1
|
Pathak S, Zajac KK, Annaji M, Govindarajulu M, Nadar RM, Bowen D, Babu RJ, Dhanasekaran M. Clinical outcomes of chemotherapy in cancer patients with different ethnicities. Cancer Rep (Hoboken) 2023; 6 Suppl 1:e1830. [PMID: 37150853 PMCID: PMC10440845 DOI: 10.1002/cnr2.1830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/09/2023] Open
Abstract
BACKGROUND Choosing the most effective chemotherapeutic agent with safest side effect profile is a common challenge in cancer treatment. Although there are standardized chemotherapy protocols in place, protocol changes made after extensive clinical trials demonstrate significant improvement in the efficacy and tolerability of certain drugs. The pharmacokinetics, pharmacodynamics, and tolerance of anti-cancer medications are all highly individualized. A driving force behind these differences lies within a person's genetic makeup. RECENT FINDINGS Pharmacogenomics, the study of how an individual's genes impact the processing and action of a drug, can optimize drug responsiveness and reduce toxicities by creating a customized medication regimen. However, these differences are rarely considered in the initial determination of standardized chemotherapeutic protocols and treatment algorithms. Because pharmacoethnicity is influenced by both genetic and nongenetic variables, clinical data highlighting disparities in the frequency of polymorphisms between different ethnicities is steadily growing. Recent data suggests that ethnic variations in the expression of allelic variants may result in different pharmacokinetic properties of the anti-cancer medication. In this article, the clinical outcomes of various chemotherapy classes in patients of different ethnicities were reviewed. CONCLUSION Genetic and nongenetic variables contribute to the interindividual variability in response to chemotherapeutic drugs. Considering pharmacoethnicity in the initial determination of standard chemotherapeutic protocols and treatment algorithms can lead to better clinical outcomes of patients of different ethnicities.
Collapse
Affiliation(s)
- Suhrud Pathak
- Department of Drug Discovery and Development, Harrison College of PharmacyAuburn UniversityAuburnAlabamaUSA
| | - Kelsee K. Zajac
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical SciencesUniversity of ToledoToledoOhioUSA
| | - Manjusha Annaji
- Department of Drug Discovery and Development, Harrison College of PharmacyAuburn UniversityAuburnAlabamaUSA
| | - Manoj Govindarajulu
- Department of Drug Discovery and Development, Harrison College of PharmacyAuburn UniversityAuburnAlabamaUSA
| | - Rishi M. Nadar
- Department of Drug Discovery and Development, Harrison College of PharmacyAuburn UniversityAuburnAlabamaUSA
| | - Dylan Bowen
- Department of Drug Discovery and Development, Harrison College of PharmacyAuburn UniversityAuburnAlabamaUSA
| | - R. Jayachandra Babu
- Department of Drug Discovery and Development, Harrison College of PharmacyAuburn UniversityAuburnAlabamaUSA
| | | |
Collapse
|
2
|
Zheng J, Cui T, Li T. Observation on the clinical efficacy and side effects of EGFR-TKI ± chemotherapy in the treatment of EGFR mutation-positive advanced lung adenocarcinoma. EUR J INFLAMM 2022. [DOI: 10.1177/1721727x221145447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Objective To assess the clinical efficacy and side effects of EGFR-TKI with or without chemotherapy in the treatment of EGFR mutation-positive advanced lung adenocarcinoma. Methods A total of 103 IIIB or IV EGFR mutation-positive lung adenocarcinoma patients admitted to the oncology department of Fujian Provincial Hospital from January 2017 to October 2020 were selected. According to genetic mutation status, patients were divided into the following groups: 19del alone, 19del combined with TP53 or other co-mutations, L858R mutation alone, and L858R mutation combined with TP53 or other co-mutations. Targeted drugs or targeted drugs combined with chemotherapy were respectively administered in the four groups. In patients with simple 19 deletion, only targeted drugs with no combined therapy were applied, resulting in seven total groups. The difference between short-term treatment and long-term treatment effects and the occurrence of adverse reactions was calculated and compared. Results There was no statistical significance of difference in the incidence of adverse reactions in seven groups ( p > 0.05). The short-term disease control rate of the combination group was higher than the targeted drug group with the difference yielding statistical significance ( p < 0.001). The short-term objective response rate of the combination group was higher than the targeted drug group, also yielding statistical significance ( p < 0.001). By October 2020, the median progression-free survival (PFS) was 16 months in the EGFR-TKI-targeted combined with chemotherapy group and 10 months in the single-drug EGFR-TKI group, and the PFS time was longer in the combination group than in the single targeted drug group, the difference being statistically significant ( p = 0.001). Conclusions In the treatment of advanced lung adenocarcinoma patients with EGFR-gene sensitive mutations, compared with single EGFR-TKI-targeted therapy, EGFR-TKI-targeted drug combined chemotherapy can control the disease progression more effectively, and does not increase adverse reactions.
Collapse
Affiliation(s)
- Jianping Zheng
- Department of Oncology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Tongjian Cui
- Department of Oncology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Ting Li
- Department of Oncology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China
| |
Collapse
|
3
|
Zeng W, Zheng W, Hu S, Zhang J, Zhang W, Xu J, Yu D, Peng J, Zhang L, Gong M, Wei Y. Application of Lipidomics for Assessing Tissue Lipid Profiles of Patients With Squamous Cell Carcinoma. Technol Cancer Res Treat 2021; 20:15330338211049903. [PMID: 34761720 PMCID: PMC8591777 DOI: 10.1177/15330338211049903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: Lipid metabolism disorders play a key role in the pathogenesis of squamous cell carcinoma (SqCC). Herein we used lipidomics to study the tissue lipid profiles of 40 patients with SqCC. Methods: Lipidomics, based on ultrahigh-performance liquid chromatography-Q Exactive hybrid quadrupole-orbitrap high-resolution accurate mass spectrometry, was applied to identify altered lipid metabolites between tumor and adjacent noninvolved tissues (ANIT), and partial least squares-discriminant analysis model facilitated the identification of differentially abundant lipids. The area under the receiver operator characteristic curve and variable importance in projection scores of the aforementioned model were calculated to select lipid profiles. Metabolic pathway analyses were completed using Kyoto Encyclopedia of Genes and Genomes and MetaboAnalyst. Results: Differences in lipid profiles were found between tumor and ANIT, early- and advanced-stage SqCC, and positive and negative lymph node metastases. The lipid profile panel was composed of five lipids-PC(44:4), diacylglycerol(36:5), sphingomyelin(d18:1/20:0), phosphatidylinositol(46:7), and HexCer-AP(t8:0/32:2 + O)-and could effectively differentiate between tumor and ANIT. Further, pathway analyses revealed alterations in several lipid metabolism pathways, including glycerophospholipid metabolism, glycosylphosphatidylinositol anchor biosynthesis, linoleic acid metabolism, glycerolipid metabolism, and sphingolipid metabolism. Conclusion: Our data revealed several changes in the tissue lipid profiles of patients with SqCC; moreover, we identified a lipid profile panel that could effectually distinguish tumor tissues from ANIT. We believe that our results provide new insights into the biological behavior of lung SqCC.
Collapse
Affiliation(s)
- Weibiao Zeng
- 196534The Second Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| | - Wen Zheng
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network34753West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Sheng Hu
- 196534The Second Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| | - Jianyong Zhang
- 74720The Affiliated Hospital of Guizhou Medical University, Guiyang, P. R. China
| | - Wenxiong Zhang
- 196534The Second Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| | - Jianjun Xu
- 196534The Second Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| | - Dongliang Yu
- 196534The Second Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| | - Jinhua Peng
- 196534The Second Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| | - Lu Zhang
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network34753West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Meng Gong
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network34753West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Yiping Wei
- 196534The Second Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| |
Collapse
|
4
|
Zhang M, Chen J. [Advances in Clinical Application of Liquid Biopsy in Non-small Cell Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2021; 24:723-728. [PMID: 34696544 PMCID: PMC8560984 DOI: 10.3779/j.issn.1009-3419.2021.102.33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Lung cancer, with the highest incidence in China, is the leading cause of death in cancer patients. Of these, about 85% are patients with non-small cell lung cancer (NSCLC). Therefore, the diagnosis and treatment of patients with lung cancer have always been a top priority nowadays. Fluid biopsy has many advantages, such as safety, convenience, repeatability, low trauma and so on, which are not available in traditional invasive biopsy. In recent years, with the rapid progress of molecular biological detection technology, fluid biopsy, as a new technology, has become the focus of attention. What's more, it contributes to the development of precision treatment and individualized treatment of lung cancer. Liquid biopsy mainly detects circulating tumor DNA (ctDNA), circulating tumor cells (CTCs) and exosomes in peripheral blood. We will make an introduce to the detection and clinical applications of ctDNA, CTCs and exocrine in this article, in order that it can provide insights into future clinical treatment for NSCLC.
.
Collapse
Affiliation(s)
- Min Zhang
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian 116000, China
| | - Jun Chen
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian 116000, China
| |
Collapse
|
5
|
Ning J, Ge T, Jiang M, Jia K, Wang L, Li W, Chen B, Liu Y, Wang H, Zhao S, He Y. Early diagnosis of lung cancer: which is the optimal choice? Aging (Albany NY) 2021; 13:6214-6227. [PMID: 33591942 PMCID: PMC7950268 DOI: 10.18632/aging.202504] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
The prognosis of lung cancer patients with different clinical stages is significantly different. The 5-year survival of stage IA groups can exceed 90%, while patients with stage IV can be less than 10%. Therefore, early diagnosis is extremely important for lung cancer patients. This research focused on various diagnosis methods of early lung cancer, including imaging screening, bronchoscopy, and emerging potential liquid biopsies, as well as volatile organic compounds, autoantibodies, aiming to improve the early diagnosis rate and explore feasible and effective early diagnosis strategies.
