosphotyrosine, we identified six PTPs by quantitative RT-PCR whose mRNA expression levels were significantly down-regulated in lung cancer-derived cell lines (ie, PTPRE, PTPRF, PTPRU, PTPRK, PTPRD, and PTPN13). After validation in primary samples of non-small cell lung cancer (NSCLC), we selected PTPN13 for further studies. The results presented here demonstrate that PTPN13 is a candidate tumor suppressor gene that is frequently inactivated in NSCLC through the loss of either mRNA and protein expression (64/87, 73%) or somatic mutation (approximately 8%). Loss of PTPN13 expression was apparently due to the loss of one or both copies of the PTPN13 locus at 4q (approximately 26% double deletion and approximately 37% single deletion) but not to promoter methylation. Finally, the manipulation of PTPN13 expression in lung cancer cells (ie, NCI-H292, A549) demonstrated that PTPN13 negatively regulates anchorage-dependent and anchorage-independent growth in vitro and restrains tumorigenicity in vivo, possibly through the control of the tyrosine phosphorylation of both EGFR and HER2. In conclusion, the expression screening of PTPs in lung cancer reported here has identified PTPN13 as a novel candidate tumor suppressor in NSCLC whose loss increases signaling from epidermal growth factor receptor and HER2 tyrosine kinase receptors.
Collapse
Affiliation(s)
- Marianna Scrima
- Biogem Scarl, the Institute for Genetic Research Gaetano Salvatore, Ariano Irpino, Italy
| | - Carmela De Marco
- Biogem Scarl, the Institute for Genetic Research Gaetano Salvatore, Ariano Irpino, Italy; Department of Experimental and Clinical Medicine, University Magna Graecia, Catanzaro, Italy
| | - Fernanda De Vita
- Biogem Scarl, the Institute for Genetic Research Gaetano Salvatore, Ariano Irpino, Italy
| | - Fernanda Fabiani
- Department of Experimental and Clinical Medicine, University Magna Graecia, Catanzaro, Italy
| | - Renato Franco
- Fondazione G. Pascale, National Cancer Institute, Naples, Italy
| | | | - Gaetano Rocco
- Fondazione G. Pascale, National Cancer Institute, Naples, Italy
| | - Donatella Malanga
- Biogem Scarl, the Institute for Genetic Research Gaetano Salvatore, Ariano Irpino, Italy; Department of Experimental and Clinical Medicine, University Magna Graecia, Catanzaro, Italy
| | - Giuseppe Viglietto
- Biogem Scarl, the Institute for Genetic Research Gaetano Salvatore, Ariano Irpino, Italy; Department of Experimental and Clinical Medicine, University Magna Graecia, Catanzaro, Italy.
| |
Collapse
|
25
|
Zhao Y, Li Y, Lu H, Chen J, Zhang Z, Zhu ZZ. Association of copy number loss of CDKN2B and PTCH1 with poor overall survival in patients with pulmonary squamous cell carcinoma. Clin Lung Cancer 2012; 12:328-34. [PMID: 21889114 DOI: 10.1016/j.cllc.2011.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 02/13/2011] [Accepted: 02/22/2011] [Indexed: 01/16/2023]
Abstract
BACKGROUND AND PURPOSE Although lung cancer is the leading cause of cancer deaths worldwide, reliable markers allowing prediction of patient survival at the time of initial diagnosis are still lacking. Copy number alterations (CNAs) in tumor tissue DNA have been associated with tumorigenesis and malignant progression. We aimed at identification of gene-level CNAs with prognostic value for survival in pulmonary squamous cell carcinoma (SCC). METHODS The CNA status of a panel of 44 genes was analyzed by high-resolution array comparative genomic hybridization (CGH) in 49 SCC samples. Overall survival information (median follow-up, 40 months) for the patients was collected and used to assess outcome correlations with gene CNAs. RESULTS Survival analysis showed that both CDKN2B loss and PTCH1 loss were associated with poor survival (both P < .001, log-rank test). Multivariate Cox analysis, including CDKN2B loss and PTCH1 loss as well as age, sex, cigarette smoking status, tumor size, tumor differentiation, and TNM stage showed that CDKN2B loss (hazard ratio [HR], 17.88; 95% confidence interval [CI], 4.40-72.67; P < .001) and PTCH1 loss (HR, 10.81; 95% CI, 1.92-60.98; P = .007) were independent prognostic factors for poor survival. In addition the PTCH1 loss was more frequently found in moderately or poorly differentiated tumors than in well-differentiated tumors (P = .007). CONCLUSION These findings suggest that 2 genes of loss, CDKN2B and PTCH1, are associated with poor overall survival in patients with SCC of the lung and may be useful as prognostic markers.
