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early stage lung cancer gene

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https://www.readbyqxmd.com/read/29022249/common-subcluster-mining-in-microarray-data-for-molecular-biomarker-discovery
#1
Arnab Sadhu, Balaram Bhattacharyya
Molecular biomarkers can be potential facilitators for detection of cancer at early stage which is otherwise difficult through conventional biomarkers. Gene expression data from microarray experiments on both normal and diseased cell samples provide enormous scope to explore genetic relations of disease using computational techniques. Varied patterns of expressions of thousands of genes at different cell conditions along with inherent experimental error make the task of isolating disease related genes challenging...
October 11, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28989534/activation-of-janus-kinase-1-confers-poor-prognosis-in-patients-with-non-small-cell-lung-cancer
#2
Dan Liu, Yi Huang, Li Zhang, Dong-Ni Liang, Li Li
The activation of Janus kinase 1 (JAK1) has been reported to occur in non-small cell lung cancer (NSCLC), activating the JAK/signal transducers and activators of transcription cascade. However, the association between JAK1 activation and the prognostic value in NSCLC remains unclear. The present study initially investigated the association between expression of the activated form of JAK1 (p-JAK1) and prognosis in patients with NSCLC. A cohort of 142 resected primary NSCLC tissue samples, including 74 adenocarcinoma (ADCC) and 68 squamous cell carcinoma samples, were analyzed...
October 2017: Oncology Letters
https://www.readbyqxmd.com/read/28977903/polymorphisms-in-mitotic-checkpoint-related-genes-can-influence-survival-outcomes-of-early-stage-non-small-cell-lung-cancer
#3
Hyo Gyoung Kang, Seung Soo Yoo, Jin Eun Choi, Mi Jeong Hong, Sook Kyung Do, Cheng Cheng Jin, Soyoun Kim, Won Kee Lee, Sun Ha Choi, So Yeon Lee, Hyun Jung Kim, Shin Yup Lee, Jaehee Lee, Seung Ick Cha, Chang Ho Kim, Yangki Seok, Eungbae Lee, Sukki Cho, Sanghoon Jheon, Jae Yong Park
This study was conducted to investigate the association between variants in mitotic checkpoint-related genes and clinical outcomes of non-small cell lung cancer (NSCLC). A total of 766 patients with NSCLC who underwent curative surgery were enrolled. Among the 73 variants evaluated, 4 variants were related with survival outcomes. BUB3 rs7897156C>T was associated with worse overall survival under a recessive model (adjusted hazard ratio = 1.58, 95% confidence interval = 1.07-2.33, P = 0.02). AURKB rs1059476G>A was associated with better overall survival under a recessive model (adjusted hazard ratio = 0...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28977863/clinical-roles-of-the-aberrantly-expressed-lncrnas-in-lung-squamous-cell-carcinoma-a-study-based-on-rna-sequencing-and-microarray-data-mining
#4
Wen-Jie Chen, Rui-Xue Tang, Rong-Quan He, Dong-Yao Li, Liang Liang, Jiang-Hui Zeng, Xiao-Hua Hu, Jie Ma, Shi-Kang Li, Gang Chen
Lung squamous cell carcinoma (LUSC) accounts for a significant proportion of lung cancer and there have been few therapeutic alternatives for recurrent LUSC due to the lack of specific driver molecules. To investigate the prospective role of lncRNAs in the tumorigenesis and progression of LUSC, the aberrantly expressed lncRNAs were calculated based on The Cancer Genome Atlas RNA-seq data. Of 7589 lncRNAs with 504 LUSC cases, 884 lncRNAs were identified as being aberrantly expressed (|log2 fold change| >2 and adjusted P<0...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28935015/-egfr-and-kras-gene-mutations-in-754-patients-with-resectable-stage-i-iiia-non-small-cell-lung-cancer-and-its-clinical-significance
#5
Jing Zhao, Jie Gao, Liping Guo, Xiaoxu Hu, Qi Liu, Jinyin Zhao, Licheng Liu, Jun Jiang, Mengzhao Wang, Zhiyong Liang, Yan Xu, Minjiang Chen, Li Zhang, Longyun Li, Wei Zhong
BACKGROUND: Epidermal growth factor receptor (EGFR) and KRAS gene are important driver genes of non-small cell lung cancer (NSCLC). The studies are mainly focused on detection of EGFR gene for advanced NSCLC, and the mutation feature of EGFR and KRAS gene in early NSCLC tissue is unknown. This study aims to investigate the mutations of EGFR and KRAS gene in NSCLC, and the relationship between the genotype and clinicopathologic features. METHODS: The hotspot mutations in EGFR and KRAS gene in 754 tissue samples of stage I-IIIa NSCLC from Department of Pathology, Peking Union Medical College Hospital were detected by modified amplification refractory mutation system (ARMS) real-time PCR kit, and analyzed their correlation with clinical variables...