Collapse
Affiliation(s)
- Jing Ning
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, People's Republic of China.,Tongji University, Shanghai 200433, People's Republic of China
| | - Tao Ge
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
| | - Minlin Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, People's Republic of China.,Tongji University, Shanghai 200433, People's Republic of China
| | - Keyi Jia
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, People's Republic of China.,Tongji University, Shanghai 200433, People's Republic of China
| | - Lei Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
| | - Wei Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
| | - Bin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
| | - Yu Liu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, People's Republic of China.,Tongji University, Shanghai 200433, People's Republic of China
| | - Hao Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, People's Republic of China.,Tongji University, Shanghai 200433, People's Republic of China
| | - Sha Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
| |
Collapse
|
6
|
Esagian SM, Grigoriadou GΙ, Nikas IP, Boikou V, Sadow PM, Won JK, Economopoulos KP. Comparison of liquid-based to tissue-based biopsy analysis by targeted next generation sequencing in advanced non-small cell lung cancer: a comprehensive systematic review. J Cancer Res Clin Oncol 2020; 146:2051-2066. [PMID: 32462295 PMCID: PMC7456570 DOI: 10.1007/s00432-020-03267-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE To explore whether targeted next generation sequencing (NGS) of liquid biopsy in advanced non-small cell lung cancer (NSCLC) could potentially overcome the innate problems that arise with standard tissue biopsy, like intratumoral heterogeneity and the inability to obtain adequate samples for analysis. METHODS The Scopus, Cochrane Library, and MEDLINE (via PubMed) databases were searched for studies with matched tissue and liquid biopsies from advanced NSCLC patients, analyzed with targeted NGS. The number of mutations detected in tissue biopsy only, liquid biopsy only, or both was assessed and the positive percent agreement (PPA) of the two methods was calculated for every clinically relevant gene. RESULTS A total of 644 unique relevant articles were retrieved and data were extracted from 38 studies fulfilling the inclusion criteria. The sample size was composed of 2000 mutations tested in matched tissue and liquid biopsies derived from 1141 patients. No studies analyzed circulating tumor cells. The calculated PPA rates were 53.6% (45/84) for ALK, 53.9% (14/26) for BRAF, 56.5% (13/23) for ERBB2, 67.8% (428/631) for EGFR, 64.2% (122/190) for KRAS, 58.6% (17/29) for MET, 54.6% (12/22) for RET, and 53.3% (8/15) for ROS1. We additionally recorded data for 65 genes that are not recommended by current guidelines for mutational testing. An extra category containing results of unspecified genes was added, with a PPA rate of 55.7% (122/219). CONCLUSION Despite many advantages, liquid biopsy might be unable to fully substitute its tissue counterpart in detecting clinically relevant mutations in advanced NSCLC patients. However, it may serve as a helpful tool when making therapeutic decisions. More studies are needed to evaluate its role in everyday clinical practice.
Collapse
Affiliation(s)
- Stepan M Esagian
- Oncology Working Group, Society of Junior Doctors, Athens, Greece
| | - Georgia Ι Grigoriadou
- Oncology Working Group, Society of Junior Doctors, Athens, Greece
- 1st Department of Medical Oncology, Theageneio Anticancer Hospital, Thessaloníki, Greece
| | - Ilias P Nikas
- School of Medicine, European University of Cyprus, Nicosia, Cyprus
| | - Vasileios Boikou
- Oncology Working Group, Society of Junior Doctors, Athens, Greece
- Athens University of Economics and Business, Athens, Greece
| | - Peter M Sadow
- Department of Pathology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Jae-Kyung Won
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Konstantinos P Economopoulos
- Oncology Working Group, Society of Junior Doctors, Athens, Greece.
- Department of Surgery, Duke University Medical Center, 2301 Erwin Rd, Durham, NC, 27710, USA.
| |
Collapse
|
7
|
Wang N, Zhang X, Wang F, Zhang M, Sun B, Yin W, Deng S, Wan Y, Lu W. The Diagnostic Accuracy of Liquid Biopsy in EGFR-Mutated NSCLC: A Systematic Review and Meta-Analysis of 40 Studies. SLAS Technol 2020; 26:42-54. [PMID: 32659150 DOI: 10.1177/2472630320939565] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Epidermal growth factor receptor (EGFR) mutations are the most common carcinogenic driver mutations in non-small-cell lung cancer (NSCLC) patients, while invasive tissue biopsy has certain inherent defects. PubMed, Ovid Medline, Embase, and the Cochrane Library were systematically searched on January 4, 2020, using the keywords "liquid biopsy," "EGFR," and "NSCLC." The pooled sensitivity and specificity of EGFR mutations in paired tissue and blood were calculated. The accuracy was assessed by receiver operating characteristic curve. The meta-regression of the subgroup was performed to analyze the heterogeneity. Hazard ratio (HR) and 95% confidence interval (CI) were combined for evaluating the impact of EGFR mutation in tissue and liquid blood biopsy. A total of 40 studies with 5,995 patients were involved in the study. The pooled sensitivity was 68% (95% CI = 60-75%), and the specificity was 98% (95% CI = 95-99%). The diagnostic odds ratio was 88 (95% CI = 40-195), and the area under the curve was 0.91 (95% CI = 0.88-0.93). In the meta-regression, the sensitivity and specificity remain lower in the Asian studies than non-Asian studies (sensitivity: 66% vs. 73%, P = 0.04; specificity: 96% vs. 97%, P = 0.03, respectively). The EGFR mutation was associated with a better progression-free survival than wild type in both tissue (HR = 0.54, 95% CI = 0.34-0.85, P = 0.007) and blood (HR = 0.81, 95% CI = 0.71-0.92, P = 0.001) detection. Peripheral blood liquid biopsy had a better specificity for detecting EGFR mutation in NSCLC patients, while tissue biopsy still needs to be undertaken for negative blood biopsy patients due to its lower sensitivity.
Collapse
Affiliation(s)
- Naiqun Wang
- Hospital Infection Management Department, The People's Hospital of Yichun City, Yichun, Jiangxi, China
| | - Xiaolian Zhang
- Laboratory Department, The People's Hospital of Yichun City, Yichun, Jiangxi, China
| | - Feilong Wang
- Thoracic Surgery Department, Jining No. 1 People's Hospital, Jining, Shandong, China
| | - Min Zhang
- Department of Stomatology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Bo Sun
- Thoracic Surgery Department, Jining No. 1 People's Hospital, Jining, Shandong, China
| | - Weihua Yin
- Oncology Department, The People's Hospital of Yichun City, Yichun, Jiangxi, China
| | - Shaorong Deng
- Blood Transfusion Department, The People's Hospital of Yichun City, Yichun, Jiangxi, China
| | - Ying Wan
- Thoracic Surgery Department, Jining No. 1 People's Hospital, Jining, Shandong, China
| | - Wei Lu
- Thoracic Surgery Department, Jining No. 1 People's Hospital, Jining, Shandong, China
| |
Collapse
|
8
|
Liam CK, Mallawathantri S, Fong KM. Is tissue still the issue in detecting molecular alterations in lung cancer? Respirology 2020; 25:933-943. [PMID: 32335992 DOI: 10.1111/resp.13823] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/23/2020] [Accepted: 03/29/2020] [Indexed: 02/07/2023]
Abstract
Molecular biomarker testing of advanced-stage NSCLC is now considered standard of care and part of the diagnostic algorithm to identify subsets of patients for molecular-targeted treatment. Tumour tissue biopsy is essential for an accurate initial diagnosis, determination of the histological subtype and for molecular testing. With the increasing use of small biopsies and cytological specimens for diagnosis and the need to identify an increasing number of predictive biomarkers, proper management of the limited amount of sampling materials available is important. Many patients with advanced NSCLC do not have enough tissue for molecular testing and/or do not have a biopsy-amenable lesion and/or do not want to go through a repeat biopsy given the potential risks. Molecular testing can be difficult or impossible if the sparse material from very small biopsy specimens has already been exhausted for routine diagnostic purposes. A limited diagnostic workup is recommended to preserve sufficient tissue for biomarker testing. In addition, tumour biopsies are limited by tumour heterogeneity, particularly in the setting of disease resistance, and thus may yield false-negative results. Hence, there have been considerable efforts to determine if liquid biopsy in which molecular alterations can be non-invasively identified in plasma cell-free ctDNA, a potential surrogate for the entire tumour genome, can overcome the issues with tissue biopsies and replace the need for the latter.
Collapse
Affiliation(s)
- Chong-Kin Liam
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Kwun M Fong
- Thoracic Medicine, The Prince Charles Hospital, The University of Queensland Thoracic Research Centre at TPCH, Brisbane, QLD, Australia
| |
Collapse
|
9
|
Cytogenetics and Cytogenomics Evaluation in Cancer. Int J Mol Sci 2019; 20:ijms20194711. [PMID: 31547595 PMCID: PMC6801775 DOI: 10.3390/ijms20194711] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/07/2023] Open
Abstract
The availability of cytogenetics and cytogenomics technologies improved the detection and identification of tumor molecular signatures as well as the understanding of cancer initiation and progression. The use of large-scale and high-throughput cytogenomics technologies has led to a fast identification of several cancer candidate biomarkers associated with diagnosis, prognosis, and therapeutics. The advent of array comparative genomic hybridization and next-generation sequencing technologies has significantly improved the knowledge about cancer biology, underlining driver genes to guide targeted therapy development, drug-resistance prediction, and pharmacogenetics. However, few of these candidate biomarkers have made the transition to the clinic with a clear benefit for the patients. Technological progress helped to demonstrate that cellular heterogeneity plays a significant role in tumor progression and resistance/sensitivity to cancer therapies, representing the major challenge of precision cancer therapy. A paradigm shift has been introduced in cancer genomics with the recent advent of single-cell sequencing, since it presents a lot of applications with a clear benefit to oncological patients, namely, detection of intra-tumoral heterogeneity, mapping clonal evolution, monitoring the development of therapy resistance, and detection of rare tumor cell populations. It seems now evident that no single biomarker could provide the whole information necessary to early detect and predict the behavior and prognosis of tumors. The promise of precision medicine is based on the molecular profiling of tumors being vital the continuous progress of high-throughput technologies and the multidisciplinary efforts to catalogue chromosomal rearrangements and genomic alterations of human cancers and to do a good interpretation of the relation genotype-phenotype.
Collapse
|
10
|
Alifano M. Obstructive lung disease in smokers and never smokers: further insights in patient-related approach in lung cancer understanding. J Thorac Dis 2019; 11:S1310-S1312. [PMID: 31245118 DOI: 10.21037/jtd.2019.04.53] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marco Alifano
- Department of Thoracic Surgery, Paris Center University Hospital, Paris Descartes University, Paris, France
| |
Collapse
|
11
|
Wu Y, Zhang Y, Liu C, Zhang Y, Wang D, Wang S, Wu Y, Liu F, Li Q, Liu X, Zaky MY, Yan D, Liu S. Amplification of USP13 drives non-small cell lung cancer progression mediated by AKT/MAPK signaling. Biomed Pharmacother 2019; 114:108831. [PMID: 30986623 DOI: 10.1016/j.biopha.2019.108831] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 12/31/2022] Open
Abstract
USP13 is emerging as a potential target in cancer therapy. However, the effect of USP13 on tumor progression is controversial. Here we focused on non-small cell lung cancer (NSCLC), a common cancer with high mortality, and studied the role of USP13 in tumor growth. By analysis of multi-level genetic database, we found USP13 is high expressed in heart among healthy primary tissues and is most amplified in lung cancer. Clinical samples of NSCLC showed tumor exhibited high USP13 level compared with adjacent normal tissues. We further utilized lung adenocarcinoma A549 and squamous carcinoma H226 cells as cell model and investigated USP13 effect by USP13 knockdown. As a results, downregulation of USP13 dramatically inhibited A549 and H226 cell proliferation by AKT/MAPK signaling and suppressed tumor growth in nude mice. Collectively, we identified USP13 as a tumor promoter in NSCLC and provide a promising target in cancer therapy.
