1
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Lin C, Lin K, Li P, Yuan H, Lin X, Dai Y, Zhang Y, Xie Z, Liu T, Wei C. A genomic instability-associated lncRNA signature for predicting prognosis and biomarkers in lung adenocarcinoma. Sci Rep 2024; 14:14460. [PMID: 38914679 PMCID: PMC11196711 DOI: 10.1038/s41598-024-65327-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/19/2024] [Indexed: 06/26/2024] Open
Abstract
Genomic instability (GI) was associated with tumorigenesis. However, GI-related lncRNA signature (GILncSig) in lung adenocarcinoma (LUAD) is still unknown. In this study, the lncRNA expression data, somatic mutation information and clinical survival information of LUAD were downloaded from The Cancer Genome Atlas (TCGA) and performed differential analysis. Functional and prognosis analysis revealed that multiple GI-related pathways were enriched. By using univariate and multivariate Cox regression analysis, 5 GI-associated lncRNAs (AC012085.2, FAM83A-AS1, MIR223HG, MIR193BHG, LINC01116) were identified and used to construct a GILncSig model. Mutation burden analysis indicated that the high-risk GI group had much higher somatic mutation count and the risk score constructed by the 5 GI-associated lncRNAs was an independent predictor for overall survival (OS) (P < 0.05). Overall, our study provides valuable insights into the involvement of GI-associated lncRNAs in LUAD and highlights their potential as therapeutic targets.
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Affiliation(s)
- Chunxuan Lin
- Department of Respiratory Medicine, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan, Guangdong, 528200, People's Republic of China
| | - Kunpeng Lin
- Department of Abdominal Oncosurgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Pan Li
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Hai Yuan
- Department of Cardio-Thoracic Surgery, Guangzhou Hospital of Integrated Chinese and Western Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Xiaochun Lin
- Department of Medical Examination Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, People's Republic of China
| | - Yong Dai
- Department of Respiratory Medicine, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan, Guangdong, 528200, People's Republic of China
| | - Yingying Zhang
- Department of Thoracic Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, 510095, People's Republic of China
| | - Zhijun Xie
- Department of Radiology Department, The Second People's Hospital of Jiangmen, Jiangmen, Guangdong, People's Republic of China
| | - Taisheng Liu
- Department of Thoracic Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, 510095, People's Republic of China.
| | - Chenggong Wei
- Department of Respiratory Medicine, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan, Guangdong, 528200, People's Republic of China.
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2
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N. Kachouie N, Deebani W, Shutaywi M, Christiani DC. Lung cancer clustering by identification of similarities and discrepancies of DNA copy numbers using maximal information coefficient. PLoS One 2024; 19:e0301131. [PMID: 38739669 PMCID: PMC11090345 DOI: 10.1371/journal.pone.0301131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/11/2024] [Indexed: 05/16/2024] Open
Abstract
Lung cancer is the second most diagnosed cancer and the first cause of cancer related death for men and women in the United States. Early detection is essential as patient survival is not optimal and recurrence rate is high. Copy number (CN) changes in cancer populations have been broadly investigated to identify CN gains and deletions associated with the cancer. In this research, the similarities between cancer and paired peripheral blood samples are identified using maximal information coefficient (MIC) and the spatial locations with substantially high MIC scores in each chromosome are used for clustering analysis. The results showed that a sizable reduction of feature set can be obtained using only a subset of locations with high MIC values. The clustering performance was evaluated using both true rate and normalized mutual information (NMI). Clustering results using the reduced feature set outperformed the performance of clustering using entire feature set in several chromosomes that are highly associated with lung cancer with several identified oncogenes.
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Affiliation(s)
- Nezamoddin N. Kachouie
- Department of Mathematics and Systems Engineering, Florida Institute of Technology, Melbourne, FL, United States of America
| | - Wejdan Deebani
- Mathematics Department, College of Science and Arts, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Meshal Shutaywi
- Mathematics Department, College of Science and Arts, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David C. Christiani
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, United States of America
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States of America
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3
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Chow SE, Hsu CC, Yang CT, Meir YJJ. YAP co-localizes with the mitotic spindle and midbody to safeguard mitotic division in lung-cancer cells. FEBS J 2023; 290:5704-5719. [PMID: 37549045 DOI: 10.1111/febs.16926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 06/22/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
YES-associated protein (YAP) is a part of the Hippo pathway, with pivotal roles in several developmental processes and dual functionality as both a tumor suppressor and an oncogene. In the present study, we identified YAP activity as a microtubular scaffold protein that maintains the stability of the mitotic spindle and midbody by physically interacting with α-tubulin during mitotic progression. The interaction of YAP and α-tubulin was evident in co-immunoprecipitation assays, as well as observing their co-localization in the microtubular structure of the mitotic spindle and midbody in immunostainings. With YAP depletion, levels of ECT2, MKLP-1, and Aurora B are reduced, which is consistent with YAP functioning in midbody formation during cytokinesis. The concomitant decrease in α-tubulin and increase in acetyl-α-tubulin during YAP depletion occurred at the post-transcriptional level. This suggests that YAP maintains the stability of the mitotic spindle and midbody, which ensures appropriate chromosome segregation during mitotic division. The increase in acetyl-α-tubulin during YAP depletion may provide a lesion-halting mechanism in maintaining the microtubule structure. The depletion of YAP also results in multinuclearity and aneuploidy, which supports its role in stabilizing the mitotic spindle and midbody.
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Affiliation(s)
- Shu-Er Chow
- Department of Otolaryngology-Head and Neck Surgery, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Nature Science, Center for General Studies, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Chi Hsu
- Department of Nature Science, Center for General Studies, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Ta Yang
- Department of Thoracic Medicine, Taoyuan Chang Gung Memorial Hospital, Taiwan
| | - Yaa-Jyuhn J Meir
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
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4
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Forder A, Zhuang R, Souza VGP, Brockley LJ, Pewarchuk ME, Telkar N, Stewart GL, Benard K, Marshall EA, Reis PP, Lam WL. Mechanisms Contributing to the Comorbidity of COPD and Lung Cancer. Int J Mol Sci 2023; 24:ijms24032859. [PMID: 36769181 PMCID: PMC9918127 DOI: 10.3390/ijms24032859] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/18/2023] [Accepted: 01/22/2023] [Indexed: 02/05/2023] Open
Abstract
Lung cancer and chronic obstructive pulmonary disease (COPD) often co-occur, and individuals with COPD are at a higher risk of developing lung cancer. While the underlying mechanism for this risk is not well understood, its major contributing factors have been proposed to include genomic, immune, and microenvironment dysregulation. Here, we review the evidence and significant studies that explore the mechanisms underlying the heightened lung cancer risk in people with COPD. Genetic and epigenetic changes, as well as the aberrant expression of non-coding RNAs, predispose the lung epithelium to carcinogenesis by altering the expression of cancer- and immune-related genes. Oxidative stress generated by tobacco smoking plays a role in reducing genomic integrity, promoting epithelial-mesenchymal-transition, and generating a chronic inflammatory environment. This leads to abnormal immune responses that promote cancer development, though not all smokers develop lung cancer. Sex differences in the metabolism of tobacco smoke predispose females to developing COPD and accumulating damage from oxidative stress that poses a risk for the development of lung cancer. Dysregulation of the lung microenvironment and microbiome contributes to chronic inflammation, which is observed in COPD and known to facilitate cancer initiation in various tumor types. Further, there is a need to better characterize and identify the proportion of individuals with COPD who are at a high risk for developing lung cancer. We evaluate possible novel and individualized screening strategies, including biomarkers identified in genetic studies and exhaled breath condensate analysis. We also discuss the use of corticosteroids and statins as chemopreventive agents to prevent lung cancer. It is crucial that we optimize the current methods for the early detection and management of lung cancer and COPD in order to improve the health outcomes for a large affected population.
