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https://www.readbyqxmd.com/read/27913729/qsea-modelling-of-genome-wide-dna-methylation-from-sequencing-enrichment-experiments
#1
Matthias Lienhard, Sabrina Grasse, Jana Rolff, Steffen Frese, Uwe Schirmer, Michael Becker, Stefan Börno, Bernd Timmermann, Lukas Chavez, Holger Sültmann, Gunda Leschber, Iduna Fichtner, Michal R Schweiger, Ralf Herwig
Genome-wide enrichment of methylated DNA followed by sequencing (MeDIP-seq) offers a reasonable compromise between experimental costs and genomic coverage. However, the computational analysis of these experiments is complex, and quantification of the enrichment signals in terms of absolute levels of methylation requires specific transformation. In this work, we present QSEA, Quantitative Sequence Enrichment Analysis, a comprehensive workflow for the modelling and subsequent quantification of MeDIP-seq data...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27911863/correlation-of-long-non-coding-rna-h19-expression-with-cisplatin-resistance-and-clinical-outcome-in-lung-adenocarcinoma
#2
Qi Wang, Ningning Cheng, Xuefei Li, Hui Pan, Chunyu Li, Shengxiang Ren, Chunxia Su, Weijing Cai, Chao Zhao, Limin Zhang, Caicun Zhou
The acquired drug resistance would influence the efficacy of cisplatin-based chemotherapy in non-small-cell lung cancer. The present study aimed to investigate the correlation of long non-coding RNA (lncRNA) H19 with cisplatin-resistance and clinical outcome in lung adenocarcinoma. In our study, the expression of H19 in cisplatin-resistant A549/DDP cells was unregulated. Knockdown of H19 restored the response of A549/DDP cells to cisplatin. H19-mediated chemosensitivity enhancement was associated with metastasis, induction of G0/G1 cell-cycle arrest, cell proliferation, and increased apoptosis...
November 29, 2016: Oncotarget
https://www.readbyqxmd.com/read/27911119/phase-ii-study-of-dasatinib-in-previously-treated-patients-with-advanced-non-small-cell-lung-cancer
#3
Michael J Kelley, Gautam Jha, Debra Shoemaker, James E Herndon, Lin Gu, William T Barry, Jeffrey Crawford, Neal Ready
The Src pathway in activated in about one-third of non-small cell lung cancer (NSCLC) tumors. Dasatinib has Src-inhibitor activity. We examined the activity of dasatinib in 37 patients with advanced, previously treated NSCLC. Among the 29 patients who underwent pre-treatment biopsy for RNA biomarker analysis, 25 were treated with dasatinib 70 mg twice daily. There were no responses. Five patients discontinued treatment due to toxicity. Three patients had minor biopsy-related pneumothoraces. Given the lack of responses, no biomarkers were analyzed...
December 2, 2016: Cancer Investigation
https://www.readbyqxmd.com/read/27906860/liquid-biopsy-for-early-detection-of-lung-cancer
#4
Paul Hofman
PURPOSE OF REVIEW: The possibility of complete recovery for a lung cancer patient depends on very early diagnosis, as it allows total surgical resection. Screening for this cancer in a high-risk population can be performed using a radiological approach, but this holds a certain number of limitations. Liquid biopsy could become an alternative and complementary screening approach to chest imaging for early diagnosis of lung cancer. RECENT FINDINGS: Several circulating biomarkers indicative of lung cancer can be investigated in blood, such as circulating tumor cells, circulating free nucleic acids (RNA and DNA) and proteins...
January 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/27906622/sensitive-liquid-chromatography-mass-spectrometry-lc-ms-assay-reveals-novel-insights-on-dna-methylation-and-incorporation-of-gemcitabine-its-metabolite-difluorodeoxyuridine-deoxyuridine-and-rx-3117-into-dna
#5
Richard J Honeywell, Dzjemma Sarkisjan, Ietje Kathmann, Michael H Kristensen, Godefridus J Peters
Antimetabolites are incorporated into DNA and RNA, affecting their function. Liquid-chromatography-mass-spectrometry (LC-MS-MS) permits the sensitive, selective analysis of normal nucleosides. The method was adapted to measure the incorporation of deoxyuridine, gemcitabine (difluorodeoxycytidine), its metabolite difluorodeoxyuridine (dFdU), and the novel compound fluorocyclopentenylcytosine (RX3117). DNA was degraded to its deoxynucleotides for quantification by LC-MS-MS, gradient chromatography on a Phenomenex prodigy-3-ODS with positive ionization...