Collapse
Affiliation(s)
- Yue Wu
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Yingqiu Zhang
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Congcong Liu
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Yang Zhang
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Duchuang Wang
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Shanshan Wang
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Yueguang Wu
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Fang Liu
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Qiong Li
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Xiuxiu Liu
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Mohamed Y Zaky
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China; Molecular Physiology Division, Department of Zoology, Faculty of Science, Beni-Suef University, Egypt
| | - Dong Yan
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China.
| | - Shuyan Liu
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China.
| |
Collapse
|
12
|
Gui J, Zhu M, Bai X, Li B, Gao M, Ma H, Li H, Wu C. [Effect of methanol-ethyl acetate partitioned fractions from Descurainia sophia on proliferation and apoptosis of human non-small cell lung cancer H1975 cells]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2019; 39:169-174. [PMID: 30890504 DOI: 10.12122/j.issn.1673-4254.2019.02.07] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVE To investigate the effects of methanol-ethyl acetate partitioned fractions from Descurainia sophia (MEDS) on the proliferation and apoptosis of human non-small cell lung cancer H1975 cells. METHODS The systemic solvent extraction method was used to preliminary separation of the effective fractions in the methanol extract of Descurainia sophia. The cytotoxicity of each extract (5, 10, 20, 40, and 80 μg/mL) was tested using MTT assay. Colony cloning method was used to assess the effect of different concentrations of methanol-ethyl acetate partitioned fractions from MEDS (5, 10, 20, 40, and 80 μg/ mL) on the proliferation of H1975 cells. Flow cytometric analysis with Annexin V-FITC/PI staining was performed to detect the apoptosis of the cells after treatment with different concentrations of MEDS fractions (10, 20, and 40 μg/mL). Western blotting was used to evaluate the effects of MEDS fractions on the expressions of apoptosis-related proteins Akt, Bax, and Bcl-2. The anti-tumor activity of 100 mg/kg MEDS fractions was tested in a nude mouse model bearing H1975 cell xenografts. RESULTS MTT assay and colony forming experiment showed that MEDS fractions significantly inhibited the proliferation of H1975 cells in a dose-and time-dependent manner (P < 0.05). The results of flow cytometry showed that MEDS fractions induced obvious apoptosis of H1975 cells in a concentration-dependent manner (P < 0.05). MEDS fractions also significantly decreased the expressions of Bcl-2 and Akt protein and increased the protein expression of Bax (P < 0.05). In the tumor-bearing nude mouse model, MEDS fractions showed potent anti-tumor effects with a low toxicity to affect the body weight and organs of the mice. CONCLUSIONS The methanol-ethyl acetate partitioned fractions from MEDS show potent anti-tumor activity both in vivo and in vitro, suggesting their value as promising therapeutic agents against lung cancer.
Collapse
Affiliation(s)
- Jiahui Gui
- School of Pharmacy, Bengbu Medical College, Bengbu 233030, China
| | - Meilin Zhu
- School of Pharmacy, Bengbu Medical College, Bengbu 233030, China
| | - Xiangjian Bai
- School of Pharmacy, Bengbu Medical College, Bengbu 233030, China
| | - Bohan Li
- School of Pharmacy, Bengbu Medical College, Bengbu 233030, China
| | - Meijia Gao
- School of Pharmacy, Bengbu Medical College, Bengbu 233030, China
| | - Hui Ma
- School of Pharmacy, Bengbu Medical College, Bengbu 233030, China
| | - Hongmei Li
- School of Pharmacy, Bengbu Medical College, Bengbu 233030, China
| | - Chengzhu Wu
- School of Pharmacy, Bengbu Medical College, Bengbu 233030, China
| |
Collapse
|
13
|
Song Z, Wang S, Liu Y. The diagnostic accuracy of liquid exosomes for lung cancer detection: a meta-analysis. Onco Targets Ther 2018; 12:181-192. [PMID: 30636881 PMCID: PMC6309778 DOI: 10.2147/ott.s188832] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Several studies have suggested that liquid exosomes can be used as biomarkers for the diagnosis of lung cancer (LC). The purpose of this meta-analysis was to investigate the comprehensive diagnostic value of liquid exosomes for LC. MATERIALS AND METHODS Relevant studies were searched from multiple electronic databases. The quality of the studies was assessed by the Quality Assessment of Diagnostic Accuracy Studies-2 criteria in RevMan 5.3 software. Stata 14.0 software and Meta-disc 1.4 software were used to synthesize the diagnostic parameters. Publication bias was judged according to the Deeks' funnel plot asymmetry test. RESULTS There were 13 eligible articles that comprised 1,338 LC patients and 1,075 paired controls for the meta-analysis. The pooled sensitivity (SEN), specificity (SPE), diagnostic likelihood ratio positive (DLR+), diagnostic likelihood ratio negative (DLR-), diagnostic OR (DOR), and area under the curve (AUC) of liquid exosomes in diagnosing LC were 0.82 (95% CI: 0.76-0.87), 0.84 (95% CI: 0.77-0.89), 5.27 (95% CI: 3.58-7.75), 0.21 (95% CI: 0.15-0.29), 25.14 (95% CI: 14.25-44.33), and 0.90 (95% CI: 0.87-0.92), respectively. Research based on serum, miRNA, the isolation kit method, one index in exosomes, patient sample size of 50 or greater, and control group size of 50 or greater obtained higher AUC values when the LC type was small cell lung cancer. CONCLUSION Liquid exosomes have shown potential as novel biomarkers that could facilitate LC diagnosis. Further prospective studies are still needed to confirm the diagnostic value of liquid exosomes.
Collapse
Affiliation(s)
- Zhipeng Song
- Department of Epidemiology, Beijing Chest Hospital, Capital Medical University, Beijing, China,
| | - Saisai Wang
- Department of Epidemiology, Beijing Chest Hospital, Capital Medical University, Beijing, China,
| | - Yang Liu
- Department of Epidemiology, Beijing Chest Hospital, Capital Medical University, Beijing, China,
| |
Collapse
|
14
|
Song Z, Liu Y. [Progress of Liquid Biopsy in Early Diagnosis of Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2018; 21:620-627. [PMID: 30172270 PMCID: PMC6105353 DOI: 10.3779/j.issn.1009-3419.2018.08.08] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
肺癌的早期诊断有利于提高患者的生存率。应用影像学方法对肺癌高风险人群进行筛查,可以起到早发现、早诊断的作用。越来越多的研究显示,液体活检(liquid biopsy)可以对该方法进行替代和补充。检测肺癌患者外周血中的循环肿瘤细胞(circulating tumor cells, CTCs)、循环肿瘤DNA(circulating tumor DNA, ctDNA)、微小核糖核酸(microRNA, miRNA)、外泌体(exosomes)、肿瘤血小板(tumor educated platelets, TEPs)可以用于肺癌的早期诊断,并且可能为影像学检查阴性的高风险人群提供相应的诊疗建议。全文就以上标志物的检测手段、在肺癌早期诊断中的价值以及存在优势与局限性进行综述,以期促进液体活检在肺癌早期诊断、与其他筛查手段相结合方面的应用。
Collapse
Affiliation(s)
- Zhipeng Song
- Department of Epidemiology, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Yang Liu
- Department of Epidemiology, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| |
Collapse
|
15
|
Patient-derived conditionally reprogrammed cells maintain intra-tumor genetic heterogeneity. Sci Rep 2018; 8:4097. [PMID: 29511269 PMCID: PMC5840339 DOI: 10.1038/s41598-018-22427-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/22/2018] [Indexed: 02/05/2023] Open
Abstract
Preclinical in vitro models provide an essential tool to study cancer cell biology as well as aid in translational research, including drug target identification and drug discovery efforts. For any model to be clinically relevant, it needs to recapitulate the biology and cell heterogeneity of the primary tumor. We recently developed and described a conditional reprogramming (CR) cell technology that addresses many of these needs and avoids the deficiencies of most current cancer cell lines, which are usually clonal in origin. Here, we used the CR cell method to generate a collection of patient-derived cell cultures from non-small cell lung cancers (NSCLC). Whole exome sequencing and copy number variations are used for the first time to address the capability of CR cells to keep their tumor-derived heterogeneity. Our results indicated that these primary cultures largely maintained the molecular characteristics of the original tumors. Using a mutant-allele tumor heterogeneity (MATH) score, we showed that CR cells are able to keep and maintain most of the intra-tumoral heterogeneity, suggesting oligoclonality of these cultures. CR cultures therefore represent a pre-clinical lung cancer model for future basic and translational studies.
Collapse
|
16
|
Detection of circulating tumor DNA in patients with advanced non-small cell lung cancer. Oncotarget 2018; 8:2130-2140. [PMID: 27791985 PMCID: PMC5356786 DOI: 10.18632/oncotarget.12883] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 10/19/2016] [Indexed: 12/18/2022] Open
Abstract
Circulating tumor DNA (ctDNA) isolated from plasma has great potential in identification of gene mutation in non-small cell lung cancers (NSCLC), which is a non-invasive technique and can avoid the inherent shortcomings of tissue biopsy. However the ability of NGS to detect gene mutation in plasma ctDNA has not been broadly explored. To assess the diagnostic ability of ctDNA for the total mutation profile, including single nucleotide variations (SNVs), insertions and deletions (indels) and gene rearrangements, we performed a targeted DNA sequencing approach to screen NSCLC related driver gene mutations in both tissue biopsies and matched blood plasma samples from 39 advanced NSCLC patients from China. The sensitivity of EGFR, KRAS, PIK3CA mutations and gene rearrangements detected in plasma ctDNA was 70.6%, 75%, 50% and 60%, respectively and the overall concordance of gene mutations between tissue DNA and plasma ctDNA was 78.21%. Our data provide evidence that ctDNA in plasma is likely to become an alternative source for cancer-related mutations profiling in advanced NSCLC patients and targeted sequencing of ctDNA offers a promising perspective on precise diagnostics and may serve as a feasible option for clinical monitoring of NSCLC patients.