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Affiliation(s)
- Aisling Forder
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Rebecca Zhuang
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Vanessa G P Souza
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
| | - Liam J Brockley
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Michelle E Pewarchuk
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nikita Telkar
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
- British Columbia Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Greg L Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Katya Benard
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Erin A Marshall
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Patricia P Reis
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
| | - Wan L Lam
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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5
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The Roles of EXO1 and RPA1 Polymorphisms in Prognosis of Lung Cancer Patients Treated with Platinum-Based Chemotherapy. DISEASE MARKERS 2022; 2022:3306189. [PMID: 36277983 PMCID: PMC9584701 DOI: 10.1155/2022/3306189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/29/2022] [Indexed: 12/24/2022]
Abstract
Background. Lung cancer is one of the major causes of cancer-related mortality worldwide. DNA repair and damage response contribute to genomic instability that accompanies tumor progression. In this study, we focus on evaluating association between DNA repair polymorphisms of EXO1, RPA1, and prognosis in lung cancer patients whom received platinum-based chemotherapy. Methods. 593 lung cancer patients were recruited in this study. We performed genotyping of 19 single nucleotide polymorphisms (SNPs) by Sequenom MassARRAY. Cox regression analysis was used to assess overall survival (OS) and progression-free survival (PFS) among SNP genotypes. Results. Significant differences in PFS and OS were observed in RPA1 rs5030740, EXO1 rs1776148, and rs1047840. Results showed that patients with CC genotype in rs5030740 (recessive model:
) had a better PFS. Patients with AA or/and AG genotypes in rs1776148 (additive model:
; dominant model:
) and AA genotype in rs1047840 (recessive model:
) had longer OS. We also demonstrated differences in subgroup analysis between rs5030740, rs1776148, rs1047840, and prognosis. Conclusions. Our results indicated that EXO1 rs1776148, rs1047840, and RPA1 rs5030740 were significantly associated with prognosis of lung cancer. Rs1776148, rs1047840, and rs5030740 may act as prognosis markers in lung cancer patients with platinum-based chemotherapy.
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6
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[DNA Damage Repair System and Antineoplastic Agents in Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2022; 25:434-442. [PMID: 35747923 PMCID: PMC9244503 DOI: 10.3779/j.issn.1009-3419.2022.101.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DNA damage repair (DDR) system plays an important role in maintaining of genomic stability. Accumulation of DNA lesions or deficiency of DDR system could drive tumorigenesis as well as promote tumor progression; meanwhile, they could also provide therapeutic opportunities and targets. Of all the antineoplastic agents of lung cancers, many of them targeted or were associated with DNA damage and repair pathways, such as chemotherapies and antibody-drug conjugates which were designed directly causing DNA damages, targeted drugs inhibiting DNA repair pathways, and immune-checkpoint inhibitors. In this review, we described the role of DNA damage and repair pathways in antitumor activity of the above agents, as well as summarized the application and clinical investigations of these antineoplastic agents in lung cancers, in order to provide more information for exploring precision and effective strategies for the treatment of lung cancer based on the mechanism of DNA damage and repair.
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7
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Nuclear p120 catenin is a component of the perichromosomal layer and coordinates sister chromatid segregation during mitosis in lung cancer cells. Cell Death Dis 2022; 13:526. [PMID: 35660718 PMCID: PMC9167299 DOI: 10.1038/s41419-022-04929-z] [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] [Received: 12/19/2021] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 01/21/2023]
Abstract
Abnormal expression of p120 catenin is associated with the malignant phenotype in human lung cancer. Numerous studies have focused on the function of p120 catenin in the juxta-membrane compartment. However, the role of nuclear p120 catenin remains unclear. In this study, the dynamic changes in nuclear p120 catenin localization during cell cycle progression were investigated. Immunofluorescent staining, FACS analysis, and western blotting revealed that nuclear p120 catenin is a major architectural constituent of the chromosome periphery during mitosis. During mitosis, granule-like p120 catenin dispersed into a cloudy-like structure and formed cordon-like structures surrounding the condensed chromosomes to create the peri-chromosomal layer. Interestingly, lumican and p120 catenin colocalized at the spindle fiber where the perichromosomal layer connects to the condensed chromosomes during mitosis. Furthermore, downregulation of p120 catenin using a specific siRNA induced cell cycle stalling in the G2/M phase and promoted aneuploidy. This study validates the role of nuclear p120 catenin in the formation of the chromosome periphery and reveals the p120 catenin-lumican interaction may couple orientation of cell division with the segregation of sister chromatids during mitosis. Our data suggest the protective role of p120 catenin in maintaining the integrity of chromosomes, and also warrants further studies to evaluate the contribution of the loss of p120 catenin to the creation of gene rearrangement in cancer evolution and tumor progression.
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8
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Khadse A, Haakensen VD, Silwal-Pandit L, Hamfjord J, Micke P, Botling J, Brustugun OT, Lingjærde OC, Helland Å, Kure EH. Prognostic Significance of the Loss of Heterozygosity of KRAS in Early-Stage Lung Adenocarcinoma. Front Oncol 2022; 12:873532. [PMID: 35574381 PMCID: PMC9098994 DOI: 10.3389/fonc.2022.873532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/31/2022] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is a common disease with a poor prognosis. Genomic alterations involving the KRAS gene are common in lung carcinomas, although much is unknown about how different mutations, deletions, and expressions influence the disease course. The first approval of a KRAS-directed inhibitor was recently approved by the FDA. Mutations in the KRAS gene have been associated with poor prognosis for lung adenocarcinomas, but implications of the loss of heterozygosity (LOH) of KRAS have not been investigated. In this study, we have assessed the LOH of KRAS in early-stage lung adenocarcinoma by analyzing DNA copy number profiles and have investigated the effect on patient outcome in association with mRNA expression and somatic hotspot mutations. KRAS mutation was present in 36% of cases and was associated with elevated mRNA expression. LOH in KRAS was associated with a favorable prognosis, more prominently in KRAS mutated than in wild-type patients. The presence of both LOH and mutation in KRAS conferred a better prognosis than KRAS mutation alone. For wild-type tumors, no difference in prognosis was observed between patients with and without LOH in KRAS. Our study indicates that LOH in KRAS is an independent prognostic factor that may refine the existing prognostic groups of lung adenocarcinomas.
