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https://www.readbyqxmd.com/read/28727569/comparing-the-performance-of-linear-and-nonlinear-principal-components-in-the-context-of-high-dimensional-genomic-data-integration
#1
Shofiqul Islam, Sonia Anand, Jemila Hamid, Lehana Thabane, Joseph Beyene
Linear principal component analysis (PCA) is a widely used approach to reduce the dimension of gene or miRNA expression data sets. This method relies on the linearity assumption, which often fails to capture the patterns and relationships inherent in the data. Thus, a nonlinear approach such as kernel PCA might be optimal. We develop a copula-based simulation algorithm that takes into account the degree of dependence and nonlinearity observed in these data sets. Using this algorithm, we conduct an extensive simulation to compare the performance of linear and kernel principal component analysis methods towards data integration and death classification...
July 26, 2017: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28727410/exosomes-mediate-epithelium-mesenchyme-crosstalk-in-organ-development
#2
Nan Jiang, Lusai Xiang, Ling He, Guodong Yang, Jinxuan Zheng, Chenglin Wang, Yimei Zhang, Sainan Wang, Yue Zhou, Tzong-Jen Sheu, Jiaqian Wu, Kenian Chen, Paulo G Coelho, Nicky M Tovar, Shin Hye Kim, Mo Chen, Yan-Heng Zhou, Jeremy J Mao
Organ development requires complex signaling by cells in different tissues. Epithelium and mesenchyme interactions are crucial for the development of the skin, hair follicles, kidney, lungs, prostate, major glands and the teeth. Despite myriad literature on cell-cell interactions and ligand-receptor binding, the roles extracellular vesicles in epithelium-mesenchyme interactions during organogenesis are poorly understood. Here, we discovered that ~100 nm exosomes were secreted by the epithelium and mesenchyme of a developing tooth organ, and diffused through the basement membrane...
July 20, 2017: ACS Nano
https://www.readbyqxmd.com/read/28727276/correlation-between-microrna-expression-clinicopathological-characteristics-and-prognosis-in-patients-with-non-small-cell-lung-cancer-a-retrospective-study
#3
Xin Wang, Yi Zhang, Xiuyi Zhi
BACKGROUND: Lung cancer prognosis is related to various factors; however, the comprehensive relationship between these factors, including microRNAs (miRNAs), and lung cancer prognosis has not been determined. Thus, the aim of this study was to identify the key factors associated with lung cancer prognosis. METHODS: We retrospectively analyzed prognosis and relevant factors in 216 non-small cell lung cancer (NSCLC) patients diagnosed from January 2008 to December 2014...
July 20, 2017: Thoracic Cancer
https://www.readbyqxmd.com/read/28726085/micrornas-in-mucosal-inflammation
#4
REVIEW
Viola Neudecker, Xiaoyi Yuan, Jessica L Bowser, Holger K Eltzschig
Of the total human body's surface, the majority is internal surface, belonging to the lungs (100 m(2)) and intestinal tract (400 m(2)). In comparison, the external surface area, belonging to the skin, comprises less than 1% (2 m(2)). Continuous exposure of the mucosal surface to external factors (e.g., pathogens, food particles) requires tight regulation to maintain homeostasis. MicroRNAs (miRNAs) have gained noticeable attention as playing important roles in maintaining the steady-state of tissues by modulating immune functions and inflammatory responses...
July 20, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/28724364/tamoxifen-reverses-epithelial-mesenchymal-transition-by-demethylating-mir-200c-in-triple-negative-breast-cancer-cells
#5
Qian Wang, Yu Cheng, Yan Wang, Yibo Fan, Ce Li, Ye Zhang, Yiding Wang, Qian Dong, Yanju Ma, Yue-E Teng, Xiujuan Qu, Yunpeng Liu
BACKGROUND: Although the efficacy of tamoxifen (TAM) for breast cancer has been attributed to inducing cell cycle arrest and apoptosis by inhibiting estrogen receptor (ER) signaling, recent evidence indicates that TAM also possesses ER-independent antitumor activity through an unclear mechanism. The present study investigated the anti-tumor mechanism of TAM on mesenchymal triple-negative breast cancer (TNBC). METHODS: The inhibitory effect of TAM on tumor migration and metastasis was analyzed by transwell chamber in vitro and by murine xenograft model in vivo...