Collapse
|
17
|
Barris DM, Weiner SB, Dubin RA, Fremed M, Zhang X, Piperdi S, Zhang W, Maqbool S, Gill J, Roth M, Hoang B, Geller D, Gorlick R, Weiser DA. Detection of circulating tumor DNA in patients with osteosarcoma. Oncotarget 2018; 9:12695-12704. [PMID: 29560102 PMCID: PMC5849166 DOI: 10.18632/oncotarget.24268] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/09/2018] [Indexed: 12/30/2022] Open
Abstract
Identification and quantification of somatic alterations in plasma-derived, circulating tumor DNA (ctDNA) is gaining traction as a non-invasive and cost effective method of disease monitoring in cancer patients, particularly to evaluate response to treatment and monitor for disease recurrence. To our knowledge, genetic analysis of ctDNA in osteosarcoma has not yet been studied. To determine whether somatic alterations can be detected in ctDNA and perhaps applied to patient management in this disease, we collected germline, tumor, and serial plasma samples from pediatric, adolescent, and young adult patients with osteosarcoma and used targeted Next Generation Sequencing (NGS) to identify somatic single nucleotide variants (SNV), insertions and deletions (INDELS), and structural variants (SV) in 7 genes commonly mutated in osteosarcoma. We demonstrate that patient-specific somatic alterations identified through comparison of tumor-germline pairs can be detected and quantified in cell-free DNA of osteosarcoma patients.
Collapse
Affiliation(s)
- David M Barris
- Department of Genetics and Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Shoshana B Weiner
- Department of Genetics and Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert A Dubin
- Computational Genomics Core, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Michael Fremed
- Department of Genetics and Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xusheng Zhang
- Computational Genomics Core, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sajida Piperdi
- Department of Pediatrics, Montefiore Medical Center, Bronx, NY, USA
| | - Wendong Zhang
- Department of Pediatrics, Montefiore Medical Center, Bronx, NY, USA
| | - Shahina Maqbool
- Department of Genetics and Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jonathan Gill
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael Roth
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bang Hoang
- Department of Orthopedic Surgery, Montefiore Medical Center, Bronx, NY, USA
| | - David Geller
- Department of Orthopedic Surgery, Montefiore Medical Center, Bronx, NY, USA
| | - Richard Gorlick
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Daniel A Weiser
- Division of Hematology/Oncology, Children's Hospital at Montefiore, Bronx, NY, USA.,Departments of Pediatrics and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| |
Collapse
|
18
|
Komseli ES, Pateras IS, Krejsgaard T, Stawiski K, Rizou SV, Polyzos A, Roumelioti FM, Chiourea M, Mourkioti I, Paparouna E, Zampetidis CP, Gumeni S, Trougakos IP, Pefani DE, O’Neill E, Gagos S, Eliopoulos AG, Fendler W, Chowdhury D, Bartek J, Gorgoulis VG. A prototypical non-malignant epithelial model to study genome dynamics and concurrently monitor micro-RNAs and proteins in situ during oncogene-induced senescence. BMC Genomics 2018; 19:37. [PMID: 29321003 PMCID: PMC5763532 DOI: 10.1186/s12864-017-4375-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/11/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Senescence is a fundamental biological process implicated in various pathologies, including cancer. Regarding carcinogenesis, senescence signifies, at least in its initial phases, an anti-tumor response that needs to be circumvented for cancer to progress. Micro-RNAs, a subclass of regulatory, non-coding RNAs, participate in senescence regulation. At the subcellular level micro-RNAs, similar to proteins, have been shown to traffic between organelles influencing cellular behavior. The differential function of micro-RNAs relative to their subcellular localization and their role in senescence biology raises concurrent in situ analysis of coding and non-coding gene products in senescent cells as a necessity. However, technical challenges have rendered in situ co-detection unfeasible until now. METHODS In the present report we describe a methodology that bypasses these technical limitations achieving for the first time simultaneous detection of both a micro-RNA and a protein in the biological context of cellular senescence, utilizing the new commercially available SenTraGorTM compound. The method was applied in a prototypical human non-malignant epithelial model of oncogene-induced senescence that we generated for the purposes of the study. For the characterization of this novel system, we applied a wide range of cellular and molecular techniques, as well as high-throughput analysis of the transcriptome and micro-RNAs. RESULTS This experimental setting has three advantages that are presented and discussed: i) it covers a "gap" in the molecular carcinogenesis field, as almost all corresponding in vitro models are fibroblast-based, even though the majority of neoplasms have epithelial origin, ii) it recapitulates the precancerous and cancerous phases of epithelial tumorigenesis within a short time frame under the light of natural selection and iii) it uses as an oncogenic signal, the replication licensing factor CDC6, implicated in both DNA replication and transcription when over-expressed, a characteristic that can be exploited to monitor RNA dynamics. CONCLUSIONS Consequently, we demonstrate that our model is optimal for studying the molecular basis of epithelial carcinogenesis shedding light on the tumor-initiating events. The latter may reveal novel molecular targets with clinical benefit. Besides, since this method can be incorporated in a wide range of low, medium or high-throughput image-based approaches, we expect it to be broadly applicable.
Collapse
Affiliation(s)
- Eirini-Stavroula Komseli
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National & Kapodistrian University of Athens, 75 Mikras Asias St, GR-11527 Athens, Greece
| | - Ioannis S. Pateras
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National & Kapodistrian University of Athens, 75 Mikras Asias St, GR-11527 Athens, Greece
| | - Thorbjørn Krejsgaard
- Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3c, DK-2200 Copenhagen, Denmark
| | - Konrad Stawiski
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 15 Mazowiecka St. 92-215, Lodz, Poland
| | - Sophia V. Rizou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National & Kapodistrian University of Athens, 75 Mikras Asias St, GR-11527 Athens, Greece
| | - Alexander Polyzos
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou St, GR-11527 Athens, Greece
| | - Fani-Marlen Roumelioti
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou St, GR-11527 Athens, Greece
| | - Maria Chiourea
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou St, GR-11527 Athens, Greece
| | - Ioanna Mourkioti
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National & Kapodistrian University of Athens, 75 Mikras Asias St, GR-11527 Athens, Greece
| | - Eleni Paparouna
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National & Kapodistrian University of Athens, 75 Mikras Asias St, GR-11527 Athens, Greece
| | - Christos P. Zampetidis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National & Kapodistrian University of Athens, 75 Mikras Asias St, GR-11527 Athens, Greece
| | - Sentiljana Gumeni
- Department of Cell Biology and Biophysics, Faculty of Biology, National & Kapodistrian University of Athens, GR-15784 Athens, Greece
| | - Ioannis P. Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, National & Kapodistrian University of Athens, GR-15784 Athens, Greece
| | - Dafni-Eleftheria Pefani
- CRUK/MRC Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ UK
| | - Eric O’Neill
- CRUK/MRC Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ UK
| | - Sarantis Gagos
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou St, GR-11527 Athens, Greece
| | - Aristides G. Eliopoulos
- Department of Biology, School of Medicine, National & Kapodistrian University of Athens, 75 Mikras Asias St, GR-11527 Athens, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research & Technology-Hellas, GR-70013 Heraklion, Crete Greece
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 15 Mazowiecka St. 92-215, Lodz, Poland
- Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215 USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215 USA
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115 USA
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Centre, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Hněvotínská, 1333/5, 779 00 Olomouc, Czech Republic
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, SE-171 77 Stockholm, Sweden
| | - Vassilis G. Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National & Kapodistrian University of Athens, 75 Mikras Asias St, GR-11527 Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou St, GR-11527 Athens, Greece
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Wilmslow Road, Manchester, M20 4QL UK
| |
Collapse
|
19
|
Fadlullah MZH, Chiang IKN, Dionne KR, Yee PS, Gan CP, Sam KK, Tiong KH, Ng AKW, Martin D, Lim KP, Kallarakkal TG, Mustafa WMW, Lau SH, Abraham MT, Zain RB, Rahman ZAA, Molinolo A, Patel V, Gutkind JS, Tan AC, Cheong SC. Genetically-defined novel oral squamous cell carcinoma cell lines for the development of molecular therapies. Oncotarget 2017; 7:27802-18. [PMID: 27050151 PMCID: PMC5053689 DOI: 10.18632/oncotarget.8533] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/18/2016] [Indexed: 12/13/2022] Open
Abstract
Emerging biological and translational insights from large sequencing efforts underscore the need for genetically-relevant cell lines to study the relationships between genomic alterations of tumors, and therapeutic dependencies. Here, we report a detailed characterization of a novel panel of clinically annotated oral squamous cell carcinoma (OSCC) cell lines, derived from patients with diverse ethnicity and risk habits. Molecular analysis by RNAseq and copy number alterations (CNA) identified that the cell lines harbour CNA that have been previously reported in OSCC, for example focal amplications in 3q, 7p, 8q, 11q, 20q and deletions in 3p, 5q, 8p, 18q. Similarly, our analysis identified the same cohort of frequently mutated genes previously reported in OSCC including TP53, CDKN2A, EPHA2, FAT1, NOTCH1, CASP8 and PIK3CA. Notably, we identified mutations (MLL4, USP9X, ARID2) in cell lines derived from betel quid users that may be associated with this specific risk factor. Gene expression profiles of the ORL lines also aligned with those reported for OSCC. By focusing on those gene expression signatures that are predictive of chemotherapeutic response, we observed that the ORL lines broadly clustered into three groups (cell cycle, xenobiotic metabolism, others). The ORL lines noted to be enriched in cell cycle genes responded preferentially to the CDK1 inhibitor RO3306, by MTT cell viability assay. Overall, our in-depth characterization of clinically annotated ORL lines provides new insight into the molecular alterations synonymous with OSCC, which can facilitate in the identification of biomarkers that can be used to guide diagnosis, prognosis, and treatment of OSCC.