December 2016: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/27904771/tumor-suppressive-function-of-long-noncoding-rna-malat1-in-glioma-cells-by-suppressing-mir-155-expression-and-activating-fbxw7-function
#6
Shuanzhu Cao, Yanzhou Wang, Jinquan Li, Mingliang Lv, Haitao Niu, Yong Tian
The human metastasis associated lung adenocarcinoma transcript 1 (MALAT1) is a long non-coding RNA associated with metastasis, and is a favorable prognostic factor for lung cancer. Recent studies have shown that MALAT1 plays an important role in many malignancies. However, little is known about the role of MALAT1 in glioma. In this study, we determined the expression of MALAT1 and explored its prognostic value in glioma. Further, we investigated the regulatory mechanism of MALAT1 in glioma progression. Our results showed that the expression of MALAT1 was significantly decreased in glioma specimens than in noncancerous brain tissues...
2016: American Journal of Cancer Research
https://www.readbyqxmd.com/read/27903834/saliva-diagnostics-current-views-and-directions
#7
Karolina Elżbieta Kaczor-Urbanowicz, Carmen Martin Carreras-Presas, Katri Aro, Michael Tu, Franklin Garcia-Godoy, David Tw Wong
In this review, we provide an update on the current and future applications of saliva for diagnostic purposes. There are many advantages of using saliva as a biofluid. Its collection is fast, easy, inexpensive, and non-invasive. In addition, saliva, as a "mirror of the body," can reflect the physiological and pathological state of the body. Therefore, it serves as a diagnostic and monitoring tool in many fields of science such as medicine, dentistry, and pharmacotherapy. Introduced in 2008, the term "Salivaomics" aimed to highlight the rapid development of knowledge about various "omics" constituents of saliva, including: proteome, transcriptome, micro-RNA, metabolome, and microbiome...
November 29, 2016: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/27900322/patterns-of-transposable-element-expression-and-insertion-in-cancer
#8
Evan A Clayton, Lu Wang, Lavanya Rishishwar, Jianrong Wang, John F McDonald, I King Jordan
Human transposable element (TE) activity in somatic tissues causes mutations that can contribute to tumorigenesis. Indeed, TE insertion mutations have been implicated in the etiology of a number of different cancer types. Nevertheless, the full extent of somatic TE activity, along with its relationship to tumorigenesis, have yet to be fully explored. Recent developments in bioinformatics software make it possible to analyze TE expression levels and TE insertional activity directly from transcriptome (RNA-seq) and whole genome (DNA-seq) next-generation sequence data...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27900045/microrna-133b-inhibits-the-migration-and-invasion-of-non-small-cell-lung-cancer-cells-via-targeting-fscn1
#9
Xucheng Yang, Pengfei Lei, Yong Huang, Zijian Zhang, Yingying Zhang
MicroRNA (miR)-133b has been reported to act as a tumor suppressor in multiple types of human cancers, including non small cell lung cancer (NSCLC). However, the underlying mechanism by which miR-133b inhibits NSCLC metastasis remains largely unclear. In the present study, reverse transcription-quantitative polymerase chain reaction and western blotting were used to detect messenger RNA and protein expression. A wound healing assay and transwell assay were used to examine the cell migration and invasion. The expression level of miR-133b was found to be significantly downregulated in NSCLC cell lines compared with normal lung epithelial BEAS-2B cells...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27897231/platycodin-d-potentiates-proliferation-inhibition-and-apoptosis-induction-upon-akt-inhibition-via-feedback-blockade-in-non-small-cell-lung-cancer-cells
#10
Ting Li, Xin Chen, Xiuping Chen, Dik Lung Ma, Chung Hang Leung, Jin Jian Lu
AKT is the frequently overexpressed and constitutively active kinase within NSCLC cells and recognized as a promising target for NSCLC treatment. However, AKT inhibition relieves the feedback inhibition of upstream receptor tyrosine kinases (RTKs) that may weaken the efficiency of AKT inhibitors. Platycodin D (PD), isolated from widely-used traditional Chinese medicine Platycodonis Radix, is now found to remarkably enhance the anti-proliferative effect of AKT inhibitors. In this study, combinatorial activity of AKT inhibitor MK2206 and PD on cell proliferation, apoptosis and related signaling were disclosed...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27896996/cerna-search-method-identified-a-met-activated-subgroup-among-egfr-dna-amplified-lung-adenocarcinoma-patients