July 19, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28719033/identification-of-driver-copy-number-alterations-in-diverse-cancer-types-and-application-in-drug-repositioning
#6
Wenbin Zhou, Zhangxiang Zhao, Ruiping Wang, Yue Han, Chengyu Wang, Fan Yang, Ya Han, Haihai Liang, Lishuang Qi, Chenguang Wang, Zheng Guo, Yunyan Gu
Results from numerous studies suggest an important role for somatic copy number alterations (SCNAs) in cancer progression. Our work aimed to identify the drivers (oncogenes or tumor suppressor genes) that reside in recurrently aberrant genomic regions, including a large number of genes or non-coding genes, which remain a challenge for decoding the SCNAs involved in carcinogenesis. Here, we propose a new approach to comprehensively identify drivers, using 8740 cancer samples involving 18 cancer types from The Cancer Genome Atlas (TCGA)...
July 18, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28716897/mcpip1-downregulation-in-clear-cell-renal-cell-carcinoma-promotes-vascularization-and-metastatic-progression
#7
Paulina Marona, Judyta Górka, Zofia Mazurek, Waclaw Wilk, Janusz Rys, Marcin Majka, Jolanta Jura, Katarzyna Miekus
<p>Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer and it forms highly vascularized tumors. The monocyte endoribonuclease MCPIP1 negatively regulates inflammation by degrading mRNA encoding proinflammatory cytokines, such as IL-6, IL-1 and IL-12. MCPIP1 is also a negative regulator of NFκB and AP1 activity and it influences a broad range of miRNA activities. Here we report that MCPIP1 protein levels are decreased during renal cancer progression. In patient-derived tumors, and xenografts established in NOD-SCID or nude mice, low MCPIP1 levels correlated strongly with increased proliferation, tumor outgrowth and vascularity...
July 17, 2017: Cancer Research
https://www.readbyqxmd.com/read/28716020/long-non-coding-rna-casc2-suppresses-epithelial-mesenchymal-transition-of-hepatocellular-carcinoma-cells-through-casc2-mir-367-fbxw7-axis
#8
Yufeng Wang, Zhikui Liu, Bowen Yao, Qing Li, Liang Wang, Cong Wang, Changwei Dou, Meng Xu, Qingguang Liu, Kangsheng Tu
BACKGROUND: Recently, it has been reported that long non-coding RNA (lncRNA) cancer susceptibility candidate 2 (CASC2), a novel tumor suppressor, participates in regulating the carcinogenesis and suppresses tumor progression by sponging microRNAs (miRNAs). However, the expression and function of CASC2 in hepatocellular carcinoma (HCC) remain unclear. METHODS: The expression of CASC2 and miR-367 in HCC specimens and cell lines were detected by real-time PCR. Western blotting and immunohistochemistry were carried out for detection of epithelial-to-mesenchymal transition (EMT) markers in HCC...
July 17, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28714414/role-of-mirna-in-lung-cancer-potential-biomarkers-and-therapies
#9
Xiaohong Du, Jitai Zhang, Juping Wang, Xiaoming Lin, Feng Ding
MicroRNAs (miRNAs) are small noncoding RNAs, which downregulate gene expression by repressing or degrading mRNA targets. Lung cancer (LC), together with liver and colorectal cancers are the three leading causes of cancer death worldwide, and 80% of LCs belong to non-small cell lung cancers (NSCLCs). Despite a great advancement in developing distinct and delicate tools for early diagnosis and targeted therapies over the last decade, only about 15% of the NSCLC patients eventually survived. MiRNAs are frequently dysregulated in carcinoma, including LC...
July 14, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28714413/mirna-based-therapeutics-for-lung-cancer
#10
Miaowei Wu, Guosheng Wang, Wei Tian, Yongchuan Deng, Yibing Xu
BACKGROUND: miRNA, a small non-coding RNA molecule containing about 22 nucleotides, functions in RNA silencing and post-transcriptional regulation of gene expression. With these qualities, miRNAs modulate multiple signaling pathways involved in cancer development, such as cellular proliferation, apoptosis, and migration. METHODS: The goal of this review is to discuss possible miRNAs-based therapeutic strategies, through defining performance of miRNAs in carcinogenesis, in particular in lung cancer...
