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early stage lung cancer gene

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https://www.readbyqxmd.com/read/28625654/line-1-hypomethylation-is-associated-to-specific-clinico-pathological-features-in-stage-i-non-small-cell-lung-cancer
#1
Andrea Imperatori, Nora Sahnane, Nicola Rotolo, Francesca Franzi, Elisa Nardecchia, Laura Libera, Chiara Romualdi, Maria Cattoni, Fausto Sessa, Lorenzo Dominioni, Daniela Furlan
OBJECTIVES: We hypothesize that selected genetic and/or epigenetic changes associated with advanced tumours may help identifying early non-small cell lung cancers (NSCLCs) that recur after resection. Among epigenetic changes, long interspersed nuclear element-1 (LINE-1) hypomethylation is seen early during carcinogenesis and may act in concert with genetic alterations to cancer progression. LINE-1 hypomethylation and gene mutations frequently involved in lung cancer, were analysed to evaluate their prognostic role in resected stage I NSCLC...
June 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/28608966/next-generation-sequencing-and-clinical-outcomes-of-patients-with-lung-adenocarcinoma-treated-with-stereotactic-body-radiotherapy
#2
Richard J Cassidy, Xinyan Zhang, Pretesh R Patel, Joseph W Shelton, Chase E Escott, Gabriel L Sica, Michael R Rossi, Charles E Hill, Conor E Steuer, Rathi N Pillai, Suresh S Ramalingam, Taofeek K Owonikoko, Madhusmita Behera, Seth D Force, Felix G Fernandez, Walter J Curran, Kristin A Higgins
BACKGROUND: Genetic aberrations are well characterized in lung adenocarcinomas (LACs) and clinical outcomes have been influenced by targeted therapies in the advanced setting. Stereotactic body radiotherapy (SBRT) is the standard-of-care therapy for patients with nonoperable, early-stage LAC, but to the authors' knowledge, no information is available regarding the impact of genomic changes in these patients. The current study sought to determine the frequency and clinical impact of genetic aberrations in this population...
June 13, 2017: Cancer
https://www.readbyqxmd.com/read/28608921/whole-exome-sequencing-reveals-critical-genes-underlying-metastasis-in-esophageal-squamous-cell-carcinoma
#3
Wei Dai, Josephine Mun Yee Ko, Sheyne Sta Ana Choi, Zhouyou Yu, Luwen Ning, Hong Zheng, Vinod Gopalan, Kin Tak Chan, Nikki Pui-Yue Lee, Kwok Wah Chan, Simon Ying-Kit Law, Alfred King-Yin Lam, Maria Li Lung
Esophageal squamous cell carcinoma (ESCC) is one of the most lethal cancers due to a high frequency of metastasis. However, little is known about the genomic landscape of metastatic ESCC. To identify the genetic alterations that underlie ESCC metastasis, whole-exome sequencing (WES) was performed for 41 primary tumors and 15 lymph nodes (LNs) with metastatic ESCC. Eleven cases included matched primary tumors, synchronous LN metastases and non-neoplastic mucosa. Approximately 50-76% of the mutations identified in primary tumors appeared in the synchronous LN metastases...
June 13, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28591748/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...
May 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28533227/detecting-the-presence-and-progression-of-premalignant-lung-lesions-via-airway-gene-expression
#5
Jennifer Beane, Sarah A Mazzilli, Anna M Tassinari, Gang Liu, Xiaohui Zhang, Hanqiao Liu, Anne Dy Buncio, Samjot S Dhillon, Suso J Platero, Marc E Lenburg, Mary E Reid, Stephen Lam, Avrum E Spira
  Lung cancer (LC) is the leading cause of cancer death in the US. The molecular events preceding the onset of disease are poorly understood and no effective tools exist to identify smokers with premalignant lesions (PMLs) that will progress to invasive cancer. Prior work identified molecular alterations in the smoke-exposed airway field of injury associated with LC.  Here we focus on an earlier stage in the disease process leveraging the airway field of injury to study PMLs and its utility in LC chemoprevention...