Collapse
Affiliation(s)
- Yushi Zhao
- Department of Cardiovascular Surgery, the Fourth Affiliated Hospital, Harbin Medical University, Heilongjiang, P.R. China
| | | | | | | | | | | |
Collapse
|
26
|
Danner BC, Hellms T, Jung K, Gunawan B, Didilis V, Füzesi L, Schöndube FA. Prognostic Value of Chromosomal Imbalances in Squamous Cell Carcinoma and Adenocarcinoma of the Lung. Ann Thorac Surg 2011; 92:1038-43. [DOI: 10.1016/j.athoracsur.2011.04.052] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 04/09/2011] [Accepted: 04/15/2011] [Indexed: 11/27/2022]
|
27
|
Matsuyama Y, Suzuki M, Arima C, Huang QM, Tomida S, Takeuchi T, Sugiyama R, Itoh Y, Yatabe Y, Goto H, Takahashi T. Proteasomal non-catalytic subunit PSMD2 as a potential therapeutic target in association with various clinicopathologic features in lung adenocarcinomas. Mol Carcinog 2011; 50:301-9. [PMID: 21465578 DOI: 10.1002/mc.20632] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We previously identified PSMD2, a subunit of the 19S regulatory complex of proteasomes, as a constituent of a signature associated with the acquisition of metastatic phenotype and poor prognosis in lung cancers. In the present study, we found that knockdown of PSMD2 decreased proteasome activity, and induced growth inhibition and apoptosis in lung cancer cell lines. These effects of siRNA-mediated PSMD2 inhibition were associated with changes in the balance between phosphorylated AKT and p38, as well as with induction of p21. In addition, patients with higher PSMD2 expression had poorer prognosis and a small fraction of lung cancer specimens carried increased copies of PSMD2. Notably, our findings clearly illustrate that lung adenocarcinomas can be divided into two groups; those with and without general upregulation of proteasome pathway genes including PSMD2. This general upregulation was significantly more prevalent in the non-terminal respiratory unit (non-TRU)-type, a recently proposed genetically and clinicopathologically relevant expression profile-defined classification of adenocarcinomas (P < 0.001 by Fisher's exact test). Patients with adenocarcinomas with general upregulation had significantly shorter survival after potentially curative resection (P = 0.0001 by log-rank test) independent of disease stage, as shown by multivariate Cox regression analysis. Our results suggest that PSMD2 may be a good molecular target candidate and that other co-regulated proteasome pathway genes and/or their common regulator(s) might also be potential targets, warranting future study including elucidation of the underlying common regulatory mechanism.
Collapse
Affiliation(s)
- Yasushi Matsuyama
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Newnham GM, Conron M, McLachlan S, Dobrovic A, Do H, Li J, Opeskin K, Thompson N, Wright GM, Thomas DM. Integrated mutation, copy number and expression profiling in resectable non-small cell lung cancer. BMC Cancer 2011; 11:93. [PMID: 21385341 PMCID: PMC3058106 DOI: 10.1186/1471-2407-11-93] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 03/07/2011] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The aim of this study was to identify critical genes involved in non-small cell lung cancer (NSCLC) pathogenesis that may lead to a more complete understanding of this disease and identify novel molecular targets for use in the development of more effective therapies. METHODS Both transcriptional and genomic profiling were performed on 69 resected NSCLC specimens and results correlated with mutational analyses and clinical data to identify genetic alterations associated with groups of interest. RESULTS Combined analyses identified specific patterns of genetic alteration associated with adenocarcinoma vs. squamous differentiation; KRAS mutation; TP53 mutation, metastatic potential and disease recurrence and survival. Amplification of 3q was associated with mutations in TP53 in adenocarcinoma. A prognostic signature for disease recurrence, reflecting KRAS pathway activation, was validated in an independent test set. CONCLUSIONS These results may provide the first steps in identifying new predictive biomarkers and targets for novel therapies, thus improving outcomes for patients with this deadly disease.
Collapse
Affiliation(s)
- Genni M Newnham
- Department of Oncology, St Vincent's Hospital, (Victoria Pde), Melbourne, (3065), Australia
- Department of Medicine, St Vincent's Hospital, The University of Melbourne, (Tin Alley), Melbourne, (3010), Australia
| | - Matthew Conron
- Department of Respiratory Medicine, St Vincent's Hospital, (Victoria Pde), Melbourne, (3065), Australia
| | - SueAnne McLachlan
- Department of Oncology, St Vincent's Hospital, (Victoria Pde), Melbourne, (3065), Australia
- Department of Medicine, St Vincent's Hospital, The University of Melbourne, (Tin Alley), Melbourne, (3010), Australia
| | - Alexander Dobrovic
- Department of Pathology, Peter MacCallum Cancer Centre, (St Andrews Place), East Melbourne, (3002), Australia
- Department of Pathology, The University of Melbourne, (Tin Alley), Melbourne, (3010), Australia
| | - Hongdo Do
- Department of Pathology, Peter MacCallum Cancer Centre, (St Andrews Place), East Melbourne, (3002), Australia
- Department of Pathology, The University of Melbourne, (Tin Alley), Melbourne, (3010), Australia
| | - Jason Li
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, (St Andrews Place), East Melbourne, (3002), Australia
| | - Kenneth Opeskin
- Department of Anatomical Pathology, St Vincent's Hospital, (Victoria Pde), Melbourne, (3065), Australia
| | - Natalie Thompson
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, (St Andrews Place), East Melbourne, (3002), Australia
| | - Gavin M Wright
- Department of Thoracic Surgery, St Vincent's Hospital, (Victoria Pde), Melbourne, (3065), Australia
| | - David M Thomas
- Centre for Genomics and Predictive Medicine, Peter MacCallum Cancer Centre, (St Andrews Place), East Melbourne, (3002), Australia
| |
Collapse
|
29
|
Abstract
Background: Lung squamous cell carcinomas (SqCCs) occur at higher rates following arsenic exposure. Somatic DNA copy-number alterations (CNAs) are understood to be critical drivers in several tumour types. We have assembled a rare panel of lung tumours from a population with chronic arsenic exposure, including SqCC tumours from patients with no smoking history. Methods: Fifty-two lung SqCCs were analysed by whole-genome tiling-set array comparative genomic hybridisation. Twenty-two were derived from arsenic-exposed patients from Northern Chile (10 never smokers and 12 smokers). Thirty additional cases were obtained for comparison from North American smokers without arsenic exposure. Twenty-two blood samples from healthy individuals from Northern Chile were examined to identify germline DNA copy-number variations (CNVs) that could be excluded from analysis. Results: We identified multiple CNAs associated with arsenic exposure. These alterations were not attributable to either smoking status or CNVs. DNA losses at chromosomes 1q21.1, 7p22.3, 9q12, and 19q13.31 represented the most recurrent events. An arsenic-associated gain at 19q13.33 contains genes previously identified as oncogene candidates. Conclusions: Our results provide a comprehensive approach to molecular characteristics of the arsenic-exposed lung cancer genome and the non-smoking lung SqCC genome. The distinct and recurrent arsenic-related alterations suggest that this group of tumours may be considered as a separate disease subclass.