Collapse
Affiliation(s)
| | - Ivy Kim-Ni Chiang
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,Oral Cancer Research and Co-ordinating Centre (OCRCC), Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Kalen R Dionne
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,Oral Cancer Research and Co-ordinating Centre (OCRCC), Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.,Medical Scientist Training Program, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO
| | - Pei San Yee
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Chai Phei Gan
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Kin Kit Sam
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Kai Hung Tiong
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,Oral Cancer Research and Co-ordinating Centre (OCRCC), Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Daniel Martin
- Oral and Pharyngeal Cancer Branch, National Institutes of Health, Bethesda, MD, USA
| | - Kue Peng Lim
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Thomas George Kallarakkal
- Oral Cancer Research and Co-ordinating Centre (OCRCC), Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.,Department of Oro-Maxillofacial Surgery and Medical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Shin Hin Lau
- Stomatology Unit, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - Mannil Thomas Abraham
- Department of Oral and Maxillofacial Surgery, Tengku Ampuan Rahimah Hospital, Klang, Selangor, Malaysia
| | - Rosnah Binti Zain
- Oral Cancer Research and Co-ordinating Centre (OCRCC), Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.,Department of Oro-Maxillofacial Surgery and Medical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Zainal Ariff Abdul Rahman
- Department of Oro-Maxillofacial Surgery and Medical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Alfredo Molinolo
- Oral and Pharyngeal Cancer Branch, National Institutes of Health, Bethesda, MD, USA
| | - Vyomesh Patel
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - J Silvio Gutkind
- Oral and Pharyngeal Cancer Branch, National Institutes of Health, Bethesda, MD, USA
| | - Aik Choon Tan
- Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sok Ching Cheong
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,Department of Oro-Maxillofacial Surgery and Medical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
20
|
Mayo-de-Las-Casas C, Garzón Ibáñez M, Jordana-Ariza N, García-Peláez B, Balada-Bel A, Villatoro S, Malapelle U, Karachaliou N, Troncone G, Rosell R, Molina-Vila MA. An update on liquid biopsy analysis for diagnostic and monitoring applications in non-small cell lung cancer. Expert Rev Mol Diagn 2017; 18:35-45. [PMID: 29172773 DOI: 10.1080/14737159.2018.1407243] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Collection of tumor samples is not always feasible in non-small cell lung cancer (NSCLC) patients, and circulating free DNA (cfDNA) extracted from blood represents a viable alternative. Different sensitive platforms have been developed for genetic cfDNA testing, some of which are already in clinical use. However, several difficulties remain, particularly the lack of standardization of these methodologies. Areas covered: Here, the authors present a review of the literature to update the applicability of cfDNA for diagnosis and monitoring of NSCLC patients. Expert commentary: Detection of somatic alterations in cfDNA is already in use in clinical practice and provides valuable information for patient management. Monitoring baseline alterations and emergence of resistance mutations is one of the most important clinical applications and can be used to non-invasively track disease evolution. Today, different technologies are available for cfDNA analysis, including whole-genome or exome sequencing and targeted methods that focus on a selection of genes of interest in a specific disease. In the case of Next Generation Sequencing (NGS) approaches, in depth coverage of candidate mutation loci can be achieved by selecting a limited number of targeted genes.
Collapse
Affiliation(s)
| | | | | | | | - Ariadna Balada-Bel
- a Pangaea Oncology , Quirón Dexeus University Hospital , Barcelona , Spain
| | - Sergio Villatoro
- a Pangaea Oncology , Quirón Dexeus University Hospital , Barcelona , Spain
| | - Umberto Malapelle
- b Department of Public Health , University of Naples Federico II , Naples , Italy
| | - Niki Karachaliou
- c Dr Rosell Oncology Institute , University Hospital Sagrat Cor , Barcelona , Spain
| | - Giancarlo Troncone
- b Department of Public Health , University of Naples Federico II , Naples , Italy
| | - Rafael Rosell
- d Cancer Biology and Precision Medicine Program, Catalan Institute of Oncology , Germans Trias i Pujol Health Sciences Institute and Hospital , Badalona , Spain
| | | |
Collapse
|
21
|
Next-generation sequencing reveals novel resistance mechanisms and molecular heterogeneity in EGFR-mutant non-small cell lung cancer with acquired resistance to EGFR-TKIs. Lung Cancer 2017; 113:106-114. [DOI: 10.1016/j.lungcan.2017.09.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 12/30/2022]
|
22
|
Özdemir BC, Dotto GP. Racial Differences in Cancer Susceptibility and Survival: More Than the Color of the Skin? Trends Cancer 2017; 3:181-197. [PMID: 28718431 DOI: 10.1016/j.trecan.2017.02.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 12/14/2022]
Abstract
Epidemiological studies point to race as a determining factor in cancer susceptibility. In US registries recording cancer incidence and survival by race (distinguishing 'black versus white'), individuals of African ancestry have a globally increased risk of malignancies compared with Caucasians and Asian Americans. Differences in socioeconomic status and health-care access play a key role. However, the lesser disease susceptibility of Hispanic populations with comparable lifestyles and socioeconomic status as African Americans (Hispanic paradox) points to the concomitant importance of genetic determinants. Here, we overview the molecular basis of racial disparity in cancer susceptibility ranging from genetic polymorphisms and cancer-driver gene mutations to obesity, chronic inflammation, and immune responses. We discuss implications for race-adapted cancer screening programs and clinical trials to reduce disparities in cancer burden.
Collapse
Affiliation(s)
- Berna C Özdemir
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Rue du Bugnon 46, 1011 Lausanne, Switzerland
| | - Gian-Paolo Dotto
- Department of Biochemistry, University of Lausanne, Chemin des Boveresses 155, 1066 Épalinges, Switzerland; Harvard Dermatology Department and Cutaneous Biology Research Center, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02129, USA.
| |
Collapse
|
23
|
Dong N, Shi L, Wang DC, Chen C, Wang X. Role of epigenetics in lung cancer heterogeneity and clinical implication. Semin Cell Dev Biol 2016; 64:18-25. [PMID: 27575638 DOI: 10.1016/j.semcdb.2016.08.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 08/24/2016] [Indexed: 12/15/2022]
Abstract
Lung cancer, as a highly heterogeneous disease, can be initiated and progressed through the interaction between permanent genetic mutations and dynamic epigenetic alterations. However, the mediating mechanisms of epigenetics in cancer heterogeneity remain unclear. The evolution of cancer, the existence of cancer stem cells (CSCs) and the phenomenon of epithelial-mesenchymal transition (EMT) have been reported to be involved in lung cancer heterogeneity. In this review, we briefly recap the definition of heterogeneity and concept of epigenetics, highlight the potential roles and mechanisms of epigenetic regulation in heterogeneity of lung cancer, and summarize the diagnostic and therapeutic implications of epigenetic alterations in lung cancer, especially the role of DNA methylation and histone acetylation. Deep understanding of epigenetic regulation in cancer heterogeneity is instrumental to the design of novel therapeutic approaches that target lung cancer.
Collapse
Affiliation(s)
- Nian Dong
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, China
| | - Lin Shi
- Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics; Zhongshan Hospital Institute of Clinical Science of Fudan University, Shanghai, China
| | - Diane C Wang
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, China
| | - Chengshui Chen
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, China.
| | - Xiangdong Wang
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, China; Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics; Zhongshan Hospital Institute of Clinical Science of Fudan University, Shanghai, China.
| |
Collapse
|
24
|
Aoi T. Biology of lung cancer: genetic mutation, epithelial-mesenchymal transition, and cancer stem cells. Gen Thorac Cardiovasc Surg 2016; 64:517-23. [PMID: 27376535 DOI: 10.1007/s11748-016-0682-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/27/2016] [Indexed: 12/13/2022]
Abstract
At present, most cases of unresectable cancer cannot be cured. Genetic mutations, EMT, and cancer stem cells are three major issues linked to poor prognosis in such cases, all connected by inter- and intra-tumor heterogeneity. Issues on inter-/intra-tumor heterogeneity of genetic mutation could be resolved with recent and future technologies of deep sequencers, whereas, regarding such issues as the "same genome, different epigenome/phenotype", we expect to solve many of these problems in the future through further research in stem cell biology. We herein review and discuss the three major issues in the biology of cancers, especially from the standpoint of stem cell biology.
Collapse
Affiliation(s)
- Takashi Aoi
- Division of Advanced Medical Science, Graduate School of Science, Technology and Innovation, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan. .,Department of iPS cell Applications, Graduate School of Medicine, Kobe University, Kobe, Japan. .,Center for Human Resource Development for Regenerative Medicine, Kobe University Hospital, Kobe, Japan.
| |
Collapse
|
25
|
Tan DSW, Yom SS, Tsao MS, Pass HI, Kelly K, Peled N, Yung RC, Wistuba II, Yatabe Y, Unger M, Mack PC, Wynes MW, Mitsudomi T, Weder W, Yankelevitz D, Herbst RS, Gandara DR, Carbone DP, Bunn PA, Mok TSK, Hirsch FR. The International Association for the Study of Lung Cancer Consensus Statement on Optimizing Management of EGFR Mutation-Positive Non-Small Cell Lung Cancer: Status in 2016. J Thorac Oncol 2016; 11:946-63. [PMID: 27229180 DOI: 10.1016/j.jtho.2016.05.008] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/12/2016] [Accepted: 05/13/2016] [Indexed: 12/11/2022]
Abstract
Mutations in the epidermal growth factor receptor gene (EGFR) represent one of the most frequent "actionable" alterations in non-small cell lung cancer (NSCLC). Typified by high response rates to targeted therapies, EGFR tyrosine kinase inhibitors (TKIs) are now established first-line treatment options and have transformed the treatment paradigm for NSCLC. With the recent breakthrough designation and approval of the third-generation EGFR TKI osimertinib, available systemic and local treatment options have expanded, requiring new clinical algorithms that take into account individual patient molecular and clinical profiles. In this International Association for the Study of Lung Cancer commissioned consensus statement, key pathologic, diagnostic, and therapeutic considerations, such as optimal choice of EGFR TKI and management of brain metastasis, are discussed. In addition, recommendations are made for clinical guidelines and research priorities, such as the role of repeat biopsies and use of circulating free DNA for molecular studies. With the rapid pace of progress in treating EGFR-mutant NSCLC, this statement provides a state-of-the-art review of the contemporary issues in managing this unique subgroup of patients.
Collapse
Affiliation(s)
- Daniel S W Tan
- National Cancer Centre Singapore and Genome Institute of Singapore, Singapore
| | - Sue S Yom
- Department of Radiation Oncology, University of California, San Francisco, California
| | - Ming S Tsao
- Departments of Pathology, University Health Network, Princess Margaret Cancer Centre, and the University of Toronto, Toronto, Ontario, Canada
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York
| | - Karen Kelly
- University of California Davis Comprehensive Cancer Center, Sacramento, California
| | - Nir Peled
- The Thoracic Cancer Unit, Davidoff Cancer Center, Tel Aviv University, Tel-Aviv, Israel
| | - Rex C Yung
- Department of Pulmonary and Critical Care Medicine, Greater Baltimore Medical Center, Baltimore, Maryland
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Michael Unger
- Sidney Kimmel Medical College and Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Philip C Mack
- University of California Davis Comprehensive Cancer Center, Sacramento, California
| | - Murry W Wynes
- International Association for the Study of Lung Cancer, Aurora, Colorado
| | - Tetsuya Mitsudomi
- Division of Thoracic Surgery, Department of Surgery, Kinki University Faculty of Medicine, Osaka-Sayama, Japan
| | - Walter Weder
- Division of Thoracic Surgery, University Hospital Zurich, Zurich, Switzerland
| | - David Yankelevitz
- Department of Radiology, Mount Sinai School of Medicine, New York, New York
| | | | - David R Gandara
- University of California Davis Comprehensive Cancer Center, Sacramento, California
| | - David P Carbone
- Division of Medical Oncology, The Ohio State University, Columbus, Ohio
| | - Paul A Bunn
- Division of Medical Oncology, University of Colorado Cancer Center, Aurora, Colorado
| | - Tony S K Mok
- State Key Laboratory of Southern China, Hong Kong Cancer Institute, Department of Clinical Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, People's Republic of China.