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Affiliation(s)
- Anand Khadse
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Faculty of Technology, Natural Sciences and Maritime Sciences, Department of Natural Sciences and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
| | - Vilde D. Haakensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Oncology, Oslo University Hospital, Oslo, Norway
- *Correspondence: Vilde D. Haakensen,
| | - Laxmi Silwal-Pandit
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Julian Hamfjord
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Odd Terje Brustugun
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Section of Oncology, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway
| | - Ole Christian Lingjærde
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Åslaug Helland
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Oncology, Oslo University Hospital, Oslo, Norway
- Department of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Elin H. Kure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Faculty of Technology, Natural Sciences and Maritime Sciences, Department of Natural Sciences and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
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9
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Bjaanæs MM, Nilsen G, Halvorsen AR, Russnes HG, Solberg S, Jørgensen L, Brustugun OT, Lingjærde OC, Helland Å. Whole genome copy number analyses reveal a highly aberrant genome in TP53 mutant lung adenocarcinoma tumors. BMC Cancer 2021; 21:1089. [PMID: 34625038 PMCID: PMC8501630 DOI: 10.1186/s12885-021-08811-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/23/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genetic alterations are common in non-small cell lung cancer (NSCLC), and DNA mutations and translocations are targets for therapy. Copy number aberrations occur frequently in NSCLC tumors and may influence gene expression and further alter signaling pathways. In this study we aimed to characterize the genomic architecture of NSCLC tumors and to identify genomic differences between tumors stratified by histology and mutation status. Furthermore, we sought to integrate DNA copy number data with mRNA expression to find genes with expression putatively regulated by copy number aberrations and the oncogenic pathways associated with these affected genes. METHODS Copy number data were obtained from 190 resected early-stage NSCLC tumors and gene expression data were available from 113 of the adenocarcinomas. Clinical and histopathological data were known, and EGFR-, KRAS- and TP53 mutation status was determined. Allele-specific copy number profiles were calculated using ASCAT, and regional copy number aberration were subsequently obtained and analyzed jointly with the gene expression data. RESULTS The NSCLC tumors tissue displayed overall complex DNA copy number profiles with numerous recurrent aberrations. Despite histological differences, tissue samples from squamous cell carcinomas and adenocarcinomas had remarkably similar copy number patterns. The TP53-mutated lung adenocarcinomas displayed a highly aberrant genome, with significantly altered copy number profiles including gains, losses and focal complex events. The EGFR-mutant lung adenocarcinomas had specific arm-wise aberrations particularly at chromosome7p and 9q. A large number of genes displayed correlation between copy number and expression level, and the PI(3)K-mTOR pathway was highly enriched for such genes. CONCLUSIONS The genomic architecture in NSCLC tumors is complex, and particularly TP53-mutated lung adenocarcinomas displayed highly aberrant copy number profiles. We suggest to always include TP53-mutation status when studying copy number aberrations in NSCLC tumors. Copy number may further impact gene expression and alter cellular signaling pathways.
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MESH Headings
- Adenocarcinoma of Lung/genetics
- Adenocarcinoma of Lung/pathology
- Alleles
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Chromosomes, Human, Pair 7
- Chromosomes, Human, Pair 9
- Class I Phosphatidylinositol 3-Kinases/genetics
- DNA Copy Number Variations
- Ex-Smokers
- Female
- Gene Dosage
- Gene Expression
- Genes, erbB-1/genetics
- Genes, p53
- Genes, ras/genetics
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Male
- Non-Smokers
- Polymorphism, Single Nucleotide
- Signal Transduction/genetics
- Smokers
- TOR Serine-Threonine Kinases/genetics
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Affiliation(s)
- Maria Moksnes Bjaanæs
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway
- Department of Oncology, Oslo University Hospital, 4950 Nydalen Oslo, Norway
| | - Gro Nilsen
- Department of Computer Science, University of Oslo, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ann Rita Halvorsen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway
| | - Hege G. Russnes
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Steinar Solberg
- Department of Cardiothoracic Surgery, Oslo University Hospital, Oslo, Norway
| | - Lars Jørgensen
- Department of Cardiothoracic Surgery, Oslo University Hospital, Oslo, Norway
| | - Odd Terje Brustugun
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway
- Section of Oncology, Vestre Viken Hospital, Drammen, Norway
| | - Ole Christian Lingjærde
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway
- Department of Computer Science, University of Oslo, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Åslaug Helland
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway
- Department of Oncology, Oslo University Hospital, 4950 Nydalen Oslo, Norway
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10
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Pisapia P, Pepe F, Sgariglia R, Nacchio M, Russo G, Gragnano G, Conticelli F, Salatiello M, De Luca C, Girolami I, Eccher A, Iaccarino A, Bellevicine C, Vigliar E, Malapelle U, Troncone G. Methods for actionable gene fusion detection in lung cancer: now and in the future. Pharmacogenomics 2021; 22:833-847. [PMID: 34525844 DOI: 10.2217/pgs-2021-0048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Although gene fusions occur rarely in non-small-cell lung cancer (NSCLC) patients, they represent a relevant target in treatment decision algorithms. To date, immunohistochemistry and fluorescence in situ hybridization are the two principal methods used in clinical trials. However, using these methods in routine clinical practice is often impractical and time consuming because they can only analyze single genes and the quantity of tissue material is often insufficient. Thus, novel technologies, able to test multiple genes in a single run with minimal sample input, are being under investigation. Here, we discuss the utility of next-generation sequencing and nCounter technologies in detecting simultaneous gene fusions in NSCLC patients.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Floriana Conticelli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Maria Salatiello
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Caterina De Luca
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Ilaria Girolami
- Division of Pathology, Central Hospital Bolzano, Bolzano, Italy
| | - Albino Eccher
- Department of Pathology & Diagnostics, University & Hospital Trust of Verona, Verona, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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11
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Huang R, Zhou PK. DNA damage repair: historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy. Signal Transduct Target Ther 2021; 6:254. [PMID: 34238917 PMCID: PMC8266832 DOI: 10.1038/s41392-021-00648-7] [Citation(s) in RCA: 234] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/28/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Genomic instability is the hallmark of various cancers with the increasing accumulation of DNA damage. The application of radiotherapy and chemotherapy in cancer treatment is typically based on this property of cancers. However, the adverse effects including normal tissues injury are also accompanied by the radiotherapy and chemotherapy. Targeted cancer therapy has the potential to suppress cancer cells' DNA damage response through tailoring therapy to cancer patients lacking specific DNA damage response functions. Obviously, understanding the broader role of DNA damage repair in cancers has became a basic and attractive strategy for targeted cancer therapy, in particular, raising novel hypothesis or theory in this field on the basis of previous scientists' findings would be important for future promising druggable emerging targets. In this review, we first illustrate the timeline steps for the understanding the roles of DNA damage repair in the promotion of cancer and cancer therapy developed, then we summarize the mechanisms regarding DNA damage repair associated with targeted cancer therapy, highlighting the specific proteins behind targeting DNA damage repair that initiate functioning abnormally duo to extrinsic harm by environmental DNA damage factors, also, the DNA damage baseline drift leads to the harmful intrinsic targeted cancer therapy. In addition, clinical therapeutic drugs for DNA damage and repair including therapeutic effects, as well as the strategy and scheme of relative clinical trials were intensive discussed. Based on this background, we suggest two hypotheses, namely "environmental gear selection" to describe DNA damage repair pathway evolution, and "DNA damage baseline drift", which may play a magnified role in mediating repair during cancer treatment. This two new hypothesis would shed new light on targeted cancer therapy, provide a much better or more comprehensive holistic view and also promote the development of new research direction and new overcoming strategies for patients.
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Affiliation(s)
- Ruixue Huang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China.