Collapse
|
30
|
Fong Y, Lin YS, Liou CP, Li CF, Tzeng CC. Chromosomal imbalances in lung adenocarcinomas with or without mutations in the epidermal growth factor receptor gene. Respirology 2010; 15:700-5. [PMID: 20409020 DOI: 10.1111/j.1440-1843.2010.01746.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND AND OBJECTIVE Epidermal growth factor receptor (EGFR) mutations are common in lung adenocarcinomas of Asian patients, implying a good response to treatment with the EGFR tyrosine kinase inhibitors, gefitinib and erlotinib. However, the distinct chromosomal imbalances between lung adenocarcinomas with and those without EGFR mutations have not been fully elucidated. METHODS Seventy-seven patients of surgically resected lung adenocarcinoma were analysed for the EGFR exon 19 deletion and the L858R mutation, using mutant-enriched PCR, and for chromosomal imbalance alterations using comparative genomic hybridization. RESULTS EGFR mutations were detected in 42 (54.5%) patients, including 22 with the exon 19 deletion and 20 with the L858R mutation. The mean number of chromosomal arms with imbalance alterations was significantly higher in tumours with EGFR mutations than in those lacking these two mutations. The minimal regions with gain on 1q23-q31, 6p12-p21.1 and 7q11.2, and loss on 3p21, 8p22-p23, 9q33, 10q25 and 13q13, differed significantly between lung adenocarcinomas with or without EGFR mutations. However, neither EGFR mutations, nor any of the common chromosomal imbalance alterations alone, exhibited significant associations with tumour stage or disease-specific survival of the patients. CONCLUSIONS These results indicate that imbalance alterations at several chromosomal regions occur significantly more frequently in lung adenocarcinomas with EGFR mutations than in those without such mutations. Tumour growth-related genes in these chromosomal regions should be further investigated to improve our understanding of the common genetic alterations in lung adenocarcinomas with EGFR mutations.
Collapse
Affiliation(s)
- Yao Fong
- Division of Thoracic Surgery, Department of Surgery, Chi Mei Medical Center, Tainan, Taiwan
| | | | | | | | | |
Collapse
|
31
|
Lonergan KM, Chari R, Coe BP, Wilson IM, Tsao MS, Ng RT, MacAulay C, Lam S, Lam WL. Transcriptome profiles of carcinoma-in-situ and invasive non-small cell lung cancer as revealed by SAGE. PLoS One 2010; 5:e9162. [PMID: 20161782 PMCID: PMC2820080 DOI: 10.1371/journal.pone.0009162] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2009] [Accepted: 01/07/2010] [Indexed: 12/29/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) presents as a progressive disease spanning precancerous, preinvasive, locally invasive, and metastatic lesions. Identification of biological pathways reflective of these progressive stages, and aberrantly expressed genes associated with these pathways, would conceivably enhance therapeutic approaches to this devastating disease. Methodology/Principal Findings Through the construction and analysis of SAGE libraries, we have determined transcriptome profiles for preinvasive carcinoma-in-situ (CIS) and invasive squamous cell carcinoma (SCC) of the lung, and compared these with expression profiles generated from both bronchial epithelium, and precancerous metaplastic and dysplastic lesions using Ingenuity Pathway Analysis. Expression of genes associated with epidermal development, and loss of expression of genes associated with mucociliary biology, are predominant features of CIS, largely shared with precancerous lesions. Additionally, expression of genes associated with xenobiotic metabolism/detoxification is a notable feature of CIS, and is largely maintained in invasive cancer. Genes related to tissue fibrosis and acute phase immune response are characteristic of the invasive SCC phenotype. Moreover, the data presented here suggests that tissue remodeling/fibrosis is initiated at the early stages of CIS. Additionally, this study indicates that alteration in copy-number status represents a plausible mechanism for differential gene expression in CIS and invasive SCC. Conclusions/Significance This study is the first report of large-scale expression profiling of CIS of the lung. Unbiased expression profiling of these preinvasive and invasive lesions provides a platform for further investigations into the molecular genetic events relevant to early stages of squamous NSCLC development. Additionally, up-regulated genes detected at extreme differences between CIS and invasive cancer may have potential to serve as biomarkers for early detection.