May 22, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28525852/absolute-quantification-of-dna-methylation-using-microfluidic-chip-based-digital-pcr
#6
Zhenhua Wu, Yanan Bai, Zule Cheng, Fangming Liu, Ping Wang, Dawei Yang, Gang Li, Qinghui Jin, Hongju Mao, Jianlong Zhao
Hypermethylation of CpG islands in the promoter region of many tumor suppressor genes downregulates their expression and in a result promotes tumorigenesis. Therefore, detection of DNA methylation status is a convenient diagnostic tool for cancer detection. Here, we reported a novel method for the integrative detection of methylation by the microfluidic chip-based digital PCR. This method relies on methylation-sensitive restriction enzyme HpaII, which cleaves the unmethylated DNA strands while keeping the methylated ones intact...
May 12, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28521438/identification-of-differentially-expressed-genes-between-early-stage-adenocarcinoma-and-squamous-cell-carcinoma-lung-cancer-using-meta-analysis-methods
#7
Tianjiao Wang, Lei Zhang, Pu Tian, Suyan Tian
Lung adenocarcinoma (AC) and squamous cell lung carcinoma (SCC) are two major subtypes of non-small cell lung cancer (NSCLC). Previous studies have demonstrated that fundamental differences exist in the underlying mechanisms of tumor development, growth and invasion between these subtypes. The investigation of differentially-expressed genes (DEGs) between these two NSCLC subtypes is useful for determining and understanding such differences. The present study aimed to identify those DEGs using meta-analysis and the data from four microarray experiments, consisting of 164 AC and 161 SCC samples...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28518058/prediction-of-nsclc-recurrence-from-microarray-data-with-gep
#8
Russul Al-Anni, Jingyu Hou, Rana Dhia'a Abdu-Aljabar, Yong Xiang
Lung cancer is one of the deadliest diseases in the world. Non-small cell lung cancer (NSCLC) is the most common and dangerous type of lung cancer. Despite the fact that NSCLC is preventable and curable for some cases if diagnosed at early stages, the vast majority of patients are diagnosed very late. Furthermore, NSCLC usually recurs sometime after treatment. Therefore, it is of paramount importance to predict NSCLC recurrence, so that specific and suitable treatments can be sought. Nonetheless, conventional methods of predicting cancer recurrence rely solely on histopathology data and predictions are not reliable in many cases...
June 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28498804/increased-s100a15-expression-and-decreased-dna-methylation-of-its-gene-promoter-are-involved-in-high-metastasis-potential-and-poor-outcome-of-lung-adenocarcinoma
#9
Yung-Che Chen, Meng-Chih Lin, Chang-Chun Hsiao, Yi-Xin Zheng, Kuang-Den Chen, Ming-Tse Sung, Chung-Jen Chen, Ting-Ya Wang, Yong-Yong Lin, Huang-Chih Chang, Yu-Mu Chen, Jen-Chieh Chang
PURPOSE: This study aims to determine the functional role of S100A15 and its promoter DNA methylation patterns in lung cancer progression. EXPERIMENTAL DESIGN: We analyzed 178 formalin-fixed paraffin embedded specimens from lung cancer patients, including 24 early stage and 91 advanced stage adenocarcinoma. S100A15 protein expression was evaluated by immunohistochemistry stain, and its DNA methylation levels were measured by pyrosequencing. RESULTS: S100A15 nuclear staining was increased in lung adenocarcinoma patients with distant metastasis versus those without distant metastasis...