September 20, 2017: Zhongguo Fei Ai za Zhi, Chinese Journal of Lung Cancer
https://www.readbyqxmd.com/read/28927388/the-suppressive-role-of-mir-542-5p-in-nsclc-the-evidence-from-clinical-data-and-in-vivo-validation-using-a-chick-chorioallantoic-membrane-model
#6
Rong-Quan He, Xiao-Jiao Li, Lu Liang, You Xie, Dian-Zhong Luo, Jie Ma, Zhi-Gang Peng, Xiao-Hua Hu, Gang Chen
BACKGROUND: Non-small cell lung cancer (NSCLC) has led to the highest cancer-related mortality for decades. To enhance the efficiency of early diagnosis and therapy, more efforts are urgently needed to reveal the origins of NSCLC. In this study, we explored the effect of miR-542-5p in NSCLC with clinical samples and in vivo models and further explored the prospective function of miR-542-5p though bioinformatics methods. METHODS: A total of 125 NSCLC tissue samples were collected, and the expression of miR-542-5p was detected by qRT-PCR...
September 19, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28922552/an-individualized-gene-expression-signature-for-prediction-of-lung-adenocarcinoma-metastases
#7
Lishuang Qi, Tianhao Li, Gengen Shi, Jiasheng Wang, Xin Li, Sainan Zhang, Libin Chen, Yuan Qin, Yunyan Gu, Wenyuan Zhao, Zheng Guo
Our laboratory previously reported an individual-level signature consisting of nine gene pairs, named 9-GPS. This signature was developed by training on microarray expression data and validated using three independent integrated microarray data sets, with samples of stage I non-small-cell lung cancer after complete surgical resection. In this study, we first validated the cross-platform robustness of 9-GPS by demonstrating that 9-GPS could significantly stratify the overall survival of 213 stage I lung adenocarcinoma (LUAD) patients detected with RNA-sequencing platform in The Cancer Genome Atlas (TCGA; log-rank P = 0...
September 18, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28891455/epigenetic-biomarkers-for-risk-assessment-of-particulate-matter-associated-lung-cancer
#8
Arpit Bhargava, Neha Bunkar, Aniket Aglawe, Kailash Chand Pandey, Rajnarayan Tiwari, Koel Chaudhury, Irina Yu Goryacheva, Pradyumna Kumar Mishra
BACKGROUND: Particulate matter directly emitted into the air by sources such as combustion processes and windblown dust, or formed in the atmosphere by transformation of emitted gases are the major contributors to air pollution that triggers a diverse array of human pathologies including lung cancer. The mortality in lung cancer is usually high as the disease is not symptomatic at its early treatable stage. Moreover, available methods for screening are costly and mainly rely on imaging techniques which lack sufficient sensitivity and specificity...
September 10, 2017: Current Drug Targets
https://www.readbyqxmd.com/read/28891208/serum-microrna-150-predicts-prognosis-for-early-stage-non-small-cell-lung-cancer-and-promotes-tumor-cell-proliferation-by-targeting-tumor-suppressor-gene-srcin1
#9
Liren Zhang, Jing Lin, Yuanqing Ye, Taro Oba, Emanuela Gentile, Jie Lian, Jing Wang, Yang Zhao, Jian Gu, Ignacio I Wistuba, Jack A Roth, Lin Ji, Xifeng Wu
This integrative multistage study was aimed to identify circulating miRNAs as prognostic biomarkers and investigate treatment target for early-stage non-small cell lung cancer (NSCLC) patients. In stage I-II NSCLC patients, we screened and validated miRNA ratio signatures predictive of prognosis in serum. In tumor, we found that the expression of miR-150 in identified miRNA signatures was also associated with survival. Increased miR-150 expression promoted NSCLC cell proliferation and migration and vice versa...