Collapse
Affiliation(s)
- Kim M. Lonergan
- Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- * E-mail:
| | - Raj Chari
- Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Bradley P. Coe
- Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Ian M. Wilson
- Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Ming-Sound Tsao
- Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Raymond T. Ng
- Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Calum MacAulay
- Imaging Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Stephen Lam
- Imaging Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Wan L. Lam
- Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| |
Collapse
|
32
|
Shen H, Gao W, Wu YJ, Qiu HR, Shu YQ. Multicolor fluorescence in situ hybridization and comparative genomic hybridization reveal molecular events in lung adenocarcinomas and squamous cell lung carcinomas. Biomed Pharmacother 2009; 63:396-403. [DOI: 10.1016/j.biopha.2008.08.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Accepted: 08/24/2008] [Indexed: 01/03/2023] Open
|
33
|
Campbell JM, Lockwood WW, Buys TPH, Chari R, Coe BP, Lam S, Lam WL. Integrative genomic and gene expression analysis of chromosome 7 identified novel oncogene loci in non-small cell lung cancer. Genome 2009; 51:1032-9. [PMID: 19088816 DOI: 10.1139/g08-086] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lung cancer accounts for over a quarter of cancer deaths, with non-small cell lung cancer (NSCLC) accounting for approximately 80% of cases. Several genome studies have been undertaken in both cell models of NSCLC and clinical samples to identify alterations underlying disease behaviour, and many have identified recurring aberrations of chromosome 7. The presence of recurring chromosome 7 alterations that do not span the well-studied oncogenes EGFR (at 7p11.2) and MET (at 7q31.2) has raised the hypothesis of additional genes on this chromosome that contribute to tumourigenesis. In this study, we demonstrated that multiple loci on chromosome 7 are indeed amplified in NSCLC, and through integrative analysis of gene dosage alterations and parallel gene expression changes, we identified new lung cancer oncogene candidates, including FTSJ2, NUDT1, TAF6, and POLR2J. Activation of these key genes was confirmed in panels of clinical lung tumour tissue as compared with matched normal lung tissue. The detection of gene activation in multiple cohorts of samples strongly supports the presence of key genes involved in lung cancer that are distinct from the EGFR and MET loci on chromosome 7.
Collapse
Affiliation(s)
- Jennifer M Campbell
- Department of Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z1L3 Canada
| | | | | | | | | | | | | |
Collapse
|
34
|
Genomic aberrations in squamous cell lung carcinoma related to lymph node or distant metastasis. Lung Cancer 2009; 66:372-8. [PMID: 19324446 DOI: 10.1016/j.lungcan.2009.02.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 02/12/2009] [Accepted: 02/15/2009] [Indexed: 11/22/2022]
Abstract
About 50% of patients presenting with resectable lung cancer develop distant metastases within 5 years. Genomic markers predicting metastatic behaviour of squamous cell lung carcinoma (SCC) are currently underexposed. We analyzed a cohort of patients with primary SCC using array-based comparative genomic hybridization (aCGH) to identify which genomic aberrations are related to metastatic behaviour. The cohort consisted of 34 patients with a follow-up of at least 5 years, 8 with metastases in regional lymph nodes only and 26 patients without any metastases at the time of surgery. Eleven of the latter 26 developed metastases in distant organs within 3 years after surgery. Copy number changes observed in at least 40% of all SCC included gains at chromosomal arms 3q, 5p, 8q, 19q, 20p, 22q and losses at 3p, 4p, 4q, 5q, 8p and 9p. High copy number amplifications were observed at 2p15-p16, 3q24-q29, 8p11-p12, 8q23-q24, and 12p12, containing candidate oncogenes such as BCL11A, REL, ECT2, PIK3CA, ADAM9, MYC and KRAS. Amplification of 2p15-p16 is a novel finding in SCC. Another novel finding is the homozygous deletion observed at 4q33-34.1 in 15% of the SCC cases. Gains at 7q36, 8p12, 10q22, 12p12, loss at 4p14 and the homozygous deletions at 4q occurred significantly more frequent in SCC from patients with lymph node metastases only. SCC from patients with distant metastases showed a significantly higher gain frequency at 8q22-q24 and loss at 8p23 and 13q21, and a significantly lower gain frequency at 2p12 and 2p16 and loss at 11q25 compared with SCC from patients without metastases. Of these, gains at 7q, 8p and 10q were restricted to SCC with lymph node metastasis and gain at 8q was restricted to patients with distant metastasis. Two genomic aberrations, i.e. loss of 4p and gain of 19q12 were observed more frequently in SCC with only lymph node metastases as compared to SCC with distant metastases. In conclusion, we identified genomic aberrations in primary SCC that were related to lymph node or distant metastases.
Collapse
|
35
|
Jung HM, Choi SJ, Kim JK. Expression profiles of SV40-immortalization-associated genes upregulated in various human cancers. J Cell Biochem 2009; 106:703-13. [DOI: 10.1002/jcb.22063] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
36
|
Gill RK, Vazquez MF, Kramer A, Hames M, Zhang L, Heselmeyer-Haddad K, Ried T, Shilo K, Henschke C, Yankelevitz D, Jen J. The use of genetic markers to identify lung cancer in fine needle aspiration samples. Clin Cancer Res 2009; 14:7481-7. [PMID: 19010865 DOI: 10.1158/1078-0432.ccr-07-5242] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE We seek to establish a genetic test to identify lung cancer using cells obtained through computed tomography-guided fine needle aspiration (FNA). EXPERIMENTAL DESIGN We selected regions of frequent copy number gains in chromosomes 1q32, 3q26, 5p15, and 8q24 in non-small cell lung cancer and tested their ability to determine the neoplastic state of cells obtained by FNA using fluorescent in situ hybridization. Two sets of samples were included. The pilot set included six paraffin-embedded, noncancerous lung tissues and 33 formalin-fixed FNA specimens. These 39 samples were used to establish the optimal fixation and single scoring criteria for the samples. The test set included 40 FNA samples. The results of the genetic test were compared with the cytology, pathology, and clinical follow-up for each case to assess the sensitivity and specificity of the genetic test. RESULTS Nontumor lung tissues had < or= 4 signals per nucleus for all tested markers, whereas tumor samples had > or = 5 signals per nucleus in five or more cells for at least one marker. Among the 40 testing cases, 36 of 40 (90%) FNA samples were analyzable. Genetic analysis identified 15 cases as tumor and 21 cases as nontumor. Clinical and pathologic diagnoses confirmed the genetic test in 15 of 16 lung cancer cases regardless of tumor subtype, stage, or size and in 20 of 20 cases diagnosed as benign lung diseases. CONCLUSIONS A set of only four genetic markers can distinguish the neoplastic state of lung lesion using small samples obtained through computed tomography-guided FNA.