| | - Fred R Hirsch
- Division of Medical Oncology, University of Colorado Cancer Center, Aurora, Colorado
| |
Collapse
|
26
|
Marien E, Meister M, Muley T, del Pulgar TG, Derua R, Spraggins JM, Van de Plas R, Vanderhoydonc F, Machiels J, Binda MM, Dehairs J, Willette-Brown J, Hu Y, Dienemann H, Thomas M, Schnabel PA, Caprioli RM, Lacal JC, Waelkens E, Swinnen JV. Phospholipid profiling identifies acyl chain elongation as a ubiquitous trait and potential target for the treatment of lung squamous cell carcinoma. Oncotarget 2016; 7:12582-97. [PMID: 26862848 PMCID: PMC4914306 DOI: 10.18632/oncotarget.7179] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/04/2016] [Indexed: 01/19/2023] Open
Abstract
Lung cancer is the leading cause of cancer death. Beyond first line treatment, few therapeutic options are available, particularly for squamous cell carcinoma (SCC). Here, we have explored the phospholipidomes of 30 human SCCs and found that they almost invariably (in 96.7% of cases) contain phospholipids with longer acyl chains compared to matched normal tissues. This trait was confirmed using in situ 2D-imaging MS on tissue sections and by phospholipidomics of tumor and normal lung tissue of the L-IkkαKA/KA mouse model of lung SCC. In both human and mouse, the increase in acyl chain length in cancer tissue was accompanied by significant changes in the expression of acyl chain elongases (ELOVLs). Functional screening of differentially expressed ELOVLs by selective gene knockdown in SCC cell lines followed by phospholipidomics revealed ELOVL6 as the main elongation enzyme responsible for acyl chain elongation in cancer cells. Interestingly, inhibition of ELOVL6 drastically reduced colony formation of multiple SCC cell lines in vitro and significantly attenuated their growth as xenografts in vivo in mouse models. These findings identify acyl chain elongation as one of the most common traits of lung SCC discovered so far and pinpoint ELOVL6 as a novel potential target for cancer intervention.
Collapse
Affiliation(s)
- Eyra Marien
- KU Leuven – University of Leuven, LKI - Leuven Cancer Institute, Department of Oncology, Laboratory of Lipid Metabolism and Cancer, Leuven, Belgium
| | - Michael Meister
- Thoraxklinik at University Hospital Heidelberg, Translational Research Unit, Heidelberg, Germany
- TLRC-H – Translational Lung Research Center Heidelberg, Member of The German Center for Lung Research, Heidelberg, Germany
| | - Thomas Muley
- Thoraxklinik at University Hospital Heidelberg, Translational Research Unit, Heidelberg, Germany
- TLRC-H – Translational Lung Research Center Heidelberg, Member of The German Center for Lung Research, Heidelberg, Germany
| | | | - Rita Derua
- KU Leuven – University of Leuven, Department of Cellular and Molecular Medicine, Laboratory of Protein Phosphorylation and Proteomics, Leuven, Belgium
| | - Jeffrey M. Spraggins
- Vanderbilt University Medical Center, Department of Biochemistry and Mass Spectrometry Research Center, Nashville, TN, USA
| | - Raf Van de Plas
- Vanderbilt University Medical Center, Department of Biochemistry and Mass Spectrometry Research Center, Nashville, TN, USA
- Delft University of Technology, Delft Center for Systems and Control, Delft, The Netherlands
| | - Frank Vanderhoydonc
- KU Leuven – University of Leuven, LKI - Leuven Cancer Institute, Department of Oncology, Laboratory of Lipid Metabolism and Cancer, Leuven, Belgium
| | - Jelle Machiels
- KU Leuven – University of Leuven, LKI - Leuven Cancer Institute, Department of Oncology, Laboratory of Lipid Metabolism and Cancer, Leuven, Belgium
| | - Maria Mercedes Binda
- KU Leuven – University of Leuven, LKI - Leuven Cancer Institute, Department of Oncology, Abdominal Surgical Oncology, Leuven, Belgium
| | - Jonas Dehairs
- KU Leuven – University of Leuven, LKI - Leuven Cancer Institute, Department of Oncology, Laboratory of Lipid Metabolism and Cancer, Leuven, Belgium
| | - Jami Willette-Brown
- National Cancer Institute, Centre for Cancer Research, Cancer and Inflammation Program, Frederick, MD, USA
| | - Yinling Hu
- National Cancer Institute, Centre for Cancer Research, Cancer and Inflammation Program, Frederick, MD, USA
| | - Hendrik Dienemann
- TLRC-H – Translational Lung Research Center Heidelberg, Member of The German Center for Lung Research, Heidelberg, Germany
- Thoraxklinik at University Hospital Heidelberg, Department of Surgery, Heidelberg, Germany
| | - Michael Thomas
- TLRC-H – Translational Lung Research Center Heidelberg, Member of The German Center for Lung Research, Heidelberg, Germany
- Thoraxklinik at University Hospital Heidelberg, Department of Thoracic Oncology, Heidelberg, Germany
| | - Philipp A. Schnabel
- TLRC-H – Translational Lung Research Center Heidelberg, Member of The German Center for Lung Research, Heidelberg, Germany
- University of The Saarland, Institut für Allgemeine und Spezielle Pathologie, Homburg/Saar, Germany
| | - Richard M. Caprioli
- Vanderbilt University Medical Center, Department of Biochemistry and Mass Spectrometry Research Center, Nashville, TN, USA
| | - Juan Carlos Lacal
- Fundación Jiménez Díaz, Division of Translational Oncology, Madrid, Spain
| | - Etienne Waelkens
- KU Leuven – University of Leuven, Department of Cellular and Molecular Medicine, Laboratory of Protein Phosphorylation and Proteomics, Leuven, Belgium
| | - Johannes V. Swinnen
- KU Leuven – University of Leuven, LKI - Leuven Cancer Institute, Department of Oncology, Laboratory of Lipid Metabolism and Cancer, Leuven, Belgium
| |
Collapse
|
27
|
Khoo BL, Chaudhuri PK, Ramalingam N, Tan DSW, Lim CT, Warkiani ME. Single-cell profiling approaches to probing tumor heterogeneity. Int J Cancer 2016; 139:243-55. [PMID: 26789729 DOI: 10.1002/ijc.30006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/10/2015] [Accepted: 01/08/2016] [Indexed: 01/08/2023]
Abstract
Tumor heterogeneity is a major hindrance in cancer classification, diagnosis and treatment. Recent technological advances have begun to reveal the true extent of its heterogeneity. Single-cell analysis (SCA) is emerging as an important approach to detect variations in morphology, genetic or proteomic expression. In this review, we revisit the issue of inter- and intra-tumor heterogeneity, and list various modes of SCA techniques (cell-based, nucleic acid-based, protein-based, metabolite-based and lipid-based) presently used for cancer characterization. We further discuss the advantages of SCA over pooled cell analysis, as well as the limitations of conventional techniques. Emerging trends, such as high-throughput sequencing, are also mentioned as improved means for cancer profiling. Collectively, these applications have the potential for breakthroughs in cancer treatment.
Collapse
Affiliation(s)
- Bee Luan Khoo
- Mechanobiology Institute, National University of Singapore.,BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore
| | | | | | - Daniel Shao Weng Tan
- Division of Medical Oncology, National Cancer Centre Singapore.,Cancer Stem Cell Biology, Genome Institute of Singapore
| | - Chwee Teck Lim
- Mechanobiology Institute, National University of Singapore.,BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore.,Department of Biomedical Engineering, National University of Singapore
| | - Majid Ebrahimi Warkiani
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore.,School of Mechanical and Manufacturing Engineering, Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| |
Collapse
|
28
|
Tan DSW, Mok TSK, Rebbeck TR. Cancer Genomics: Diversity and Disparity Across Ethnicity and Geography. J Clin Oncol 2015; 34:91-101. [PMID: 26578615 DOI: 10.1200/jco.2015.62.0096] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ethnic and geographic differences in cancer incidence, prognosis, and treatment outcomes can be attributed to diversity in the inherited (germline) and somatic genome. Although international large-scale sequencing efforts are beginning to unravel the genomic underpinnings of cancer traits, much remains to be known about the underlying mechanisms and determinants of genomic diversity. Carcinogenesis is a dynamic, complex phenomenon representing the interplay between genetic and environmental factors that results in divergent phenotypes across ethnicities and geography. For example, compared with whites, there is a higher incidence of prostate cancer among Africans and African Americans, and the disease is generally more aggressive and fatal. Genome-wide association studies have identified germline susceptibility loci that may account for differences between the African and non-African patients, but the lack of availability of appropriate cohorts for replication studies and the incomplete understanding of genomic architecture across populations pose major limitations. We further discuss the transformative potential of routine diagnostic evaluation for actionable somatic alterations, using lung cancer as an example, highlighting implications of population disparities, current hurdles in implementation, and the far-reaching potential of clinical genomics in enhancing cancer prevention, diagnosis, and treatment. As we enter the era of precision cancer medicine, a concerted multinational effort is key to addressing population and genomic diversity as well as overcoming barriers and geographical disparities in research and health care delivery.
Collapse
Affiliation(s)
- Daniel S W Tan
- Daniel S.W. Tan, National Cancer Centre Singapore and Genome Institute of Singapore, Singapore; Tony S.K. Mok, The Chinese University of Hong Kong, Sir Y. K. Pau Cancer Center, State Key Laboratory of Southern China, Prince of Wales Hospital, Hong Kong, China; and Timothy R. Rebbeck, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Tony S K Mok
- Daniel S.W. Tan, National Cancer Centre Singapore and Genome Institute of Singapore, Singapore; Tony S.K. Mok, The Chinese University of Hong Kong, Sir Y. K. Pau Cancer Center, State Key Laboratory of Southern China, Prince of Wales Hospital, Hong Kong, China; and Timothy R. Rebbeck, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA.
| | - Timothy R Rebbeck
- Daniel S.W. Tan, National Cancer Centre Singapore and Genome Institute of Singapore, Singapore; Tony S.K. Mok, The Chinese University of Hong Kong, Sir Y. K. Pau Cancer Center, State Key Laboratory of Southern China, Prince of Wales Hospital, Hong Kong, China; and Timothy R. Rebbeck, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| |
Collapse
|
29
|
Circulating tumor DNA identified by targeted sequencing in advanced-stage non-small cell lung cancer patients. Cancer Lett 2015; 370:324-31. [PMID: 26582655 DOI: 10.1016/j.canlet.2015.11.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/13/2015] [Accepted: 11/04/2015] [Indexed: 12/18/2022]
Abstract
Non-small cell lung cancers (NSCLC) have unique mutation patterns, and some of these mutations may be used to predict prognosis or guide patient treatment. Mutation profiling before and during treatment often requires repeated tumor biopsies, which is not always possible. Recently, cell-free, circulating tumor DNA (ctDNA) isolated from blood plasma has been shown to contain genetic mutations representative of those found in the primary tumor tissue DNA (tDNA), and these samples can readily be obtained using non-invasive techniques. However, there are still no standardized methods to identify mutations in ctDNA. In the current study, we used a targeted sequencing approach with a semi-conductor based next-generation sequencing (NGS) platform to identify gene mutations in matched tDNA and ctDNA samples from 42 advanced-stage NSCLC patients from China. We identified driver mutations in matched tDNA and ctDNA in EGFR, KRAS, PIK3CA, and TP53, with an overall concordance of 76%. In conclusion, targeted sequencing of plasma ctDNA may be a feasible option for clinical monitoring of NSCLC in the near future.