September 10, 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/28864950/correlation-of-early-pet-findings-with-tumor-response-to-molecular-targeted-agents-in-patients-with-advanced-driver-mutated-non-small-cell-lung-cancer
#10
Tomonobu Koizumi, Toshirou Fukushima, Daisuke Gomi, Takashi Kobayashi, Nodoka Sekiguchi, Keiko Mamiya, Kazunari Tateishi, Akane Katou, Kazuhiro Oguchi
Recent advances in positron emission tomography with fluorine-18-fluorodeoxyglucose (FDG-PET) have facilitated not only the diagnosis and staging of lung cancer, but also the prediction of treatment outcome. The present study was designed to assess the usefulness of early FDG-PET examination for predicting subsequent tumor size reduction in response to molecular targeted agents in metastatic non-small cell lung cancer (NSCLC) with sensitive gene anomalies. I. In 29 targeted lesions of 10 NSCLC patients, changes in FDG uptake before and on day 7 after the initiation of molecular targeted therapy (gefitinib, n = 7; crizotinib, n = 3) were compared with subsequent radiographic tumor size reduction by RECIST...
September 1, 2017: Medical Oncology
https://www.readbyqxmd.com/read/28855354/a-panel-of-novel-detection-and-prognostic-methylated-dna-markers-in-primary-non-small-cell-lung-cancer-and-serum-dna
#11
Akira Ooki, Zahra Maleki, Jun-Chieh J Tsay, Chandra M Goparaju, Mariana Brait, Nitesh Turaga, Hae-Seong Nam, William Rom, Harvey Pass, David Sidransky, Rafael Guerrero-Preston, Mohammad O Hoque
PURPOSE: To establish a novel panel of cancer-specific methylated genes for cancer detection and prognostic stratification of early stage non-small cell lung cancer (NSCLC). EXPERIMENTAL DESIGN: Identification of differentially methylated regions (DMRs) was performed with bumphunter on "The Cancer Genome Atlas (TCGA)" dataset, and clinical utility was assessed using quantitative methylation-specific PCR assay in multiple sets of primary NSCLC and body fluids that included serum, pleural effusion, and ascites samples...
August 29, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28842574/using-the-new-cellcollector-to-capture-circulating-tumor-cells-from-blood-in-different-groups-of-pulmonary-disease-a-cohort-study
#12
Yutong He, Jin Shi, Gaofeng Shi, Xiaoli Xu, Qingyi Liu, Congmin Liu, Zhaoyu Gao, Jiaoteng Bai, Baoen Shan
Circulating tumor cells (CTCs) are promising biomarkers for clinical application. Cancer screening with Low-Dose Computed Tomography (LDCT) and CTC detections in pulmonary nodule patients has never been reported. The aim of this study was to explore the effectiveness of the combined methods to screen lung cancer. Out of 8313 volunteers screened by LDCT, 32 ground-glass nodules (GGNs) patients and 19 healthy volunteers were randomly selected. Meanwhile, 15 lung cancer patients also enrolled. CellCollector, a new CTC capturing device, was applied for CTCs detection...
August 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28831115/a-mir-snp-biomarker-linked-to-an-increased-lung-cancer-survival-by-mirna-mediated-down-regulation-of-fzd4-expression-and-wnt-signaling
#13
Jing Lin, Roza Zandi, Ruping Shao, Jian Gu, Yuanqin Ye, Jing Wang, Yang Zhao, Alexander Pertsemlidis, Ignacio I Wistuba, Xifeng Wu, Jack A Roth, Lin Ji
Through a new hypothesis-driven and microRNA-pathway-based SNP (miR-SNP) association study we identified a novel miR-SNP (rs713065) in the 3'UTR region of FZD4 gene linked with decreased risk of death in early stage NSCLC patients. We determined biological function and mechanism of action of this FZD4-miR-SNP biomarker in a cellular platform. Our data suggest that FZD4-miR-SNP loci may significantly influence overall survival in NSCLC patients by specifically interacting with miR-204 and modulating FZD4 expression and cellular function in the Wnt-signaling-driven tumor progression...