Collapse
Affiliation(s)
- Rajbir K Gill
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
McCaughan F, Darai-Ramqvist E, Bankier AT, Konfortov BA, Foster N, George PJ, Rabbitts TH, Kost-Alimova M, Rabbitts PH, Dear PH. Microdissection molecular copy-number counting (microMCC)--unlocking cancer archives with digital PCR. J Pathol 2008; 216:307-16. [PMID: 18773450 DOI: 10.1002/path.2413] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Most cancer genomes are characterized by the gain or loss of copies of some sequences through deletion, amplification or unbalanced translocations. Delineating and quantifying these changes is important in understanding the initiation and progression of cancer, in identifying novel therapeutic targets, and in the diagnosis and prognosis of individual patients. Conventional methods for measuring copy-number are limited in their ability to analyse large numbers of loci, in their dynamic range and accuracy, or in their ability to analyse small or degraded samples. This latter limitation makes it difficult to access the wealth of fixed, archived material present in clinical collections, and also impairs our ability to analyse small numbers of selected cells from biopsies. Molecular copy-number counting (MCC), a digital PCR technique, has been used to delineate a non-reciprocal translocation using good quality DNA from a renal carcinoma cell line. We now demonstrate microMCC, an adaptation of MCC which allows the precise assessment of copy number variation over a significant dynamic range, in template DNA extracted from formalin-fixed paraffin-embedded clinical biopsies. Further, microMCC can accurately measure copy number variation at multiple loci, even when applied to picogram quantities of grossly degraded DNA extracted after laser capture microdissection of fixed specimens. Finally, we demonstrate the power of microMCC to precisely interrogate cancer genomes, in a way not currently feasible with other methodologies, by defining the position of a junction between an amplified and non-amplified genomic segment in a bronchial carcinoma. This has tremendous potential for the exploitation of archived resources for high-resolution targeted cancer genomics and in the future for interrogating multiple loci in cancer diagnostics or prognostics.
Collapse
Affiliation(s)
- F McCaughan
- Centre for Respiratory Research, Department of Medicine, Royal Free and University College Medical School, The Rayne Institute, London WC1E 6JJ, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Baik SH, Jee BK, Choi JS, Yoon HK, Lee KH, Kim YH, Lim Y. DNA profiling by array comparative genomic hybridization (CGH) of peripheral blood mononuclear cells (PBMC) and tumor tissue cell in non-small cell lung cancer (NSCLC). Mol Biol Rep 2008; 36:1767-78. [DOI: 10.1007/s11033-008-9380-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Accepted: 10/09/2008] [Indexed: 11/28/2022]
|
39
|
Newnham GM, Thomas DM, McLachlan SA, Wright G, Conron M. Molecular profiling of non-small cell lung cancer: of what value in clinical practice? Heart Lung Circ 2008; 17:451-62. [PMID: 18676201 DOI: 10.1016/j.hlc.2007.11.144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Accepted: 11/14/2007] [Indexed: 10/21/2022]
Abstract
Future improvements in lung cancer survival are likely to come from delineating its putative oncogenic pathways. The development of microarray technology to perform thousands of simultaneous genetic experiments and the linking of this to clinical information is an imperative for refining our current treatments and developing new ones. This paper reviews the state of this research, describes a typical microarray experiment and the implications for diagnosis and treatment of non-small cell lung cancer.
Collapse
Affiliation(s)
- Genni M Newnham
- Department of Medical Oncology, St Vincent's Hospital, Melbourne, Australia
| | | | | | | | | |
Collapse
|
40
|
Xu X, Page JL, Surtees JA, Liu H, Lagedrost S, Lu Y, Bronson R, Alani E, Nikitin AY, Weiss RS. Broad overexpression of ribonucleotide reductase genes in mice specifically induces lung neoplasms. Cancer Res 2008; 68:2652-60. [PMID: 18413732 DOI: 10.1158/0008-5472.can-07-5873] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the rate-limiting step in nucleotide biosynthesis and plays a central role in genome maintenance. Although a number of regulatory mechanisms govern RNR activity, the physiologic effect of RNR deregulation had not previously been examined in an animal model. We show here that overexpression of the small RNR subunit potently and selectively induces lung neoplasms in transgenic mice and is mutagenic in cultured cells. Combining RNR deregulation with defects in DNA mismatch repair, the cellular mutation correction system, synergistically increased RNR-induced mutagenesis and carcinogenesis. Moreover, the proto-oncogene K-ras was identified as a frequent mutational target in RNR-induced lung neoplasms. Together, these results show that RNR deregulation promotes lung carcinogenesis through a mutagenic mechanism and establish a new oncogenic activity for a key regulator of nucleotide metabolism. Importantly, RNR-induced lung neoplasms histopathologically resemble human papillary adenocarcinomas and arise stochastically via a mutagenic mechanism, making RNR transgenic mice a valuable model for lung cancer.