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12
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Geng W, Lv Z, Fan J, Xu J, Mao K, Yin Z, Qing W, Jin Y. Identification of the Prognostic Significance of Somatic Mutation-Derived LncRNA Signatures of Genomic Instability in Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:657667. [PMID: 33855028 PMCID: PMC8039462 DOI: 10.3389/fcell.2021.657667] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/11/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Lung adenocarcinoma (LUAD) is a highly heterogeneous tumor with substantial somatic mutations and genome instability, which are emerging hallmarks of cancer. Long non-coding RNAs (lncRNAs) are promising cancer biomarkers that are reportedly involved in genomic instability. However, the identification of genome instability-related lncRNAs (GInLncRNAs) and their clinical significance has not been investigated in LUAD. Methods: We determined GInLncRNAs by combining somatic mutation and transcriptome data of 457 patients with LUAD and probed their potential function using co-expression network and Gene Ontology (GO) enrichment analyses. We then filtered GInLncRNAs by Cox regression and LASSO regression to construct a genome instability-related lncRNA signature (GInLncSig). We subsequently evaluated GInLncSig using correlation analyses with mutations, external validation, model comparisons, independent prognostic significance analyses, and clinical stratification analyses. Finally, we established a nomogram for prognosis prediction in patients with LUAD and validated it in the testing set and the entire TCGA dataset. Results: We identified 161 GInLncRNAs, of which seven were screened to develop a prognostic GInLncSig model (LINC01133, LINC01116, LINC01671, FAM83A-AS1, PLAC4, MIR223HG, and AL590226.1). GInLncSig independently predicted the overall survival of patients with LUAD and displayed an improved performance compared to other similar signatures. Furthermore, GInLncSig was related to somatic mutation patterns, suggesting its ability to reflect genome instability in LUAD. Finally, a nomogram comprising the GInLncSig and tumor stage exhibited improved robustness and clinical practicability for predicting patient prognosis. Conclusion: Our study identified a signature for prognostic prediction in LUAD comprising seven lncRNAs associated with genome instability, which may provide a useful indicator for clinical stratification management and treatment decisions for patients with LUAD.
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Affiliation(s)
- Wei Geng
- NHC Key Laboratory of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhilei Lv
- NHC Key Laboratory of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinshuo Fan
- NHC Key Laboratory of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juanjuan Xu
- NHC Key Laboratory of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kaimin Mao
- NHC Key Laboratory of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhengrong Yin
- NHC Key Laboratory of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wanlu Qing
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yang Jin
- NHC Key Laboratory of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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13
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Andonegui-Elguera SD, Zamora-Fuentes JM, Espinal-Enríquez J, Hernández-Lemus E. Loss of Long Distance Co-Expression in Lung Cancer. Front Genet 2021; 12:625741. [PMID: 33777098 PMCID: PMC7987938 DOI: 10.3389/fgene.2021.625741] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/29/2021] [Indexed: 12/13/2022] Open
Abstract
Lung cancer is one of the deadliest, most aggressive cancers. Abrupt changes in gene expression represent an important challenge to understand and fight the disease. Gene co-expression networks (GCNs) have been widely used to study the genomic regulatory landscape of human cancer. Here, based on 1,143 RNA-Seq experiments from the TCGA collaboration, we constructed GCN for the most common types of lung tumors: adenocarcinoma (TAD) and squamous cells (TSCs) as well as their respective control networks (NAD and NSC). We compared the number of intra-chromosome (cis-) and inter-chromosome (trans-) co-expression interactions in normal and cancer GCNs. We compared the number of shared interactions between TAD and TSC, as well as in NAD and NSC, to observe which phenotypes were more alike. By means of an over-representation analysis, we associated network topology features with biological functions. We found that TAD and TSC present mostly cis- small disconnected components, whereas in control GCNs, both types have a giant trans- component. In both cancer networks, we observed cis- components in which genes not only belong to the same chromosome but to the same cytoband or to neighboring cytobands. This supports the hypothesis that in lung cancer, gene co-expression is constrained to small neighboring regions. Despite this loss of distant co-expression observed in TAD and TSC, there are some remaining trans- clusters. These clusters seem to play relevant roles in the carcinogenic processes. For instance, some clusters in TAD and TSC are associated with the immune system, response to virus, or control of gene expression. Additionally, other non-enriched trans- clusters are composed of one gene and several associated pseudo-genes, as in the case of the FTH1 gene. The appearance of those common trans- clusters reflects that the gene co-expression program in lung cancer conserves some aspects for cell maintenance. Unexpectedly, 0.48% of the edges are shared between control networks; conversely, 35% is shared between lung cancer GCNs, a 73-fold larger intersection. This suggests that in lung cancer a process of de-differentiation may be occurring. To further investigate the implications of the loss of distant co-expression, it will become necessary to broaden the investigation with other omic-based approaches. However, the present approach provides a basis for future work toward an integrative perspective of abnormal transcriptional regulatory programs in lung cancer.
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Affiliation(s)
| | | | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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14
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Zhou CS, Feng MT, Chen X, Gao Y, Chen L, Li LD, Li DH, Cao YQ. Exonuclease 1 (EXO1) is a Potential Prognostic Biomarker and Correlates with Immune Infiltrates in Lung Adenocarcinoma. Onco Targets Ther 2021; 14:1033-1048. [PMID: 33623391 PMCID: PMC7894803 DOI: 10.2147/ott.s286274] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/16/2021] [Indexed: 12/16/2022] Open
Abstract
Background Exonuclease 1 (EXO1) has been identified to be highly expressed in different human malignancies, but its expression and prognostic role in lung adenocarcinoma (LUAD) remain unknown. Materials and Methods Two independent cohorts extracted from public databases and one cohort from our center were analyzed in this study. Expression levels of EXO1 in LUAD tissues and paired para-cancer tissues were detected. The prognostic value of EXO1 in LUAD patients was evaluated in the three cohorts. Enrichment analyses were performed to explore the possible underlying biological pathways. Moreover, we also explored the correlations between EXO1 and tumor-infiltrating immune cells and evaluated the impact of EXO1 knock-down on the migration of lung cancer cells. Results In this study, we found that EXO1 was highly expressed in LUAD tissues compared with para-cancerous tissues in public databases (p < 0.01), which was consistent with our data (p < 0.01). Survival analysis indicated that high expression of EXO1 was associated with poor prognosis in LUAD (p < 0.01). Enrichment analyses indicated that biological pathways like cell cycle regulation, DNA damage and repair, immune response, neuroactive ligand-receptor interaction, may be associated with EXO1 aberrant expression. Moreover, high expression of EXO1 was correlated with decreased infiltrating B cells (p < 0.01) and CD4+ T cells (p < 0.01) levels, and low infiltrating levels of B cells (p < 0.01) and dendritic cells (DCs) (p < 0.05) indicated poor overall survival (OS) in LUAD. Additionally, in vitro experiments suggested that knockdown of EXO1 may inhibit the migratory ability of lung cancer cells. Conclusion In conclusion, EXO1 is a potential prognostic biomarker in LUAD, and correlates with infiltrating levels of immune cells in the tumor microenvironment. Further prospective validation of EXO1 in lung cancer is warranted.