July 14, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28714412/regulation-mechanism-of-micrornas-in-non-small-cell-lung-cancer
#11
Feng-Yun Gong, Tao Bai, Ding-Yu Zhang, Chao-Lin Huang, Jing Lv, Jing-Li Wang, Xu-Dong Hu, Juan Wang, Wei Liu
MicroRNAs are small non-coding RNAs with regulatory biological activity, by modulating target genes on epigenetic, transcriptional, post-transciptional and translational levels. Hundreds of reports indicated that miRNAs play important roles in non-small cell lung cancer (NSCLC). Actually, microRNAs are both regulation targets and regulators targeting effector genes. This article reviewed multifaceted role of microRNAs associated to NSCLC, not only targeting to but also targeted by tumor related genes, to help us understand microRNAs related complex regulation networks...
July 14, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28714018/mir-125a-5p-upregulation-suppresses-the-proliferation-and-induces-the-cell-apoptosis-of-lung-adenocarcinoma-by-targeting-nedd9
#12
Hong Zheng, Jianbo Wu, Jiachen Shi, Chunya Lu, Yuanyuan Wang, Qianqian Sun, Guojun Zhang, Guoqiang Zhao
MicroRNAs (miRNAs) are critical translational regulators that act as oncogenes or tumor-suppressor genes. qRT-PCR assay results showed that the expression levels of miR-125a-5p are lower in lung adenocarcinoma (AD) tissues than expression levels in adjacent non-neoplastic tissues. This relative expression was found to be significantly associated with lymph node metastases. Cell growth, apoptosis, caspase activity and Transwell invasion assay results showed that in two lung adenocarcinoma cell lines transfected with a miR-125a-5p mimic, proliferation and invasion rates were found to be significantly reduced, whereas the apoptosis rate of the miR-125a-5p mimic group was enhanced...
July 13, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28714014/microrna-219-is-downregulated-in-non-small-cell-lung-cancer-and-inhibits-cell-growth-and-metastasis-by-targeting-hmga2
#13
Xiaoping Sun, Min Xu, Haiyan Liu, Kunxiu Ming
Lung cancer is the most commonly diagnosed cancer and the leading cause of cancer-associated mortality worldwide. Non-small cell lung cancer (NSCLC) is the predominant type of lung cancer, and accounts for ~85% of all lung cancer cases. An increasing number of studies suggest that microRNAs (miRs) may be involved in the regulation of NSCLC carcinogenesis and progression. However, the expression and function of miRNA-219 in NSCLC, and its underlying mechanisms of action, remain unknown. In the present study, miR-219 expression in NSCLC tissues and cell lines was determined using reverse transcription-quantitative polymerase chain reaction...
July 15, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28713998/identification-of-micrornas-in-acute-respiratory-distress-syndrome-based-on-microrna-expression-profile-in-rats
#14
Yinghui Guan, Xiang Jin, Xingang Liu, Yuanping Huang, Man Wang, Xiaodan Li
Acute respiratory distress syndrome (ARDS) remains a severe disease associated with an ~40% mortality rate and as many as 200,000 new cases annually. MicroRNAs (miRNAs) have important roles in gene regulation and cancer development. The present study aimed to identify the potential roles of miRNAs in the pathogenesis and progression of ARDS. The miRNA expression profile of the GSE57223 dataset was downloaded from the Gene Expression Omnibus database. Following data normalization, differentially expressed miRNAs were identified using the t‑test method...
July 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28713980/mirna%C3%A2-1284-inhibits-cell-growth-and-induces-apoptosis-of-lung-cancer-cells
#15
Jie Li, Hairong Jin, Hua Yu, Bin Wang, Jian Tang
Lung cancer is the most common cancer worldwide, and morbidity and mortality associated with lung cancer has been increasing annually in recent decades. MicroRNAs (miRNAs), which are short non‑coding RNA sequences that are involved in the regulation of gene expression, have been previously demonstrated to be key regulators in cancer. The present study aimed to clarify the role of miRNA (miR)‑1284 in lung cancer. A549 lung carcinoma cells were transfected with miR‑1284 mimic or miR‑1284 inhibitor using Lipofectamine 2000...
July 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28713974/mirna-125b-regulates-apoptosis-of-human-non-small-cell-lung-cancer-via-the-pi3k-akt-gsk3%C3%AE-signaling-pathway
#16
Yingyi Wang, Ming Zhao, Jieying Liu, Zhao Sun, Jianjiao Ni, Hongsheng Liu
The present investigation demonstrated that regulation of microRNA (miR)-125b affected the apoptosis of human non-small cell lung cancer (NSCLC) through targeting of the PI3K/Akt and Wnt/β-catenin signaling pathways. The expression of miR-125b was assessed in patients with NSCLC, which demonstrated that miR-125b expression in NSCLC tissue was higher than that in para-carcinoma tissue. Furthermore, survival analysis of patients with NSCLC over 3 years indicated that the overall survival (OS) and disease-free survival (DFS) rates of patients with low miR-125b expression were higher than those of patients with high miR-125b expression...