Collapse
Affiliation(s)
- Xia Xu
- Department of Biomedical Sciences, Cornell University, Ithaca, New York 14853, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Glatt S, Halbauer D, Heindl S, Wernitznig A, Kozina D, Su KC, Puri C, Garin-Chesa P, Sommergruber W. hGPR87 contributes to viability of human tumor cells. Int J Cancer 2008; 122:2008-16. [PMID: 18183596 DOI: 10.1002/ijc.23349] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Emerging in vitro and in vivo data underline the crucial role of G-protein-coupled receptors (GPCRs) in tumorigenesis. Here, we report the contribution of hGPR87, a predicted member of the P2Y subfamily of GPCRs, to proliferation and survival of human tumor cell lines. hGPR87 mRNA transcript was found to be preferentially overexpressed in squamous cell carcinomas (SCCs) of different locations and in their lymph node metastases. Up-regulation of both, transcript and protein, was detected in samples of SCC of the lung, cervix, skin and head and neck (pharynx, larynx and epiglottis). In addition to the expression of hGPR87 in tumors which originate from stratified epithelia, we identified other hGPR87-positive tumor types including subsets of large cell and adenocarcinomas of the lung and transitional cell carcinomas of the urinary bladder. Loss of function studies using siRNA in human cancer cell lines lead to antiproliferative effects and induction of apoptosis. Like other known P2Y receptors, hGPR87 was found to be mainly located on the cell surface. The overexpression of hGPR87 preferentially in SCCs together with our functional data suggests a common molecular mechanism for SCC tumorigenesis and may provide a novel intervention site for mechanism-based antitumor therapies.
Collapse
Affiliation(s)
- Sebastian Glatt
- Boehringer-Ingelheim Austria GmbH, Dr. Boehringer-Gassse 5-11, Vienna, Austria
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Identification of genes involved in squamous cell carcinoma of the lung using synchronized data from DNA copy number and transcript expression profiling analysis. Lung Cancer 2008; 59:315-31. [DOI: 10.1016/j.lungcan.2007.08.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Revised: 07/16/2007] [Accepted: 08/22/2007] [Indexed: 12/12/2022]
|
43
|
|
44
|
Garnis C. Diagnostic methods of lung cancer and its subtypes by comparative genomic hybridization. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2007; 1:541-544. [PMID: 23496360 DOI: 10.1517/17530059.1.4.541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Comparative genomic hybridization technologies have been applied to study genome-wide detection of copy number alterations in virtually all commonly diagnosed cancer types and several other diseases. The patent under evaluation describes a tool that can be used in principle to produce genome signatures with diagnostic and prognostic utility in lung cancer. Specific regions of genomic alterations correlate with either disease subtype, patient age or overall survival. The ability to characterize these phenotype-associated genome alterations in a clinical setting would presumably facilitate more robust disease diagnosis and also have potential for tailoring treatment strategies.
Collapse
Affiliation(s)
- Cathie Garnis
- Massachusetts Institute of Technology Center for Cancer Research, Room E17 529, 77 Massachusetts Avenue, Cambridge MA 02139, USA
| |
Collapse
|
45
|
Kume M, Taguchi T, Okada H, Anayama T, Tominaga A, Shuin T, Sasaguri S. Establishment and molecular cytogenetic characterization of non-small cell lung cancer cell line KU-T1 by multicolor fluorescence in situ hybridization, comparative genomic hybridization, and chromosome microdissection. ACTA ACUST UNITED AC 2007; 179:93-101. [PMID: 18036395 DOI: 10.1016/j.cancergencyto.2007.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 07/21/2007] [Accepted: 07/31/2007] [Indexed: 10/22/2022]
Abstract
A human lung adenocarcinoma cell line, designated KU-T1, was established from a Japanese man in Kochi Medical School. Conventional banding and multicolor fluorescence in situ hybridization (M-FISH) analyses of KU-T1 cells revealed a hyperdiploid chromosomal constitution and complex karyotypes. Comparative genomic hybridization showed several chromosomal copy number changes, and five regions that were highly amplified. Two of the five highly amplified regions, 1q and 3q, were identified from distributions of DNA sequences on a metaphase cell by FISH using chromosome microdissection-generated probes hybridized to 1q32 approximately q34 and 3q26 approximately q28, respectively. The 3q probe depicted a homogeneously staining region (hsr) in a derivative chromosome 3 of KU-T1. An hsr probe was regenerated by chromosome microdissection and was hybridized back to KU-T1 and normal metaphases. This hybridization experiment confirmed the probe derived from an hsr and indicated original locations of DNA sequences of hsr on normal chromosome 3. Intense hybridized signals shown at three loci (3p12, 3q26.3, and 3q28) suggests that oncogenes may be involved in the hsr formation. The present study provides a comprehensive analysis of the chromosomal abnormalities, including hsr formation and related oncogenes, in the KU-T1 cell line.