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Affiliation(s)
- Chang-Shuai Zhou
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Ming-Tao Feng
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Xin Chen
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Yang Gao
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Lei Chen
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Liang-Dong Li
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - De-Heng Li
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Yi-Qun Cao
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
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15
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Platelet-Activating Factor-Receptor Signaling Mediates Targeted Therapies-Induced Microvesicle Particles Release in Lung Cancer Cells. Int J Mol Sci 2020; 21:ijms21228517. [PMID: 33198218 PMCID: PMC7696385 DOI: 10.3390/ijms21228517] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/25/2022] Open
Abstract
Microvesicle particles (MVP) secreted by a variety of cell types in response to reactive oxygen species (ROS)-generating pro-oxidative stressors have been implicated in modifying the cellular responses including the sensitivity to therapeutic agents. Our previous studies have shown that expression of a G-protein coupled, platelet-activating factor-receptor (PAFR) pathway plays critical roles in pro-oxidative stressors-mediated cancer growth and MVP release. As most therapeutic agents act as pro-oxidative stressors, the current studies were designed to determine the role of the PAFR signaling in targeted therapies (i.e., gefitinib and erlotinib)-mediated MVP release and underlying mechanisms using PAFR-expressing human A549 and H1299 non-small cell lung cancer (NSCLC) cell lines. Our studies demonstrate that both gefitinib and erlotinib generate ROS in a dose-dependent manner in a process blocked by antioxidant and PAFR antagonist, verifying their pro-oxidative stressor’s ability, and the role of the PAFR in this effect. We observed that these targeted therapies induce MVP release in a dose- and time-dependent manner, similar to a PAFR-agonist, carbamoyl-PAF (CPAF), and PAFR-independent agonist, phorbol myristate acetate (PMA), used as positive controls. To confirm the PAFR dependency, we demonstrate that siRNA-mediated PAFR knockdown or PAFR antagonist significantly blocked only targeted therapies- and CPAF-mediated but not PMA-induced MVP release. The use of pharmacologic inhibitor strategy suggested the involvement of the lipid ceramide-generating enzyme, acid sphingomyelinase (aSMase) in MVP biogenesis, and observed that regardless of the stimuli used, aSMase inhibition significantly blocked MVP release. As mitogen-activated protein kinase (MAPK; ERK1/2 and p38) pathways crosstalk with PAFR, their inhibition also significantly attenuated targeted therapies-mediated MVP release. These findings indicate that PAFR signaling could be targeted to modify cellular responses of targeted therapies in lung cancer cells.
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16
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Association between Metabolites and the Risk of Lung Cancer: A Systematic Literature Review and Meta-Analysis of Observational Studies. Metabolites 2020; 10:metabo10090362. [PMID: 32899527 PMCID: PMC7570231 DOI: 10.3390/metabo10090362] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022] Open
Abstract
Globally, lung cancer is the most prevalent cancer type. However, screening and early detection is challenging. Previous studies have identified metabolites as promising lung cancer biomarkers. This systematic literature review and meta-analysis aimed to identify metabolites associated with lung cancer risk in observational studies. The literature search was performed in PubMed and EMBASE databases, up to 31 December 2019, for observational studies on the association between metabolites and lung cancer risk. Heterogeneity was assessed using the I2 statistic and Cochran’s Q test. Meta-analyses were performed using either a fixed-effects or random-effects model, depending on study heterogeneity. Fifty-three studies with 297 metabolites were included. Most identified metabolites (252 metabolites) were reported in individual studies. Meta-analyses were conducted on 45 metabolites. Five metabolites (cotinine, creatinine riboside, N-acetylneuraminic acid, proline and r-1,t-2,3,c-4-tetrahydroxy-1,2,3,4-tetrahydrophenanthrene) and five metabolite groups (total 3-hydroxycotinine, total cotinine, total nicotine, total 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (sum of concentrations of the metabolite and its glucuronides), and total nicotine equivalent (sum of total 3-hydroxycotinine, total cotinine and total nicotine)) were associated with higher lung cancer risk, while three others (folate, methionine and tryptophan) were associated with lower lung cancer risk. Significant heterogeneity was detected across most studies. These significant metabolites should be further evaluated as potential biomarkers for lung cancer.
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17
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Chen J, Mi X, Ning J, He X, Hu J. A tail-based test to detect differential expression in RNA-sequencing data. Stat Methods Med Res 2020; 30:261-276. [PMID: 32867604 DOI: 10.1177/0962280220951907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RNA sequencing data have been abundantly generated in biomedical research for biomarker discovery and other studies. Such data at the exon level are usually heavily tailed and correlated. Conventional statistical tests based on the mean or median difference for differential expression likely suffer from low power when the between-group difference occurs mostly in the upper or lower tail of the distribution of gene expression. We propose a tail-based test to make comparisons between groups in terms of a specific distribution area rather than a single location. The proposed test, which is derived from quantile regression, adjusts for covariates and accounts for within-sample dependence among the exons through a specified correlation structure. Through Monte Carlo simulation studies, we show that the proposed test is generally more powerful and robust in detecting differential expression than commonly used tests based on the mean or a single quantile. An application to TCGA lung adenocarcinoma data demonstrates the promise of the proposed method in terms of biomarker discovery.
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Affiliation(s)
- Jiong Chen
- Data Science, LinkedIn, Mountain View, CA, USA
| | - Xinlei Mi
- Department of Biostatistics, Columbia University, New York, NY, USA
| | - Jing Ning
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xuming He
- Department of Statistics, University of Michigan at Ann Arbor, Ann Arbor, MI, USA
| | - Jianhua Hu
- Department of Biostatistics, Columbia University, New York, NY, USA
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18
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Burgess JT, Rose M, Boucher D, Plowman J, Molloy C, Fisher M, O'Leary C, Richard DJ, O'Byrne KJ, Bolderson E. The Therapeutic Potential of DNA Damage Repair Pathways and Genomic Stability in Lung Cancer. Front Oncol 2020; 10:1256. [PMID: 32850380 PMCID: PMC7399071 DOI: 10.3389/fonc.2020.01256] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/17/2020] [Indexed: 12/16/2022] Open
Abstract
Despite advances in our understanding of the molecular biology of the disease and improved therapeutics, lung cancer remains the most common cause of cancer-related deaths worldwide. Therefore, an unmet need remains for improved treatments, especially in advanced stage disease. Genomic instability is a universal hallmark of all cancers. Many of the most commonly prescribed chemotherapeutics, including platinum-based compounds such as cisplatin, target the characteristic genomic instability of tumors by directly damaging the DNA. Chemotherapies are designed to selectively target rapidly dividing cells, where they cause critical DNA damage and subsequent cell death (1, 2). Despite the initial efficacy of these drugs, the development of chemotherapy resistant tumors remains the primary concern for treatment of all lung cancer patients. The correct functioning of the DNA damage repair machinery is essential to ensure the maintenance of normal cycling cells. Dysregulation of these pathways promotes the accumulation of mutations which increase the potential of malignancy. Following the development of the initial malignancy, the continued disruption of the DNA repair machinery may result in the further progression of metastatic disease. Lung cancer is recognized as one of the most genomically unstable cancers (3). In this review, we present an overview of the DNA damage repair pathways and their contributions to lung cancer disease occurrence and progression. We conclude with an overview of current targeted lung cancer treatments and their evolution toward combination therapies, including chemotherapy with immunotherapies and antibody-drug conjugates and the mechanisms by which they target DNA damage repair pathways.