August 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28817650/snorna-and-pirna-expression-levels-modified-by-tobacco-use-in-women-with-lung-adenocarcinoma
#14
Natasha Andressa Nogueira Jorge, Gabriel Wajnberg, Carlos Gil Ferreira, Benilton de Sa Carvalho, Fabio Passetti
Lung cancer is one of the most frequent types of cancer worldwide. Most patients are diagnosed at advanced stage and thus have poor prognosis. Smoking is a risk factor for lung cancer, however most smokers do not develop lung cancer while 20% of women with lung adenocarcinoma are non-smokers. Therefore, it is possible that these two groups present differences besides the smoking status, including differences in their gene expression signature. The altered expression patterns of non-coding RNAs in complex diseases make them potential biomarkers for diagnosis and treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28814544/direct-detection-of-early-stage-cancers-using-circulating-tumor-dna
#15
Jillian Phallen, Mark Sausen, Vilmos Adleff, Alessandro Leal, Carolyn Hruban, James White, Valsamo Anagnostou, Jacob Fiksel, Stephen Cristiano, Eniko Papp, Savannah Speir, Thomas Reinert, Mai-Britt Worm Orntoft, Brian D Woodward, Derek Murphy, Sonya Parpart-Li, David Riley, Monica Nesselbush, Naomi Sengamalay, Andrew Georgiadis, Qing Kay Li, Mogens Rørbæk Madsen, Frank Viborg Mortensen, Joost Huiskens, Cornelis Punt, Nicole van Grieken, Remond Fijneman, Gerrit Meijer, Hatim Husain, Robert B Scharpf, Luis A Diaz, Siân Jones, Sam Angiuoli, Torben Ørntoft, Hans Jørgen Nielsen, Claus Lindbjerg Andersen, Victor E Velculescu
Early detection and intervention are likely to be the most effective means for reducing morbidity and mortality of human cancer. However, development of methods for noninvasive detection of early-stage tumors has remained a challenge. We have developed an approach called targeted error correction sequencing (TEC-Seq) that allows ultrasensitive direct evaluation of sequence changes in circulating cell-free DNA using massively parallel sequencing. We have used this approach to examine 58 cancer-related genes encompassing 81 kb...
August 16, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28810146/swarm-intelligence-enhanced-detection-of-non-small-cell-lung-cancer-using-tumor-educated-platelets
#16
Myron G Best, Nik Sol, Sjors G J G In 't Veld, Adrienne Vancura, Mirte Muller, Anna-Larissa N Niemeijer, Aniko V Fejes, Lee-Ann Tjon Kon Fat, Anna E Huis In 't Veld, Cyra Leurs, Tessa Y Le Large, Laura L Meijer, Irsan E Kooi, François Rustenburg, Pepijn Schellen, Heleen Verschueren, Edward Post, Laurine E Wedekind, Jillian Bracht, Michelle Esenkbrink, Leon Wils, Francesca Favaro, Jilian D Schoonhoven, Jihane Tannous, Hanne Meijers-Heijboer, Geert Kazemier, Elisa Giovannetti, Jaap C Reijneveld, Sander Idema, Joep Killestein, Michal Heger, Saskia C de Jager, Rolf T Urbanus, Imo E Hoefer, Gerard Pasterkamp, Christine Mannhalter, Jose Gomez-Arroyo, Harm-Jan Bogaard, David P Noske, W Peter Vandertop, Daan van den Broek, Bauke Ylstra, R Jonas A Nilsson, Pieter Wesseling, Niki Karachaliou, Rafael Rosell, Elizabeth Lee-Lewandrowski, Kent B Lewandrowski, Bakhos A Tannous, Adrianus J de Langen, Egbert F Smit, Michel M van den Heuvel, Thomas Wurdinger
Blood-based liquid biopsies, including tumor-educated blood platelets (TEPs), have emerged as promising biomarker sources for non-invasive detection of cancer. Here we demonstrate that particle-swarm optimization (PSO)-enhanced algorithms enable efficient selection of RNA biomarker panels from platelet RNA-sequencing libraries (n = 779). This resulted in accurate TEP-based detection of early- and late-stage non-small-cell lung cancer (n = 518 late-stage validation cohort, accuracy, 88%; AUC, 0.94; 95% CI, 0...