Collapse
|
30
|
Hasenahuer MA, Parisi G, Gautier M, Lazarowski A, Bramuglia GF, Fornasari MS. Twenty-One Novel EGFR Kinase Domain variants in Patients with Nonsmall Cell Lung Cancer. Ann Hum Genet 2015; 79:385-93. [PMID: 26420346 DOI: 10.1111/ahg.12127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Revised: 06/01/2015] [Accepted: 06/03/2015] [Indexed: 01/11/2023]
Abstract
Somatic sequence variants in the epidermal growth factor receptor (EGFR) kinase domain are associated with sensitivity to tyrosine kinase inhibitors (TKIs) in patients with nonsmall cell lung cancer (NSCLC). Patients exhibiting sequence variants in this domain that produce kinase activity enhancement, are more likely to benefit from TKIs than patients with EGFR wild-type disease. Although most NSCLC EGFR-related alleles are concentrated in a few positions, established protocols recommend sequencing EGFR exons 18-21. In this study, 21 novel somatic variants belonging to such exons in adult Argentinean patients affected with NSCLC are reported. Of these, 18 were single amino acid substitutions (SASs), occurring alone or in combination with another genetic alteration (complex cases), one was a short deletion, one was a short deletion-short insertion combination, and one was a duplication. New variants and different combinations of previously reported variants were also found. Moreover, two of the reported SASs occurred in previously unreported positions of the EGFR kinase domain. In order to characterize the new sequence variants, physicochemical, sequence and conformational analyses were also performed. A better understanding of sequence variants in NSCLC may facilitate the most appropriate treatment choice for this complex disease.
Collapse
Affiliation(s)
- Marcia A Hasenahuer
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Saenz Peña 352, Bernal, (B1876BXD), Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Saenz Peña 352, Bernal, (B1876BXD), Buenos Aires, Argentina
| | - Marien Gautier
- Fundación Investigar. Riobamba 429 Piso 15, Ciudad Autónoma de Buenos Aires, (C1022AAT), Argentina
| | - Alberto Lazarowski
- Fundación Investigar. Riobamba 429 Piso 15, Ciudad Autónoma de Buenos Aires, (C1022AAT), Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, Ciudad Autónoma de Buenos Aires, (C1113AAD), Argentina
| | - Guillermo F Bramuglia
- Fundación Investigar. Riobamba 429 Piso 15, Ciudad Autónoma de Buenos Aires, (C1022AAT), Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, Ciudad Autónoma de Buenos Aires, (C1113AAD), Argentina
| | - Maria Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Saenz Peña 352, Bernal, (B1876BXD), Buenos Aires, Argentina
| |
Collapse
|
31
|
Fallet V, Saffroy R, Girard N, Mazieres J, Lantuejoul S, Vieira T, Rouquette I, Thivolet-Bejui F, Ung M, Poulot V, Schlick L, Moro-Sibilot D, Antoine M, Cadranel J, Lemoine A, Wislez M. High-throughput somatic mutation profiling in pulmonary sarcomatoid carcinomas using the LungCarta™ Panel: exploring therapeutic targets. Ann Oncol 2015; 26:1748-53. [DOI: 10.1093/annonc/mdv232] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 05/07/2015] [Indexed: 02/06/2023] Open
|
32
|
Mbogning C, Perdry H, Broët P. A Bagged, Partially Linear, Tree-Based Regression Procedure for Prediction and Variable Selection. Hum Hered 2015. [PMID: 26201703 DOI: 10.1159/000380850] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES In genomics, variable selection and prediction accounting for the complex interrelationships between explanatory variables represent major challenges. Tree-based methods are powerful alternatives to classical regression models. We have recently proposed the generalized, partially linear, tree-based regression (GPLTR) procedure that integrates the advantages of generalized linear regression (allowing the incorporation of confounding variables) and of tree-based models. In this work, we use bagging to address a classical concern of tree-based methods: their instability. METHODS We present a bagged GPLTR procedure and three scores for variable importance. The prediction accuracy and the performance of the scores are assessed by simulation. The use of this procedure is exemplified by the analysis of a lung cancer data set. The aim is to predict the epidermal growth factor receptor (EGFR) mutation based on gene expression measurements, taking into account the ethnicity (confounder variable) and perform variable selection. RESULTS The procedure performs well in terms of prediction accuracy. The scores differentiate predictive variables from noise variables. Based on a lung adenocarcinoma data set, the procedure achieves good predictive performance for EGFR mutation and selects relevant genes. CONCLUSION The proposed bagged GPLTR procedure performs well for prediction and variable selection.
Collapse
|
33
|
Jain A, Lim C, Gan EM, Ng DZ, Ng QS, Ang MK, Takano A, Chan KS, Tan WM, Kanesvaran R, Toh CK, Loo CM, Hsu AAL, Devanand A, Lim CH, Koong HN, Koh T, Fong KW, Yap SP, Kim SW, Chowbay B, Oon L, Lim KH, Lim WT, Tan EH, Tan DSW. Impact of Smoking and Brain Metastasis on Outcomes of Advanced EGFR Mutation Lung Adenocarcinoma Patients Treated with First Line Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors. PLoS One 2015; 10:e0123587. [PMID: 25955322 PMCID: PMC4425557 DOI: 10.1371/journal.pone.0123587] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 03/04/2015] [Indexed: 11/19/2022] Open
Abstract
Objectives This purpose of this study was to examine clinical-pathologic factors – particularly smoking and brain metastases – in EGFR mutation positive (M+) lung adenocarcinoma (ADC) to determine their impact on survival in patients treated with first line EGFR TKI. Methods A retrospective review of EGFR mutation reflex testing experience for all ADC diagnosed at a tertiary Asian cancer centre from January 2009 to April 2013. Amongst this cohort, patients with advanced EGFR M+ ADC treated with first line EGFR TKI were identified to determine factors that influence progression free and overall survival. Results 444/742 (59.8%) ADC reflex tested for EGFR mutations were EGFR M+. Amongst never-smokers (n=468), EGFR M+ were found in 74.5% of females and 76.3% of males, and amongst ever smokers (n=283), in 53.3% of females and 35.6% of males. Exon 20 mutations were found more commonly amongst heavy smokers (> 50 pack years and > 20 pack years, Pearson’s chi square p=0.044, and p=0.038 respectively). 211 patients treated with palliative first line TKI had a median PFS and OS of 9.2 and 19.6 months respectively. 26% of patients had brain metastasis at diagnosis. This was significantly detrimental to overall survival (HR 1.85, CI 1.09-3.16, p=0.024) on multivariate analysis. There was no evidence that smoking status had a significant impact on survival. Conclusions The high prevalence of EGFR M+ in our patient population warrants reflex testing regardless of gender and smoking status. Smoking status and dosage did not impact progression free or overall survival in patients treated with first line EGFR TKI. The presence of brain metastasis at diagnosis negatively impacts overall survival.
Collapse
Affiliation(s)
- Amit Jain
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Cindy Lim
- Clinical Trials & Epidemiological Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Eugene MingJin Gan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - David Zhihao Ng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Quan Sing Ng
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Mei Kim Ang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Angela Takano
- Department of Pathology, Academia, Level 7, Singapore General Hospital, Singapore, Singapore
| | - Kian Sing Chan
- Department of Pathology, Academia, Level 7, Singapore General Hospital, Singapore, Singapore
| | - Wu Meng Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Ravindran Kanesvaran
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Chee Keong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Chian Min Loo
- Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Anne Ann Ling Hsu
- Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Anantham Devanand
- Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Chong Hee Lim
- Department of Cardiothoracic Surgery, National Heart Centre Singapore, Singapore, Singapore
| | - Heng Nung Koong
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Tina Koh
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Kam Weng Fong
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Swee Peng Yap
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Su Woon Kim
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Balram Chowbay
- Clinical Pharmacology Laboratory, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Lynette Oon
- Department of Pathology, Academia, Level 7, Singapore General Hospital, Singapore, Singapore
| | - Kiat Hon Lim
- Department of Pathology, Academia, Level 7, Singapore General Hospital, Singapore, Singapore
| | - Wan Teck Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Eng Huat Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Daniel Shao Weng Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Cancer Therapeutics Research Laboratory, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
- Cancer Stem Cell Biology, Genome Institute of Singapore, Singapore, Singapore
- * E-mail:
| |
Collapse
|
34
|
Eberlein CA, Stetson D, Markovets AA, Al-Kadhimi KJ, Lai Z, Fisher PR, Meador CB, Spitzler P, Ichihara E, Ross SJ, Ahdesmaki MJ, Ahmed A, Ratcliffe LE, O'Brien ELC, Barnes CH, Brown H, Smith PD, Dry JR, Beran G, Thress KS, Dougherty B, Pao W, Cross DAE. Acquired Resistance to the Mutant-Selective EGFR Inhibitor AZD9291 Is Associated with Increased Dependence on RAS Signaling in Preclinical Models. Cancer Res 2015; 75:2489-500. [PMID: 25870145 DOI: 10.1158/0008-5472.can-14-3167] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/17/2015] [Indexed: 12/30/2022]
Abstract
Resistance to targeted EGFR inhibitors is likely to develop in EGFR-mutant lung cancers. Early identification of innate or acquired resistance mechanisms to these agents is essential to direct development of future therapies. We describe the detection of heterogeneous mechanisms of resistance within populations of EGFR-mutant cells (PC9 and/or NCI-H1975) with acquired resistance to current and newly developed EGFR tyrosine kinase inhibitors, including AZD9291. We report the detection of NRAS mutations, including a novel E63K mutation, and a gain of copy number of WT NRAS or WT KRAS in cell populations resistant to gefitinib, afatinib, WZ4002, or AZD9291. Compared with parental cells, a number of resistant cell populations were more sensitive to inhibition by the MEK inhibitor selumetinib (AZD6244; ARRY-142886) when treated in combination with the originating EGFR inhibitor. In vitro, a combination of AZD9291 with selumetinib prevented emergence of resistance in PC9 cells and delayed resistance in NCI-H1975 cells. In vivo, concomitant dosing of AZD9291 with selumetinib caused regression of AZD9291-resistant tumors in an EGFRm/T790M transgenic model. Our data support the use of a combination of AZD9291 with a MEK inhibitor to delay or prevent resistance to AZD9291 in EGFRm and/or EGFRm/T790M tumors. Furthermore, these findings suggest that NRAS modifications in tumor samples from patients who have progressed on current or EGFR inhibitors in development may support subsequent treatment with a combination of EGFR and MEK inhibition.