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Affiliation(s)
- Joshua T Burgess
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Maddison Rose
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Didier Boucher
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Jennifer Plowman
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Christopher Molloy
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Mark Fisher
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Connor O'Leary
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia.,Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Derek J Richard
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Kenneth J O'Byrne
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia.,Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Emma Bolderson
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia.,Princess Alexandra Hospital, Brisbane, QLD, Australia
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19
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Chauhan V, Sherman S, Said Z, Yauk CL, Stainforth R. A case example of a radiation-relevant adverse outcome pathway to lung cancer. Int J Radiat Biol 2020; 97:68-84. [PMID: 31846388 DOI: 10.1080/09553002.2019.1704913] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Adverse outcome pathways (AOPs) describe how a measurable sequence of key events, beginning from a molecular initiator, can lead to an adverse outcome of relevance to risk assessment. An AOP is modular by design, comprised of four main components: (1) a Molecular Initiating Event (MIE), (2) Key Events (KEs), (3) Key Event Relationships (KERs) and (4) an Adverse Outcome (AO). PURPOSE Here, we illustrate the utility of the AOP concept through a case example in the field of ionizing radiation, using the Organisation for Economic Cooperation and Development (OECD) Users' Handbook. This AOP defines a classic targeted response to a radiation insult with an AO of lung cancer that is relevant to radon gas exposure. MATERIALS AND METHODS To build this AOP, over 500 papers were reviewed and categorized based on the modified Bradford-Hill Criteria. Data-rich key events from the MIE, to several measurable KEs and KERs related to DNA damage response/repair were identified. RESULTS The components for this AOP begin with direct deposition of energy as the MIE. Energy deposited into a cell can lead to multiple ionization events to targets such as DNA. This energy can damage DNA leading to double-strand breaks (DSBs) (KE1), this will initiate repair activation (KE2) in higher eukaryotes through mechanisms that are quick and efficient, but error-prone. If DSBs occur in regions of the DNA transcribing critical genes, then mutations (KE3) generated through faulty repair may alter the function of these genes or may cause chromosomal aberrations (KE4). This can impact cellular pathways such as cell growth, cell cycling and then cellular proliferation (KE5). This will form hyperplasia in lung cells, leading eventually to lung cancer (AO) induction and metastasis. The weight of evidence for the KERs was built using biological plausibility, incidence concordance, dose-response, time-response and essentiality studies. The uncertainties and inconsistencies surrounding this AOP are centered on dose-response relationships associated with dose, dose-rates and radiation quality. CONCLUSION Overall, the AOP framework provided an effective means to organize the scientific knowledge surrounding the KERs and identify those with strong dose-response relationships and those with inconsistencies. This case study is an example of how the AOP methodology can be applied to sources of radiation to help support areas of risk assessment.
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Affiliation(s)
- Vinita Chauhan
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Samantha Sherman
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Zakaria Said
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Robert Stainforth
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
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20
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Zito Marino F, Bianco R, Accardo M, Ronchi A, Cozzolino I, Morgillo F, Rossi G, Franco R. Molecular heterogeneity in lung cancer: from mechanisms of origin to clinical implications. Int J Med Sci 2019; 16:981-989. [PMID: 31341411 PMCID: PMC6643125 DOI: 10.7150/ijms.34739] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 05/05/2019] [Indexed: 12/13/2022] Open
Abstract
Molecular heterogeneity is a frequent event in cancer responsible of several critical issues in diagnosis and treatment of oncologic patients. Lung tumours are characterized by high degree of molecular heterogeneity associated to different mechanisms of origin including genetic, epigenetic and non-genetic source. In this review, we provide an overview of recognized mechanisms underlying molecular heterogeneity in lung cancer, including epigenetic mechanisms, mutant allele specific imbalance, genomic instability, chromosomal aberrations, tumor mutational burden, somatic mutations. We focus on the role of spatial and temporal molecular heterogeneity involved in therapeutic implications in lung cancer patients.
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Affiliation(s)
| | - Roberto Bianco
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | - Marina Accardo
- Pathology Unit, University of Campania "L. Vanvitelli", Naples, Italy
| | - Andrea Ronchi
- Pathology Unit, University of Campania "L. Vanvitelli", Naples, Italy
| | | | - Floriana Morgillo
- Medical Oncology, Department of Precision Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Giulio Rossi
- Pathology Unit, Hospital S. Maria delle Croci, Azienda Romagna, Ravenna, Italy
| | - Renato Franco
- Pathology Unit, University of Campania "L. Vanvitelli", Naples, Italy
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21
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Qi X, Yu Y, Ji N, Ren S, Xu Y, Liu H. Genetic risk analysis for an individual according to the theory of programmed onset, illustrated by lung and liver cancers. Gene 2018; 673:107-111. [PMID: 29913241 DOI: 10.1016/j.gene.2018.06.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/31/2018] [Accepted: 06/14/2018] [Indexed: 11/19/2022]
Abstract
OBJECTIVE To investigate cancer association in the genome and the genetic risk of death from major cancers according to the theory of programmed onset for an individual. METHODS Alleles of 15 randomly selected short tandem repeat (STR) loci, including D6S1043, D12S391, CSF1PO, D7S820, D2S1338, D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D16S539 and D19S433, were determined in 50 patients with lung cancer and 50 patients with liver cancer. The onset age of patients with and without the alleles was compared with Cox regression. Frequencies of significant alleles from Cox regression between the cancer group and control population were analysed through logistic regression for cross-validation. The death probability in an individual carrying two or one of two cancer-related alleles or not carrying two cancer-related alleles was calculated with outcomes of case-control studies translated into the results of the cohort studies. RESULTS It was confirmed that D18S51-20 was a lung cancer-related allele and that D21S11-30.2 and D6S1043-18 were liver cancer-related alleles. Probabilities of death from lung or liver cancers ranged from 0.115 to 0.395, respectively, for those who carry and/or do not carry D18S51-20, D21S11-30.2, D6S1043-18. CONCLUSIONS A more efficient method could be devised for genetic risk analysis according to the theory of programmed onset. The analysis of the CODIS-STR loci (STR loci listed in the US combined DNA indexing system) as genetic markers may provide an efficient and reliable approach to estimate an individual's genetic predisposition.
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Affiliation(s)
- Xia Qi
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
| | - Yuanjun Yu
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
| | - Na Ji
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
| | - Sashuang Ren
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
| | - Yongcheng Xu
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
| | - Hui Liu
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China.
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22
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Lee RC, Thapa B, John T. LACES and bootstraps: the hunt for prognostic and predictive markers for adjuvant therapy in NSCLC. Transl Lung Cancer Res 2018; 7:S239-S242. [PMID: 30393612 PMCID: PMC6193923 DOI: 10.21037/tlcr.2018.09.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/03/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Rachael Chang Lee
- Olivia Newton-John Cancer Centre, Austin Health, Melbourne, Australia
| | - Bibhusal Thapa
- Olivia Newton-John Cancer Centre, Austin Health, Melbourne, Australia
| | - Thomas John
- Olivia Newton-John Cancer Centre, Austin Health, Melbourne, Australia
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23
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Tsiambas E, Mastronikolis NS, Lefas AY, Georgiannos SN, Ragos V, Fotiades PP, Tsoukalas N, Kavantzas N, Karameris A, Peschos D, Patsouris E, Syrigos K. Chromosome 7 Multiplication in EGFR-positive Lung Carcinomas Based on Tissue Microarray Analysis. ACTA ACUST UNITED AC 2018; 31:641-648. [PMID: 28652432 DOI: 10.21873/invivo.11106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 05/07/2017] [Accepted: 05/08/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND/AIM Epidermal growth factor receptor (EGFR) over-activation is observed in significant proportions of non-small cell lung carcinomas (NSCLC). Our aim was to investigate the role of chromosome 7 multiplication with regard to its influence in EGFR expression, combined or not with gene amplification. MATERIALS AND METHODS Using tissue microarray technology, fifty (n=50) primary NSCLCs were cored and re-embedded into the final recipient block. Immunohistochemistry (IHC) and also chromogenic in situ hybridization (CISH) were performed. RESULTS EGFR expression at any level was detected in 40/50 (80%) cores. Over-expression was observed in 23/40 (57.5%) cases. Gene amplification was identified in 11/50 (22%) cases whereas chromosome 7 polysomy in 8/50 (16%) cases. Pure chromosome 7 multiplication alone led to low or moderate levels of expression. Overall EGFR expression was correlated with gene (p=0.001) and interestingly with chromosome 7 centromere numerical imbalances (p=0.004). CONCLUSION EGFR expression is associated not only with amplification, but also with chromosome 7 centromere multiple copies. Chromosome 7 multiplication -due to centromere region amplification or true polysomy- is critical for applying monoclonal antibody targeted therapeutic strategies excluding the pure non-amplified cases.