July 12, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28710117/genetic-and-epigenetic-drivers-of-neuroendocrine-tumors-net
#17
Annunziata Di Domenico, Tabea Wiedmer, Ilaria Marinoni, Aurel Perren
Neuroendocrine tumors (NET) of the gastrointestinal tract and the lung are a rare and heterogeneous group of tumors. The molecular characterization and the clinical classification of these tumors have been evolving slowly and show differences according to organs of origin. Novel technologies such as next-generation sequencing revealed new molecular aspects of NET over the last years. Notably, whole exome/genome sequencing (WES/WGS) approaches underlined the very low mutation rate of well differentiated NET of all organs compared to other malignancies, while the engagement of epigenetic changes in driving NET evolution is emerging...
July 14, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28697764/long-non-coding-rna-linc00673-regulated-non-small-cell-lung-cancer-proliferation-migration-invasion-and-epithelial-mesenchymal-transition-by-sponging-mir-150-5p
#18
Wei Lu, Honghe Zhang, Yuequn Niu, Yongfeng Wu, Wenjie Sun, Hongyi Li, Jianlu Kong, Kefeng Ding, Han-Ming Shen, Han Wu, Dajing Xia, Yihua Wu
BACKGROUND: The function of a new long non-coding RNA linc00673 remains unclear. While identified as an oncogenic player in non-small cell lung cancer (NSCLC), linc00673 was found to be anti-oncogenic in pancreatic ductal adenocarcinoma (PDAC). However whether linc00673 regulated malignancy and epithelial mesenchymal transition (EMT) has not been characterized. METHODS: Cell proliferation was assessed using CCK-8 and EdU assays, and cell migration and invasion were assessed using scratch assays and transwell invasion assays...
July 11, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28694795/modulation-of-host-mirnas-transcriptome-in-lung-and-spleen-of-peste-des-petits-ruminants-virus-infected-sheep-and-goats
#19
Aruna Pandey, Amit R Sahu, Sajad A Wani, Shikha Saxena, Sonam Kanchan, Vaishali Sah, Kaushal K Rajak, Alok Khanduri, Aditya P Sahoo, Ashok K Tiwari, Bina Mishra, D Muthuchelvan, Bishnu P Mishra, Raj K Singh, Ravi K Gandham
Peste des petits ruminants (PPR) is one of the highly contagious viral disease, characterized by fever, sore mouth, conjunctivitis, gastroenteritis, and pneumonia, primarily affecting sheep and goats. Reports suggested variable host response in goats and sheep and this host response vis-a-vis the expression of microRNAs (miRNAs) has not been investigated. Here, miRNAs were sequenced and proteomics data were generated to identify the role of differentially expressed miRNA (DEmiRNA) in PPR virus (PPRV) infected lung and spleen tissues of sheep and goats...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28692419/long-term-cigarette-smoke-exposure-and-changes-in-mirna-expression-and-proteome-in-non-small-cell-lung-cancer
#20
Jayshree Advani, Yashwanth Subbannayya, Krishna Patel, Aafaque Ahmad Khan, Arun H Patil, Ankit P Jain, Hitendra S Solanki, Aneesha Radhakrishnan, Sneha M Pinto, Nandini A Sahasrabuddhe, Joji K Thomas, Premendu P Mathur, Bipin G Nair, Xiaofei Chang, T S Keshava Prasad, David Sidransky, Harsha Gowda, Aditi Chatterjee
Chronic exposure to cigarette smoke markedly increases the risk for lung cancer. Regulation of gene expression at the post-transcriptional level by miRNAs influences a variety of cancer-related interactomes. Yet, relatively little is known on the effects of long-term cigarette smoke exposure on miRNA expression and gene regulation. NCI-H292 (H292) is a cell line sensitive to cigarette smoke with mucoepidermoid characteristics in culture. We report, in this study, original observations on long-term (12 months) cigarette smoke effects in the H292 cell line, using microarray-based miRNA expression profiling, and stable isotopic labeling with amino acids in cell culture-based quantitative proteomic analysis...
July 2017: Omics: a Journal of Integrative Biology
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