April 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28472989/circulating-mutational-portrait-of-cancer-manifestation-of-aggressive-clonal-events-in-both-early-and-late-stages
#10
Meng Yang, Umit Topaloglu, W Jeffrey Petty, Matthew Pagni, Kristie L Foley, Stefan C Grant, Mac Robinson, Rhonda L Bitting, Alexandra Thomas, Angela T Alistar, Rodwige J Desnoyers, Michael Goodman, Carol Albright, Mercedes Porosnicu, Mihaela Vatca, Shadi A Qasem, Barry DeYoung, Ville Kytola, Matti Nykter, Kexin Chen, Edward A Levine, Edgar D Staren, Ralph B D'Agostino, Robin M Petro, William Blackstock, Bayard L Powell, Edward Abraham, Boris Pasche, Wei Zhang
BACKGROUND: Solid tumors residing in tissues and organs leave footprints in circulation through circulating tumor cells (CTCs) and circulating tumor DNAs (ctDNA). Characterization of the ctDNA portraits and comparison with tumor DNA mutational portraits may reveal clinically actionable information on solid tumors that is traditionally achieved through more invasive approaches. METHODS: We isolated ctDNAs from plasma of patients of 103 lung cancer and 74 other solid tumors of different tissue origins...
May 4, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28459463/mycn-induces-neuroblastoma-in-primary-neural-crest-cells
#11
R R Olsen, J H Otero, J García-López, K Wallace, D Finkelstein, J E Rehg, Z Yin, Y-D Wang, K W Freeman
Neuroblastoma (NBL) is an embryonal cancer of the sympathetic nervous system (SNS), which causes 15% of pediatric cancer deaths. High-risk NBL is characterized by N-Myc amplification and segmental chromosomal gains and losses. Owing to limited disease models, the etiology of NBL is largely unknown, including both the cell of origin and the majority of oncogenic drivers. We have established a novel system for studying NBL based on the transformation of neural crest cells (NCCs), the progenitor cells of the SNS, isolated from mouse embryonic day 9...
May 1, 2017: Oncogene
https://www.readbyqxmd.com/read/28456114/gene-expression-signature-differentiates-histology-but-not-progression-status-of-early-stage-nsclc
#12
Radoslaw Charkiewicz, Jacek Niklinski, Jürgen Claesen, Anetta Sulewska, Miroslaw Kozlowski, Anna Michalska-Falkowska, Joanna Reszec, Marcin Moniuszko, Wojciech Naumnik, Wieslawa Niklinska
Advances in molecular analyses based on high-throughput technologies can contribute to a more accurate classification of non-small cell lung cancer (NSCLC), as well as a better prediction of both the disease course and the efficacy of targeted therapies. Here we set out to analyze whether global gene expression profiling performed in a group of early-stage NSCLC patients can contribute to classifying tumor subtypes and predicting the disease prognosis. Gene expression profiling was performed with the use of the microarray technology in a training set of 108 NSCLC samples...
June 2017: Translational Oncology
https://www.readbyqxmd.com/read/28445112/tracking-the-evolution-of-non-small-cell-lung-cancer
#13
Mariam Jamal-Hanjani, Gareth A Wilson, Nicholas McGranahan, Nicolai J Birkbak, Thomas B K Watkins, Selvaraju Veeriah, Seema Shafi, Diana H Johnson, Richard Mitter, Rachel Rosenthal, Max Salm, Stuart Horswell, Mickael Escudero, Nik Matthews, Andrew Rowan, Tim Chambers, David A Moore, Samra Turajlic, Hang Xu, Siow-Ming Lee, Martin D Forster, Tanya Ahmad, Crispin T Hiley, Christopher Abbosh, Mary Falzon, Elaine Borg, Teresa Marafioti, David Lawrence, Martin Hayward, Shyam Kolvekar, Nikolaos Panagiotopoulos, Sam M Janes, Ricky Thakrar, Asia Ahmed, Fiona Blackhall, Yvonne Summers, Rajesh Shah, Leena Joseph, Anne M Quinn, Phil A Crosbie, Babu Naidu, Gary Middleton, Gerald Langman, Simon Trotter, Marianne Nicolson, Hardy