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Affiliation(s)
- Evangelos Tsiambas
- Department of IHC & Molecular Biology, 401 GAH, Athens, Greece .,Department of Pathology, Medical School, University of Athens, Athens, Greece
| | | | - Alicia Y Lefas
- Faculty of Medicine, University of Southampton, Southampton, U.K
| | - Stavros N Georgiannos
- Department of Breast Surgery, Blue Cross Hospital Breast Cancer Action Fund, London, U.K
| | - Vasileios Ragos
- Department of Maxillofacial, School of Medicine, University of Ioannina, Ioannina, Greece
| | | | | | - Nikolaos Kavantzas
- Department of Pathology, Medical School, University of Athens, Athens, Greece
| | | | - Dimitrios Peschos
- Department of Physiology, Medical School, University of Ioannina, Ioannina, Greece
| | | | - Konstantinos Syrigos
- 3rd Department of Medicine, Athens School of Medicine, "Sotiria" General Hospital, Athens, Greece
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24
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Chromosome aberrations in peripheral blood lymphocytes of lung cancer patients exposed to radon and air pollution. Eur J Cancer Prev 2018; 27:6-12. [DOI: 10.1097/cej.0000000000000270] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Gazdar AF, Bunn PA, Minna JD. Small-cell lung cancer: what we know, what we need to know and the path forward. Nat Rev Cancer 2017; 17:725-737. [PMID: 29077690 DOI: 10.1038/nrc.2017.87] [Citation(s) in RCA: 423] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Small-cell lung cancer (SCLC) is a deadly tumour accounting for approximately 15% of lung cancers and is pathologically, molecularly, biologically and clinically very different from other lung cancers. While the majority of tumours express a neuroendocrine programme (integrating neural and endocrine properties), an important subset of tumours have low or absent expression of this programme. The probable initiating molecular events are inactivation of TP53 and RB1, as well as frequent disruption of several signalling networks, including Notch signalling. SCLC, when diagnosed, is usually widely metastatic and initially responds to cytotoxic therapy but nearly always rapidly relapses with resistance to further therapies. There were no important therapeutic clinical advances for 30 years, leading SCLC to be designated a 'recalcitrant cancer'. Scientific studies are hampered by a lack of tissue availability. However, over the past 5 years, there has been a worldwide resurgence of studies on SCLC, including comprehensive molecular analyses, the development of relevant genetically engineered mouse models and the establishment of patient-derived xenografts. These studies have led to the discovery of new potential therapeutic vulnerabilities for SCLC and therefore to new clinical trials. Thus, while the past has been bleak, the future offers greater promise.
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Affiliation(s)
- Adi F Gazdar
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75230-8593, USA
- Department of Pathology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75230-8593, USA
| | - Paul A Bunn
- Division of Medical Oncology, University of Colorado Cancer Center, 12801 East 17th Avenue, Aurora, Colorado 80045, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75230-8593, USA
- Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75230-8593, USA
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26
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Li YW, Bai L, Dai LX, He X, Zhou XP. Chromosomal and Genetic Analysis of a Human Lung Adenocarcinoma Cell Line OM. Chin Med J (Engl) 2017; 129:405-9. [PMID: 26879013 PMCID: PMC4800840 DOI: 10.4103/0366-6999.176066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Background: Lung cancer has become the leading cause of death in many regions. Carcinogenesis is caused by the stepwise accumulation of genetic and chromosomal changes. The aim of this study was to investigate the chromosome and gene alterations in the human lung adenocarcinoma cell line OM. Methods: We used Giemsa banding and multiplex fluorescence in situ hybridization focusing on the human lung adenocarcinoma cell line OM to analyze its chromosome alterations. In addition, the gains and losses in the specific chromosome regions were identified by comparative genomic hybridization (CGH) and the amplifications of cancer-related genes were also detected by polymerase chain reaction (PCR). Results: We identified a large number of chromosomal numerical alterations on all chromosomes except chromosome X and 19. Chromosome 10 is the most frequently involved in translocations with six different interchromosomal translocations. CGH revealed the gains on chromosome regions of 3q25.3-28, 5p13, 12q22-23.24, and the losses on 3p25-26, 6p25, 6q26-27, 7q34-36, 8p22-23, 9p21-24, 10q25-26.3, 12p13.31-13.33 and 17p13.1-13.3. And PCR showed the amplification of genes: Membrane metalloendopeptidase (MME), sucrase-isomaltase (SI), butyrylcholinesterase (BCHE), and kininogen (KNG). Conclusions: The lung adenocarcinoma cell line OM exhibited multiple complex karyotypes, and chromosome 10 was frequently involved in chromosomal translocation, which may play key roles in tumorigenesis. We speculated that the oncogenes may be located at 3q25.3-28, 5p13, 12q22-23.24, while tumor suppressor genes may exist in 3p25-26, 6p25, 6q26-27, 7q34-36, 8p22-23, 9p21-24, 10q25-26.3, 12p13.31-13.33, and 17p13.1-13.3. Moreover, at least four genes (MME, SI, BCHE, and KNG) may be involved in the human lung adenocarcinoma cell line OM.
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Affiliation(s)
| | | | | | | | - Xian-Ping Zhou
- Experiment Teaching Center of Clinical Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, China
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27
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Revisiting tumour aneuploidy - the place of ploidy assessment in the molecular era. Nat Rev Clin Oncol 2015; 13:291-304. [PMID: 26598944 DOI: 10.1038/nrclinonc.2015.208] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chromosome instability (CIN) is gaining increasing interest as a central process in cancer. CIN, either past or present, is indicated whenever tumour cells harbour an abnormal quantity of DNA, termed 'aneuploidy'. At present, the most widely used approach to detecting aneuploidy is DNA cytometry - a well-known research assay that involves staining of DNA in the nuclei of cells from a tissue sample, followed by analysis using quantitative flow cytometry or microscopic imaging. Aneuploidy in cancer tissue has been implicated as a predictor of a poor prognosis. In this Review, we have explored this hypothesis by surveying the current landscape of peer-reviewed research in which DNA cytometry has been applied in studies with disease-appropriate clinical follow up. This area of research is broad, however, and we restricted our survey to results published since 2000 relating to seven common epithelial cancers (those of the breast; endometrium, ovary, and uterine cervix; oesophagus; colon and rectum; lung; prostate; and bladder). We placed particular emphasis on results from multivariate analyses to pinpoint situations in which the prognostic value of aneuploidy as a biomarker is strong compared with that of existing indicators, such as clinical stage, histological grade, and specific molecular markers. We summarize the implications of our findings for the prognostic use of ploidy analysis in the clinic and for the theoretical understanding of the role of CIN in carcinogenesis.