#11
Halla Kabat, Leo Tunkle, Inhan Lee
Given the diverse molecular pathways involved in tumorigenesis, identifying subgroups among cancer patients is crucial in precision medicine. While most targeted therapies rely on DNA mutation status in tumors, responses to such therapies vary due to the many molecular processes involved in propagating DNA changes to proteins (which constitute the usual drug targets). Though RNA expressions have been extensively used to categorize tumors, identifying clinically important subgroups remains challenging given the difficulty of discerning subgroups within all possible RNA-RNA networks...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896272/long-noncoding-rna-let-suppresses-tumor-growth-and-emt-in-lung-adenocarcinoma
#12
Bin Liu, Chun-Feng Pan, Zhi-Cheng He, Jun Wang, Peng-Li Wang, Teng Ma, Yang Xia, Yi-Jiang Chen
Recently, many studies showed that long noncoding RNAs (lncRNAs) are involved in tumor progression. It is reported that lncRNA-LET is downregulated and has antitumor effect on several types of cancer. This study focuses on the role of lncRNA-LET on lung adenocarcinoma (LAC) progression. RT-PCR results indicated that frequent downregulation of lncRNA-LET in LAC tissues was related to clinicopathologic factors. lncRNA-LET knockdown significantly promoted LAC cell proliferation, invasion, and migration while lncRNA-LET overexpression obviously inhibited LAC cell proliferation, invasion, and migration, indicating a tumor inhibition of lncRNA-LET in LAC progression...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27895786/sprouty4-mrna-variants-and-protein-expressions-in-breast-and-lung-derived-cells
#13
Angelina Doriguzzi, Jihen Salhi, Hedwig Sutterlüty-Fall
Sprouty proteins are modulators of mitogen-induced signalling processes and are therefore hypothesized to affect malignant diseases. As a member of the Sprouty family, Sprouty4 has been previously shown to function as a tumour suppressor in lung and breast cancer. The present study analysed the expression of two known Sprouty4 splice variants in cells established from malignant and normal lung and breast tissues using semi-quantitative reverse transcription-polymerase chain reaction and immunoblotting. The results indicated that the expression of the two messenger RNA (mRNA) variants was reduced in the cells derived from malignant tissue in comparison to the normal counterparts...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27895785/expression-and-clinicopathological-significance-of-the-lncrna-hoxa11-as-in-colorectal-cancer
#14
Tong Li, Chengfei Xu, Bin Cai, Meng Zhang, Feng Gao, Jialiang Gan
HOXA11 antisense RNA (HOXA11-AS) is a long non-coding RNA (lncRNA) that is important in determining cancer progression. HOXA11-AS was recently identified as a novel biomarker in lung cancer progression. However, its role in colorectal cancer (CRC) remains poorly understood. The present study aimed to analyze lncRNA HOXA11-AS expression in CRC and investigate a possible association between HOXA11-AS and clinicopathological factors. HOXA11-AS expression was examined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in 84 CRC tissues and adjacent non-cancerous tissues, in addition to 3 CRC cell lines and 1 human normal colorectal cell line...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27895738/cyclooxygenase-2-is-associated-with-malignant-phenotypes-in-human-lung-cancer
#15
Weiying Li, Wentao Yue, Hui Wang, Baitang Lai, Xuehui Yang, Chunyan Zhang, Yue Wang, Meng Gu
The objective of the present study was to investigate whether cyclooxygenase-2 (COX-2) is associated with malignancy, and to investigate its molecular mechanisms in human lung cancer tumor malignancy. The present study used RNA interference (RNAi) methodology and celecoxib, a COX-2 inhibitor, to investigate the effect of COX-2 knockdown on the proliferation and invasion abilities of lung cancer cells and the molecular mechanisms involved. Human lung adenocarcinoma A549-si10 and LTEP-A2 cells transfected with a specific small interfering RNA (A549-si10 and LTEP-A2-si10, respectively) grew more slowly compared with parental cell lines and cells transfected with pU6...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27895663/mir-30a-5p-overexpression-may-overcome-egfr-inhibitor-resistance-through-regulating-pi3k-akt-signaling-pathway-in-non-small-cell-lung-cancer-cell-lines