Remmen, Keith Kerr, Mahendran Chetty, Lesley Gomersall, Dean A Fennell, Apostolos Nakas, Sridhar Rathinam, Girija Anand, Sajid Khan, Peter Russell, Veni Ezhil, Babikir Ismail, Melanie Irvin-Sellers, Vineet Prakash, Jason F Lester, Malgorzata Kornaszewska, Richard Attanoos, Haydn Adams, Helen Davies, Stefan Dentro, Philippe Taniere, Brendan O'Sullivan, Helen L Lowe, John A Hartley, Natasha Iles, Harriet Bell, Yenting Ngai, Jacqui A Shaw, Javier Herrero, Zoltan Szallasi, Roland F Schwarz, Aengus Stewart, Sergio A Quezada, John Le Quesne, Peter Van Loo, Caroline Dive, Allan Hackshaw, Charles Swanton
BACKGROUND: Among patients with non-small-cell lung cancer (NSCLC), data on intratumor heterogeneity and cancer genome evolution have been limited to small retrospective cohorts. We wanted to prospectively investigate intratumor heterogeneity in relation to clinical outcome and to determine the clonal nature of driver events and evolutionary processes in early-stage NSCLC. METHODS: In this prospective cohort study, we performed multiregion whole-exome sequencing on 100 early-stage NSCLC tumors that had been resected before systemic therapy...
June 1, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28425640/profiling-of-the-silica-induced-molecular-events-in-lung-epithelial-cells-using-the-rna-seq-approach
#14
Judy Y W Chan, Joseph C C Tsui, Patrick T W Law, Winnie K W So, Doris Y P Leung, Michael M K Sham, Stephen K W Tsui, Carmen W H Chan
Silicosis is a prolonged, irreversible and incurable occupational disease, and there is a significant number of newly diagnosed cases every year in Hong Kong. Due to the long latency of the disease, the diagnosis can be missed until detailed clinical examination at a later stage. For a better control of this deadly disease, detailing the pro-inflammatory and fibrotic events in the macrophage would be instrumental in understanding the pathogenesis of the disease and essential for the significant biomarkers discovery...
April 20, 2017: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/28423489/target-of-obstructive-sleep-apnea-syndrome-merge-lung-cancer-based-on-big-data-platform
#15
Lifeng Li, Jingli Lu, Wenhua Xue, Liping Wang, Yunkai Zhai, Zhirui Fan, Ge Wu, Feifei Fan, Jieyao Li, Chaoqi Zhang, Yi Zhang, Jie Zhao
Based on our hospital database, the incidence of lung cancer diagnoses was similar in obstructive sleep apnea Syndrome (OSAS) and hospital general population; among individual with a diagnosis of lung cancer, the presence of OSAS was associated with an increased risk for mortality. In the gene expression and network-level information, we revealed significant alterations of molecules related to HIF1 and metabolic pathways in the hypoxic-conditioned lung cancer cells. We also observed that GBE1 and HK2 are downstream of HIF1 pathway important in hypoxia-conditioned lung cancer cell...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28410204/clinical-verification-of-plasma-messenger-rna-as-novel-noninvasive-biomarker-identified-through-bioinformatics-analysis-for-lung-cancer
#16
Dan Zhou, Weiwei Tang, Xinli Liu, Han-Xiang An, Yun Zhang
Lung cancer (LC) remains associated with significant mortality worldwide. The lack of reliable noninvasive biomarkers and targeted therapies contributes to poor survival rate. Herein, we initially took advantage of the public microarray data from Oncomine database to filter messenger RNAs (mRNAs) as potential biomarkers. Subsequently, clinical validation was applied to identify candidate noninvasive biomarkers in plasma from patients with LC. Through comprehensive analysis of transcriptional expression profiles across 12 studies, top 6 over- and underexpressed mRNAs were generated...