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28
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Franco R, Rocco G, Marino FZ, Pirozzi G, Normanno N, Morabito A, Sperlongano P, Stiuso P, Luce A, Botti G, Caraglia M. Anaplastic lymphoma kinase: a glimmer of hope in lung cancer treatment? Expert Rev Anticancer Ther 2013; 13:407-20. [PMID: 23560836 DOI: 10.1586/era.13.18] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Anaplastic lymphoma kinase (ALK) rearrangements (ALK-Rs) have been identified in 3-7% of all non-small-cell lung cancers (NSCLCs) and represent an important molecular target for NSCLC treatment. The authors discuss the role of ALK-Rs in the prediction of clinical-pathological features of NSCLCs and the technical problems related to their determination in specimens. The authors also describe the preclinical and clinical results derived from the use of ALK inhibitors. ALK-R is generally detected in patients with specific clinical-pathological features: never-smokers, young males, adenocarcinoma histotype and EGF receptor/KRAS wild-type. The diagnosis of ALK-R remains a challenge, implicating the need of a careful filtering of patients. NSCLC patients harboring ALK-R have shown sensitivity to ALK inhibitors even if their activity is limited at the time by the occurrence of mechanisms of resistance. The authors summarize the strategies that in the future could overcome these mechanisms of escape.
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Affiliation(s)
- Renato Franco
- Pathology Unit, National Cancer Institute, Pascale Hospital, Naples, Italy.
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29
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Wang L, Stueckle TA, Mishra A, Derk R, Meighan T, Castranova V, Rojanasakul Y. Neoplastic-like transformation effect of single-walled and multi-walled carbon nanotubes compared to asbestos on human lung small airway epithelial cells. Nanotoxicology 2013; 8:485-507. [PMID: 23634900 DOI: 10.3109/17435390.2013.801089] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Accumulating evidence indicates that carbon nanotubes (CNTs) are biopersistent and can cause lung damage. With similar fibrous morphology and mode of exposure to asbestos, a known human carcinogen, growing concern has arisen for elevated risk of CNT-induced lung carcinogenesis; however, relatively little is known about the long-term carcinogenic effect of CNT. Neoplastic transformation is a key early event leading to carcinogenesis. We studied the ability of single- and multi-walled CNTs to induce neoplastic transformation of human lung epithelial cells compared to asbestos. Long-term (6-month) exposure of the cells to occupationally relevant concentrations of CNT in culture caused a neoplastic-like transformation phenotype as demonstrated by increased cell proliferation, anchorage-independent growth, invasion and angiogenesis. Whole-genome expression signature and protein expression analyses showed that single- and multi-walled CNTs shared similar signaling signatures which were distinct from asbestos. These results provide novel toxicogenomic information and suggest distinct particle-associated mechanisms of neoplasia promotion induced by CNTs and asbestos.
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Affiliation(s)
- Liying Wang
- HELD/PPRB, National Institute for Occupational Safety and Health , Morgantown, WV 26505 , USA
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30
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Ţuţulan-Cunită AC, Papuc SM, Arghir A, Rötzer KM, Deshpande C, Lungeanu A, Budişteanu M. 3p interstitial deletion: novel case report and review. J Child Neurol 2012; 27:1062-6. [PMID: 22290856 DOI: 10.1177/0883073811431016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
3p interstitial deletions have emerged in recent years as a new cause of neurodevelopmental delay and intellectual disability. Since the first report of this condition in 1979, 16 cases have been described in the literature, delineating it as a presumptive syndrome. Here, we add a novel case presenting severely delayed neurodevelopment and psychomotor development; facial dysmorphism (square facies, broad forehead, short palpebral fissures, epicanthic folds, broad nasal bridge, and low-set malformed ears); cerebral, cardiac, and genital malformations; hand and feet anomalies; sacral sinus; and hearing impairment. Genetic investigations revealed a del(3)(p12.3p14.1) of 12.5 Mb, including 31 ORFs, among which ROBO2, PDZRN3, MITF, and FOXP1 are known to act in neurodevelopment. The clinical features of our patient are compared with those previously reported in the literature, thus providing further support for the delineation of the 3p interstitial deletion syndrome.
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31
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Sang H, Zhang L, Li J. Anti-benzopyrene-7,8-diol-9,10-epoxide induces apoptosis via mitochondrial pathway in human bronchiolar epithelium cells independent of the mitochondria permeability transition pore. Food Chem Toxicol 2012; 50:2417-23. [DOI: 10.1016/j.fct.2012.04.041] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 03/31/2012] [Accepted: 04/26/2012] [Indexed: 11/16/2022]
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32
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Wistuba II. Molecular testing of non-small cell lung carcinoma biopsy and cytology specimens. Am Soc Clin Oncol Educ Book 2012:459-64. [PMID: 24451780 DOI: 10.14694/edbook_am.2012.32.44] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
During the past decade, substantial progress has been made in the characterization of molecular abnormalities in non-small cell carcinoma (NSCLC) tumors that are being used as molecular targets and predictive biomarkers for selection of targeted therapy. These recent advances in NSCLC targeted therapy require the analysis of a panel of molecular abnormalities in tumor specimens, including gene mutations (e.g., EGFR, KRAS, BRAF, DDR2), gene amplifications (e.g., MET, FGFR1), and fusions (e.g., EML4-ALK) by applying different methods to tumor tissue (biopsy) and cell (cytology) samples. However, the biopsy and cytology samples available for molecular testing in advanced metastatic NSCLC tumors are likely to be small specimens, including core needle biopsies and/or fine needle aspiration, which may limit the molecular and genomic analysis with currently available methods and technologies. In this process, the role of the pathologist is becoming increasingly important to adequately integrate both routine histopathologic assessment and molecular testing into the clinical pathology for proper tumor diagnosis and subsequent selection of the most appropriate therapy.
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Affiliation(s)
- Ignacio I Wistuba
- From the Departments of Pathology and Thoracic/Head and Neck Medical Oncology, University of Texas M. D. Anderson Cancer Center, Houston, TX
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33
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Postel-Vinay S, Vanhecke E, Olaussen KA, Lord CJ, Ashworth A, Soria JC. The potential of exploiting DNA-repair defects for optimizing lung cancer treatment. Nat Rev Clin Oncol 2012; 9:144-55. [PMID: 22330686 DOI: 10.1038/nrclinonc.2012.3] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The tumor genome is commonly aberrant as a consequence of mutagenic insult and incomplete DNA repair. DNA repair as a therapeutic target has recently received considerable attention owing to the promise of drugs that target tumor-specific DNA-repair enzymes and potentiate conventional cytotoxic therapy through mechanism-based approaches, such as synthetic lethality. Treatment for non-small-cell lung cancer (NSCLC) consists mainly of platinum-based chemotherapy regimens and improvements are urgently needed. Optimizing treatment according to tumor status for DNA-repair biomarkers, such as ERCC1, BRCA1 or RRM1, could predict response to platinum, taxanes and gemcitabine-based therapies, respectively, and might improve substantially the response of individual patients' tumors. Finally, recent data on germline variation in DNA-repair genes may also be informative. Here, we discuss how a molecular and functional DNA-repair classification of NSCLC may aid clinical decision making and improve patient outcome.
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Affiliation(s)
- Sophie Postel-Vinay
- INSERM U981, Department of Medicine, Université Paris-Sud XI-Institut Gustave Roussy, 114 rue Edouard Vaillant, 94805 Villejuif, France
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Ruppert AM, Beau-Faller M, Belmont L, Lavolé A, Gounant V, Cadranel J, Wislez M. Un regard simple sur la biologie du cancer bronchique : MET. Rev Mal Respir 2011; 28:1241-9. [DOI: 10.1016/j.rmr.2011.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 05/12/2011] [Indexed: 12/11/2022]
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