Collapse
Affiliation(s)
- Motohiko Kume
- Department of Surgery II, Kochi Medical School, Nankoku, Kochi 783-8505, Japan
| | | | | | | | | | | | | |
Collapse
|
46
|
Kang JU, Koo SH, Kwon KC, Park JW, Shin SY, Kim JM, Jung SS. High frequency of genetic alterations in non-small cell lung cancer detected by multi-target fluorescence in situ hybridization. J Korean Med Sci 2007; 22 Suppl:S47-51. [PMID: 17923754 PMCID: PMC2694384 DOI: 10.3346/jkms.2007.22.s.s47] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Detection of genetic alterations could provide a tool as an adjuvant for the diagnosis of non-small cell lung cancer (NSCLC) and to define patients at risk for early relapse. In this study, a multi-target fluorescence in situ hybridization (FISH) assay was conducted to investigate the correlation between the alterations of chromosomes, including 5p15.2, 6p11.1-q11, 7p12, and 8q24.12-q24.13 (LaVysion Test), and clinicopathological variables, and to clarify the potential of the multi-target FISH assay in 37 NSCLC. The most notable finding was the higher frequency of a gain in chromosome 5p15.2 in early-stage (I+IIa) lung cancers. The frequency of the gain was 81.3% (16/22) in stage I tumors. The frequencies of gains in 6p11.1-q11 and 8q24.12-q24.13 were 61.5% (8/13) and 84.6% (11/13) in stage IIIa cancers, as compared with lower frequencies in stage I tumors at 25.0% and 31.3%, respectively. There was also a significant difference in the histological type. Our results suggest that a gain in 6p11.1-q11 and 8q24.12-q24.13 plays an important role in tumor progression and is associated with histological differentiation. On the other hand, gene amplification in the 5p region was one of the most consistent alterations in early-stage lung cancer, and thus a series of genes in the critical 5p15.2 region might potentially associated with the development of lung cancer.
Collapse
MESH Headings
- Aged
- Biomarkers, Tumor/genetics
- Carcinoma, Non-Small-Cell Lung/diagnosis
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Chromosome Aberrations
- Chromosomes, Human, Pair 5/genetics
- Chromosomes, Human, Pair 6/genetics
- Chromosomes, Human, Pair 8/genetics
- Female
- Gene Amplification
- Humans
- In Situ Hybridization, Fluorescence
- Lung Neoplasms/diagnosis
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Male
- Middle Aged
- Neoplasm Staging
Collapse
Affiliation(s)
- Ji Un Kang
- Department of Laboratory Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - Sun Hoe Koo
- Department of Laboratory Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - Kye Chul Kwon
- Department of Laboratory Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - Jong Woo Park
- Department of Laboratory Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - So Youn Shin
- Department of Laboratory Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - Jin Man Kim
- Department of Pathology, Chungnam National University Hospital, Daejeon, Korea
| | - Sung Su Jung
- Department of Internal Medicine, Chungnam National University Hospital, Daejeon, Korea
| |
Collapse
|
47
|
Xie H, Holmes AL, Wise SS, Huang S, Peng C, Wise JP. Neoplastic transformation of human bronchial cells by lead chromate particles. Am J Respir Cell Mol Biol 2007; 37:544-52. [PMID: 17585109 PMCID: PMC2048681 DOI: 10.1165/rcmb.2007-0058oc] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Particulate hexavalent chromium (Cr(VI)) is a well-established human lung carcinogen with widespread exposure among people in occupational settings and the general public. However, no studies have examined the chromate-induced malignant transformation of human lung epithelial cells, its predominant target. Human papillomavirus-immortalized human bronchial epithelial (BEP2D) cells were used to better understand the mechanisms involved in human bronchial carcinogenesis induced by particulate chromate. We found that aneuploid cells increased in a concentration-dependent manner after chronic exposure to lead chromate. Moreover, chronic exposure to lead chromate induced BEP2D cell transformation. Transformed BEP2D cells developed through a series of sequential steps, including altered cell morphology, loss of cell contact inhibition and anchorage-independent growth. Specifically, a 5-day exposure to lead chromate induced foci formation with 0, 1, 5, and 10 microg/cm2 lead chromate inducing 0, 7, 3, and 15 foci in 10 dishes. Anchorage independence was observed in cell lines derived from these foci. These foci-derived cells also showed centrosome amplification and increases in aneuploid metaphases. Our study demonstrates that particulate Cr(VI) is able to transform human bronchial epithelial cells, and that chromosome instability may play an important role in particulate Cr(VI)-induced neoplastic transformation.
Collapse
Affiliation(s)
- Hong Xie
- Wise Laboratory of Environmental and Genetic Toxicology, University of Southern Maine, Portland, Maine 04104, USA
| | | | | | | | | | | |
Collapse
|
48
|
Hong KM, Yang SH, Chowdhuri SR, Player A, Hames M, Fukuoka J, Meerzaman D, Dracheva T, Sun Z, Yang P, Jen J. Inactivation of LLC1 gene in nonsmall cell lung cancer. Int J Cancer 2007; 120:2353-8. [PMID: 17304513 PMCID: PMC1907378 DOI: 10.1002/ijc.22577] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Serial analysis of gene expression studies led us to identify a previously unknown gene, c20orf85, that is present in the normal lung epithelium but absent or downregulated in most primary nonsmall cell lung cancers and lung cancer cell lines. We named this gene LLC1 for Low in Lung Cancer 1. LLC1 is located on chromosome 20q13.3 and has a 70% GC content in the promoter region. It has 4 exons and encodes a protein containing 137 amino acids. By in situ hybridization, we observed that LLC1 message is localized in normal lung bronchial epithelial cells but absent in 13 of 14 lung adenocarcinoma and 9 out of 10 lung squamous carcinoma samples. Methylation at CpG sites of the LLC1 promoter was frequently observed in lung cancer cell lines and in a fraction of primary lung cancer tissues. Treatment with 5-aza deoxycytidine resulted in a reduced methylation of the LLC1 promoter concomitant with the increase of LLC1 expression. These results suggest that inactivation of LLC1 by means of promoter methylation is a frequent event in nonsmall cell lung cancer and may play a role in lung tumorigenesis.