#16
Fei Meng, Fengfeng Wang, Lili Wang, S C Cesar Wong, William C S Cho, Lawrence W C Chan
Lung cancer is one of the most common deadly diseases worldwide, most of which is non-small cell lung cancer (NSCLC). The epidermal growth factor receptor (EGFR) mutant NSCLCs frequently respond to the EGFR tyrosine kinase inhibitors (EGFR-TKIs) treatment, such as Gefitinib and Erlotinib, but the development of acquired resistance limits the utility. Multiple resistance mechanisms have been explored, e.g., the activation of alternative tyrosine kinase receptors (TKRs) sharing similar downstream pathways to EGFR...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27895463/lentivirus-mediated-knockdown-of-nlk-inhibits-small-cell-lung-cancer-growth-and-metastasis
#17
Mutian Lv, Yaming Li, Xin Tian, Shundong Dai, Jing Sun, Guojiang Jin, Shenyi Jiang
Nemo-like kinase (NLK), an evolutionarily conserved serine/threonine kinase, has been recognized as a critical regulator of various cancers. In this study, we investigated the role of NLK in human small-cell lung cancer (SCLC), which is the most aggressive form of lung cancer. NLK expression was evaluated by quantitative real-time polymerase chain reaction in 20 paired fresh SCLC tissue samples and found to be noticeably elevated in tumor tissues. Lentivirus-mediated RNAi efficiently suppressed NLK expression in NCI-H446 cells, resulting in a significant reduction in cell viability and proliferation in vitro...
2016: Drug Design, Development and Therapy
https://www.readbyqxmd.com/read/27893417/genetic-and-epigenetic-silencing-of-mircorna-506-3p-enhances-cotl1-oncogene-expression-to-foster-non-small-lung-cancer-progression
#18
Shanqi Guo, Peiying Yang, Xingkang Jiang, Xiaojiang Li, Yuanyuan Wang, Xin Zhang, Binxu Sun, Yao Zhang, Yingjie Jia
Although previous studies suggested that microRNA-506-3p (miR-506-3p) was frequently downregulated, and functioned as a tumor suppressor in several cancers, the biological role and intrinsic regulatory mechanisms of miR-506-3p in non-small cell lung cancer (NSCLC) remain elusive. The present study found miR-506-3p expression was downregulated in advanced NSCLC tissues and cell lines. The expression of miR-506-3p in NSCLC was inversely correlated with larger tumor size, advanced TNM stage and lymph node metastasis...
November 22, 2016: Oncotarget
https://www.readbyqxmd.com/read/27887846/long-non-coding-rna-metastasis-associated-lung-adenocarcinoma-transcript-1-regulates-the-expression-of-gli2-by-mir-202-to-strengthen-gastric-cancer-progression
#19
Yue Zhang, Zhuo Chen, Ming-Jing Li, Huan-Yu Guo, Nian-Cai Jing
BACKGROUND: Gastric cancer (GC) is one of the most common malignancies and ranks the second leading cause of cancer death worldwide. Some studies had reported the tumor-promoting effects of long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) as a competing endogenous RNA (ceRNA) by sponging to microRNAs. However, the molecular mechanism of ceRNA regulatory pathway involving MALAT1 in GC remains unclear. METHODS: MALAT1 and miR -202 expression was detected by quantitative real time PCR (qRT-PCR) in 60 gastric cancer tissues and adjacent normal tissues, CCK8 cell proliferation assays, cell cycle analysis and cell apoptosis assays were performed to detect the GC cell proliferation and apoptosis...
November 22, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/27878984/sulforaphane-induced-apoptosis-in-xuanwei-lung-adenocarcinoma-cell-line-xwlc-05
#20
Lan Zhou, Qian Yao, Yan Li, Yun-Chao Huang, Hua Jiang, Chuan-Qiong Wang, Lei Fan
BACKGROUND: Xuanwei district in Yunnan Province has the highest incidence of lung cancer in China, especially among non-smoking women. Cruciferous vegetables can reduce lung cancer risk by prompting a protective mechanism against respiratory tract inflammation caused by air pollution, and are rich in sulforaphane, which can induce changes in gene expression. We investigated the effect of sulforaphane-induced apoptosis in Xuanwei lung adenocarcinoma cell line (XWCL-05) to explore the value of sulforaphane in lung cancer prevention and treatment...
November 23, 2016: Thoracic Cancer
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