August 14, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28807247/interleukins-as-new-prognostic-genetic-biomarkers-in-non-small-cell-lung-cancer
#17
Cristina Pérez-Ramírez, Marisa Cañadas-Garre, Ahmed Alnatsha, Miguel Ángel Molina, Ana I Robles, Eduardo Villar, Juan Ramón Delgado, María José Faus-Dáder, Miguel Ángel Calleja-Hernández
BACKGROUND: Surgery is the standard treatment for early-stage NSCLC, and platinum-based chemotherapy remains as the treatment of choice for advanced-stage NSCLC patients with naïve EGFR status. However, overall 5-years relative survival rates are low. Interleukins (ILs) are crucial for processes associated with tumor development. In NSCLC, IL1B, IL6, IL12A, IL13 and IL16 gene polymorphisms may contribute to individual variation in terms of patient survival. The purpose of this study was to evaluate the association between IL gene polymorphisms and survival in NSCLC patients...
September 2017: Surgical Oncology
https://www.readbyqxmd.com/read/28805673/alk-status-assessment-with-liquid-biopsies-of-lung-cancer-patients
#18
REVIEW
Paul Hofman
Patients with advanced stage non-small cell lung carcinoma (NSCLC) harboring an anaplastic lymphoma kinase ALK gene rearrangement, detected from a tissue sample, can benefit from targeted ALK inhibitor treatment. However, while treatment is initially effective in most cases, relapse or progression occurs due to different resistance mechanisms including mutations in the tyrosine kinase domain of echinoderm microtubule-associated protein-like 4 (EML44)-ALK. The liquid biopsy concept has recently radically changed the clinical care of NSCLC patients, in particular for those harboring an epidermal growth factor receptor (EGFR) gene mutation...
August 12, 2017: Cancers
https://www.readbyqxmd.com/read/28799568/association-of-long-non-coding-rna-h19-and-microrna-21-expression-with-the-biological-features-and-prognosis-of-non-small-cell-lung-cancer
#19
Y Zhou, B Sheng, Q Xia, X Guan, Y Zhang
In recent years, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been shown to play important roles in tumor biological function. The aim of this study was to investigate the diagnostic and prognostic value of lncRNA H19 and miR-21 expression in non-small-cell lung cancer (NSCLC). H19 and miR-21 expression was measured in tumor tissues and corresponding non-tumor lung tissues from 200 patients by quantitative reverse transcription polymerase chain reaction. Moreover, the in vitro and in vivo effects of H19 knock out in A549 cells were investigated...
August 2017: Cancer Gene Therapy
https://www.readbyqxmd.com/read/28791371/comprehensive-analysis-of-aberrantly-expressed-microrna-profiles-reveals-potential-biomarkers-of-human-lung-adenocarcinoma-progression
#20
Jing Sui, Ru-Song Yang, Si-Yi Xu, Yan-Qiu Zhang, Cheng-Yun Li, Sheng Yang, Li-Hong Yin, Yue-Pu Pu, Ge-Yu Liang
Lung adenocarcinoma (LUAD) is a complex disease that poses challenges for diagnosis and treatment. The aim of the present study is to investigate LUAD-specific key microRNAs (miRNAs) from large-scale samples in The Cancer Genome Atlas (TCGA) database. We used an integrative computational method to identify LUAD-specific key miRNAs related to TNM stage and lymphatic metastasis from the TCGA database. Twenty-five LUAD-specific key miRNAs (fold change >2, p<0.05) from the TCGA database were investigated, and 15 were found to be aberrantly expressed with respect to clinical features...
August 4, 2017: Oncology Reports
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