Collapse
Affiliation(s)
- Kyeong-Man Hong
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Comtesse N, Keller A, Diesinger I, Bauer C, Kayser K, Huwer H, Lenhof HP, Meese E. Frequent overexpression of the genes FXR1, CLAPM1 and EIF4G located on amplicon 3q26-27 in squamous cell carcinoma of the lung. Int J Cancer 2007; 120:2538-44. [PMID: 17290396 DOI: 10.1002/ijc.22585] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Previously, we reported gene amplification at chromosome 3q26-27 in more than one third of squamous cell carcinomas of the lung. Frequent amplification of eukaryotic translation initiation factor 4G on 3q27.1 indicated a possible role of this amplification in translation initiation. The analysis of 61 squamous cell lung carcinomas shows that the percentage of carcinomas with a 3q27.1 amplification increases in higher malignant tumors. Non-invasive (T1) and minimal-invasive (T2) tumor stages showed similar percentages of amplified and non-amplified tumors, whereas locally-invasive (T3) tumors revealed a statistically significant (p < 0.05) increased percentage of amplified tumors. Microarrays were used to analyze the expression pattern of genes mapping in the amplified domain and its flanking regions (3q25-28) as well as the expression of genes directly or indirectly associated with translation initiation in squamous cell carcinoma, large cell carcinoma, adenocarcinoma and small cell carcinoma. Three genes, namely FXR1, CLAPM1 and EIF4G, are most frequently overexpressed in the center of the amplified domain in squamous cell carcinomas. The eukaryotic translation initiation factors 4A1, 2B and 4B as well as the poly(A)-binding protein PABPC1 where found to be overexpressed in all lung cancer entities. We found, however, no overexpression of eIF4E. Our results contribute to the understanding of the frequent amplification processes in squamous cell carcinomas of the lung and to the understanding of the translation initiation that appears not to require eIF4E in lung carcinogenesis.
Collapse
Affiliation(s)
- Nicole Comtesse
- Department of Human Genetics, Medical School, Saarland University, Homburg, Germany
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Yen CC, Liang SC, Jong YJ, Chen YJ, Lin CH, Chen YM, Wu YC, Su WC, Huang CYF, Tseng SW, Whang-Peng J. Chromosomal aberrations of malignant pleural effusions of lung adenocarcinoma: different cytogenetic changes are correlated with genders and smoking habits. Lung Cancer 2007; 57:292-301. [PMID: 17553591 DOI: 10.1016/j.lungcan.2007.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Revised: 03/30/2007] [Accepted: 04/06/2007] [Indexed: 11/26/2022]
Abstract
Chromosomal aberrations of malignant cells from pleural effusions of 31 cases of lung adenocarcinoma were analyzed. Pooled CGH results showed frequent amplifications on chromosome arms 1p (22.6%), 1q (35.5%), 2q (25.8%), 3q (38.7%), 4q (41.9%), 5p (41.9%), 5q (51.6%), 6p (19.4%), 6q (25.8%), 7p (41.9%), 7q (35.5%), 8q (32.3%), 12q (38.7%), 13q (22.6%), 14q (35.5%), 17q (19.4%), Xp (22.6%), and Xq (38.7%). Frequent deletions were found on 1p (19.4%), 3p (16.1%), 4q (16.1%), 8p (25.8%), 9p (22.6%), 9q (29.0%), 10q (22.6%), 13q (22.6%), 16p (19.4%), 16q (22.6%), 17p (29.0%), 18q (16.1%), 19p (41.9%), 19q (32.3%), 20p (19.4%) and 22q (29%). These genomic changes were generally found consistent with previous reports of CGH analysis of primary tumors of lung adenocarcinoma. Loss of 19q and 22q were more frequently found in our studies (32.3% and 29.0%, respectively) than studies of primary tumors (less than 7% for both genetic changes). Gain of 11p, although not a frequent finding, was relatively more common in this (16%) than other studies (range, 2.9-11.8%). Interestingly, occurrences of 3p loss and 11p gain were higher in smokers than non-smokers, and deletion of 3p and increased copy number of 11p and Xp appeared more often in male than female patients. Among 17 male patients, gain of chromosomal 11p was a frequent aberration in tumors of smokers, while gain of Xp was more easily found in tumors of non-smokers. One candidate gene located within 11p15, lactate dehydrogenase C (LDHC), was selected for further study. Three cases with 11p gain had amplified FISH signals of LDHC. Also tumors from smokers or male had significantly higher transcript level of LDHC than non-smokers or female, respectively. The results demonstrate that different cytogenetic changes of malignant pleural effusions from lung adenocarcinoma are correlated with genders and smoking habits. The role of LDHC in the carcinogenesis of smoking-related lung adenocarcinoma, especially in male patients with pleural effusions, deserves further investigations.
Collapse
Affiliation(s)
- Chueh-Chuan Yen
- Division of Hematology and Oncology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|