March 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28387364/identification-of-prognostic-genes-and-gene-sets-for-early-stage-non-small-cell-lung-cancer-using-bi-level-selection-methods
#17
Suyan Tian, Chi Wang, Howard H Chang, Jianguo Sun
In contrast to feature selection and gene set analysis, bi-level selection is a process of selecting not only important gene sets but also important genes within those gene sets. Depending on the order of selections, a bi-level selection method can be classified into three categories - forward selection, which first selects relevant gene sets followed by the selection of relevant individual genes; backward selection which takes the reversed order; and simultaneous selection, which performs the two tasks simultaneously usually with the aids of a penalized regression model...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28381877/the-genomic-dynamics-during-progression-of-lung-adenocarcinomas
#18
Bin Yang, Longhai Luo, Wen Luo, Yong Zhou, Chao Yang, Teng Xiong, Xiangchun Li, Xuan Meng, Lin Li, Xiaopin Zhang, Zhe Wang, Zhixin Wang
Intra-tumor heterogeneity is a big barrier to precision medicine. To explore the underlying clonal diversity in lung adenocarcinomas, we selected nine individuals with whole-genome sequencing data from primary and matched metastatic tumors as a cohort for study. Similar global pattern of arm-level copy number changes and large variations of somatic single-nucleotide variant between the primary and metastasis are observed in the majority of cases. Importantly, we found breakage-fusion-bridge (BFB) cycles acting as an important mechanism for underlying cancer gene amplification, such as amplification of CDK4, CDKN3 and FGFR1 in early stage...
April 6, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28380452/detection-of-oncogenic-mutations-in-resected-bronchial-margins-by-next-generation-sequencing-indicates-early-relapse-in-stage-ia-lung-adenocarcinoma-patients
#19
Tangfeng Lv, Jiawei Zou, Hongbing Liu, Qin Shen, Zhenfeng Lu, XiaoJun Zhou, Xiaonan Wang, Yong Song
Stage I non-small cell lung cancer (NSCLC) patients experience a relatively high rate of recurrence, ranging from about 30-35%. We hypothesized that this elevated risk of recurrence is due to the presence of tumor cells at bronchial margins which was undetected by conventional light microscopy.Patients with clinical stage IA (T1N0M0) NSCLC were enrolled in this study,which included 8 early-relapse(ER) and 6 no-relapse(NR) patients. Primary tumor, bronchial margin,and normal lung tissues were collected and sent to a central site for targeted next-generation sequencing analysis...
June 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28371134/strandadvantage-test-for-early-line-and-advanced-stage-treatment-decisions-in-solid-tumors
#20
Manimala Sen, Shanmukh Katragadda, Aarthi Ravichandran, Gouri Deshpande, Minothi Parulekar, Swetha Nayanala, Vikram Vittal, Weiming Shen, Melanie Phooi Nee Yong, Jemima Jacob, Sravanthi Parchuru, Kalpana Dhanuskodi, Kenneth Eyring, Pooja Agrawal, Smita Agarwal, Ashwini Shanmugam, Satish Gupta, Divya Vishwanath, Kiran Kumari, Arun K Hariharan, Sai A Balaji, Qiaoling Liang, Belen Robolledo, Vijayashree Gauribidanur Raghavendrachar, Mohammed Oomer Farooque, Cary J Buresh, Preveen Ramamoorthy, Urvashi Bahadur, Kalyanasundaram Subramanian, Ramesh Hariharan, Vamsi Veeramachaneni, Satish Sankaran, Vaijayanti Gupta
Comprehensive genetic profiling of tumors using next-generation sequencing (NGS) is gaining acceptance for guiding treatment decisions in cancer care. We designed a cancer profiling test combining both deep sequencing and immunohistochemistry (IHC) of relevant cancer targets to aid therapy choices in both standard-of-care (SOC) and advanced-stage treatments for solid tumors. The SOC report is provided in a short turnaround time for four tumors, namely lung, breast, colon, and melanoma, followed by an investigational report...
May 2017: Cancer Medicine
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