Collapse
Affiliation(s)
- Catherine A Eberlein
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Daniel Stetson
- AstraZeneca Oncology Innovative Medicines, Gatehouse Park, Waltham, Massachusetts
| | | | - Katherine J Al-Kadhimi
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Zhongwu Lai
- AstraZeneca Oncology Innovative Medicines, Gatehouse Park, Waltham, Massachusetts
| | - Paul R Fisher
- AstraZeneca, Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Catherine B Meador
- Department of Medicine and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Paula Spitzler
- Department of Medicine and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Eiki Ichihara
- Department of Medicine and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Sarah J Ross
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Miika J Ahdesmaki
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Ambar Ahmed
- AstraZeneca Oncology Innovative Medicines, Gatehouse Park, Waltham, Massachusetts
| | | | | | - Claire H Barnes
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Henry Brown
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Paul D Smith
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Jonathan R Dry
- AstraZeneca Oncology Innovative Medicines, Gatehouse Park, Waltham, Massachusetts
| | - Garry Beran
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, Cheshire, United Kingdom
| | - Kenneth S Thress
- AstraZeneca Oncology Innovative Medicines, Gatehouse Park, Waltham, Massachusetts
| | - Brian Dougherty
- AstraZeneca Oncology Innovative Medicines, Gatehouse Park, Waltham, Massachusetts
| | - William Pao
- Department of Medicine and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Darren A E Cross
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, Cheshire, United Kingdom.
| |
Collapse
|
35
|
Marien E, Meister M, Muley T, Fieuws S, Bordel S, Derua R, Spraggins J, Van de Plas R, Dehairs J, Wouters J, Bagadi M, Dienemann H, Thomas M, Schnabel PA, Caprioli RM, Waelkens E, Swinnen JV. Non-small cell lung cancer is characterized by dramatic changes in phospholipid profiles. Int J Cancer 2015; 137:1539-48. [PMID: 25784292 PMCID: PMC4503522 DOI: 10.1002/ijc.29517] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 02/16/2015] [Accepted: 03/05/2015] [Indexed: 12/18/2022]
Abstract
Non-small cell lung cancer (NSCLC) is the leading cause of cancer death globally. To develop better diagnostics and more effective treatments, research in the past decades has focused on identification of molecular changes in the genome, transcriptome, proteome, and more recently also the metabolome. Phospholipids, which nevertheless play a central role in cell functioning, remain poorly explored. Here, using a mass spectrometry (MS)-based phospholipidomics approach, we profiled 179 phospholipid species in malignant and matched non-malignant lung tissue of 162 NSCLC patients (73 in a discovery cohort and 89 in a validation cohort). We identified 91 phospholipid species that were differentially expressed in cancer versus non-malignant tissues. Most prominent changes included a decrease in sphingomyelins (SMs) and an increase in specific phosphatidylinositols (PIs). Also a decrease in multiple phosphatidylserines (PSs) was observed, along with an increase in several phosphatidylethanolamine (PE) and phosphatidylcholine (PC) species, particularly those with 40 or 42 carbon atoms in both fatty acyl chains together. 2D-imaging MS of the most differentially expressed phospholipids confirmed their differential abundance in cancer cells. We identified lipid markers that can discriminate tumor versus normal tissue and different NSCLC subtypes with an AUC (area under the ROC curve) of 0.999 and 0.885, respectively. In conclusion, using both shotgun and 2D-imaging lipidomics analysis, we uncovered a hitherto unrecognized alteration in phospholipid profiles in NSCLC. These changes may have important biological implications and may have significant potential for biomarker development.
Collapse
Affiliation(s)
- Eyra Marien
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, KU Leuven-University of Leuven, Leuven, Belgium
| | - Michael Meister
- Thoraxklinik at University Hospital Heidelberg, Translational Research Unit, Heidelberg, Germany.,TLRC-H - Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany
| | - Thomas Muley
- Thoraxklinik at University Hospital Heidelberg, Translational Research Unit, Heidelberg, Germany.,TLRC-H - Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany
| | - Steffen Fieuws
- Department of Public Health and Primary Care, I-Biostat KU Leuven-University of Leuven and Universiteit Hasselt, Leuven, Belgium
| | - Sergio Bordel
- Department of Chemical and Biological Engineering, Systems Biology Group, Chalmers University of Technology, Gothenburg, Sweden
| | - Rita Derua
- Department of Cellular and Molecular Medicine, Laboratory of Protein Phosphorylation and Proteomics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Jeffrey Spraggins
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN
| | - Raf Van de Plas
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN.,Delft University of Technology, Delft Center for Systems and Control, CD Delft, The Netherlands
| | - Jonas Dehairs
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, KU Leuven-University of Leuven, Leuven, Belgium
| | - Jens Wouters
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, KU Leuven-University of Leuven, Leuven, Belgium
| | - Muralidhararao Bagadi
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, KU Leuven-University of Leuven, Leuven, Belgium
| | - Hendrik Dienemann
- TLRC-H - Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany.,Department of Surgery, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Thomas
- TLRC-H - Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany.,Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Philipp A Schnabel
- TLRC-H - Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany.,University Hospital Heidelberg, Institute of Pathology, Heidelberg, Germany
| | - Richard M Caprioli
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN
| | - Etienne Waelkens
- Department of Cellular and Molecular Medicine, Laboratory of Protein Phosphorylation and Proteomics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Johannes V Swinnen
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, KU Leuven-University of Leuven, Leuven, Belgium
| |
Collapse
|
36
|
Beck TN, Chikwem AJ, Solanki NR, Golemis EA. Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer. Physiol Genomics 2014; 46:699-724. [PMID: 25096367 PMCID: PMC4187119 DOI: 10.1152/physiolgenomics.00062.2014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 08/04/2014] [Indexed: 12/22/2022] Open
Abstract
Bioinformatic approaches are intended to provide systems level insight into the complex biological processes that underlie serious diseases such as cancer. In this review we describe current bioinformatic resources, and illustrate how they have been used to study a clinically important example: epithelial-to-mesenchymal transition (EMT) in lung cancer. Lung cancer is the leading cause of cancer-related deaths and is often diagnosed at advanced stages, leading to limited therapeutic success. While EMT is essential during development and wound healing, pathological reactivation of this program by cancer cells contributes to metastasis and drug resistance, both major causes of death from lung cancer. Challenges of studying EMT include its transient nature, its molecular and phenotypic heterogeneity, and the complicated networks of rewired signaling cascades. Given the biology of lung cancer and the role of EMT, it is critical to better align the two in order to advance the impact of precision oncology. This task relies heavily on the application of bioinformatic resources. Besides summarizing recent work in this area, we use four EMT-associated genes, TGF-β (TGFB1), NEDD9/HEF1, β-catenin (CTNNB1) and E-cadherin (CDH1), as exemplars to demonstrate the current capacities and limitations of probing bioinformatic resources to inform hypothesis-driven studies with therapeutic goals.
Collapse
Affiliation(s)
- Tim N Beck
- Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, Pennsylvania; and
| | - Adaeze J Chikwem
- Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Temple University School of Medicine, Philadelphia, Pennsylvania; and
| | - Nehal R Solanki
- Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Program in Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Erica A Golemis
- Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Temple University School of Medicine, Philadelphia, Pennsylvania; and Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, Pennsylvania; and
| |
Collapse
|
37
|
Tan DSW, Wang W, Leong HS, Sew PH, Lau DP, Chong FT, Krisna SS, Lim TKH, Iyer NG. Tongue carcinoma infrequently harbor common actionable genetic alterations. BMC Cancer 2014; 14:679. [PMID: 25234657 PMCID: PMC4177593 DOI: 10.1186/1471-2407-14-679] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Oral tongue squamous cell carcinomas (TSCC) are a unique subset of head and neck cancers with a distinct demographic profile, where up to half of the cases are never smokers. A small proportion of patients with OSCC are known to respond to EGFR TKI. We used a high-sensitivity mass spectrometry-based mutation profiling platform to determine the EGFR mutation status, as well as other actionable alterations in a series of Asian TSCC. METHODS 66 TSCC patients treated between 1998-2009 with complete clinico-pathologic data were included in this study. Somatic mutation profiling was performed using Sequenom LungCarta v1.0, and correlated with clinical parameters. RESULTS Mutations were identified in 20/66(30.3%) of samples and involved TP53, STK11, MET, PIK3CA, BRAF and NRF2. No activating EGFR mutations or KRAS mutations were discovered in our series, where just over a third were never smokers. The most common mutations were in p53 (10.6%; n = 7) and MET (10.6%, n = 11) followed by STK11 (9.1%, n = 6) and PIK3CA (4.5%, n = 3). BRAF and NRF2 mutations, which are novel in TSCC, were demonstrated in one sample each. There was no significant correlation between overall mutation status and smoking history (p = 0.967) or age (p = 0.360). Positive MET alteration was associated with poorer loco-regional recurrence free survival (LRFS) of 11 months [vs 90 months in MET-negative group (p = 0.008)]. None of the other mutations were significantly correlated with LRFS or overall survival. Four of these tumors were propagated as immortalized cell lines and demonstrated the same mutations as the original tumor. CONCLUSIONS Using the Sequenom multiplexed LungCarta panel, we identified mutations in 6 genes, TP53, STK11, MET, PIK3CA, BRAF and NRF2, with the notable absence of EGFR and HER2 mutations in our series of Asian OSCC. Primary cell line models recapitulated the mutation profiles of the original primary tumours and provide an invaluable resource for experimental cancer therapeutics.
Collapse
Affiliation(s)
- Daniel SW Tan
- />Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
- />Department of Medical Oncology, National Cancer Centre, 11 Hospital Drive, Singapore, 169610 Singapore
| | - Weining Wang
- />Department of Surgical Oncology, National Cancer Centre, 11 Hospital Drive, Singapore, 169610 Singapore
| | - Hui Sun Leong
- />Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
| | - Pui Hoon Sew
- />Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
| | - Dawn P Lau
- />Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
| | - Fui Teen Chong
- />Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
| | - Sai Sakktee Krisna
- />Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
| | - Tony KH Lim
- />Department of Pathology, Singapore General Hospital, Outram Road, Singapore, 169610 Singapore
| | - N Gopalakrishna Iyer
- />Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
- />Department of Surgical Oncology, National Cancer Centre, 11 Hospital Drive, Singapore, 169610 Singapore
| |
Collapse
|