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https://www.readbyqxmd.com/read/28436883/a-bipartite-network-and-resource-transfer-based-approach-to-infer-lncrna-environmental-factor-associations
#1
Jie Zhou, Yuan-Yuan Shi
Phenotypes and diseases are often determined by the complex interactions between genetic factors and environmental factors (EFs). However, compared with protein-coding genes and microRNAs, there is a paucity of computational methods for understanding the associations between long non-coding RNAs (lncRNAs) and EFs. In this study, we focused on the associations between lncRNA and EFs. By using the common miRNA partners of any pair of lncRNA and EF, based on the competing endogenous RNA (ceRNA) hypothesis and the technique of resources transfer within the experimentally-supported lncRNA-miRNA and miRNA-EF association bipartite networks, we propose an algorithm for predicting new lncRNA-EF associations...
April 18, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28435289/long-noncoding-rna-nbat-1-suppresses-tumorigenesis-and-predicts-favorable-prognosis-in-ovarian-cancer
#2
Changsheng Yan, Yi Jiang, Yicong Wan, Lin Zhang, Jinhui Liu, Shulin Zhou, Wenjun Cheng
Long noncoding RNA (lncRNA) has been proven to be involved in many biological processes in ovarian cancer (OC). However, the mechanism still remains unknown. In this study, we screened significantly downregulated NBAT-1, which has been proven to play a significant role in breast cancer, clear cell renal cell carcinoma, and neuroblastoma, but not in OC, in two independent datasets with relatively more samples (GSE18520 and GSE38666) from Gene Expression Omnibus. We found that lncRNA NBAT-1 was obviously downregulated in OC tissue compared to normal ovarian tissue (P<0...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28433650/long-noncoding-rna-malat1-is-a-potent-autophagy-inducer-protecting-brain-microvascular-endothelial-cells-against-oxygen-glucose-deprivation-reoxygenation-induced-injure-by-sponing-mir-26b-and-upregulating-ulk2-expression
#3
Zhijun Li, Jing Li, Na Tang
Brain microvascular endothelial cell (BMEC) injury induced by ischemia-reperfusion (I/R) is the initial stage of blood-brain barrier (BBB) disruption, which results in a poor prognosis in ischemic stroke patients. Autophagy has been shown to have protective effects on BMECs against cerebral ischemic insults. However, molecular mechanism of BMEC autophagy during I/R is unclear. Long noncoding RNAs (lncRNAs) are emerging as new factors involved in cell autophagy. LncRNA Malat1 is one of the most highly upregulated I/R or OGD/R-responsive endothelial lncRNA and plays a protective role in BMECs against cerebral ischemic insults...
April 19, 2017: Neuroscience
https://www.readbyqxmd.com/read/28431932/the-lncrna-zbed3-as1-induces-chondrogenesis-of-human-synovial-fluid-mesenchymal-stem-cells
#4
Farong Ou, Kai Su, Jiadong Sun, Wenting Liao, Yu Yao, Youhua Zheng, Zhiguang Zhang
Human synovial fluid-derived mesenchymal stem cells (SFMSCs) have great potential for cartilage induction and are promising for cell-based strategies for articular cartilage repair. Many long non-coding RNAs (lncRNAs) regulate chondrogenesis of MSCs. We hypothesized that the divergent lncRNA ZBED3-AS1, which binds locally to chromatin, could promote the expression of zbed3, a novel Axin-interacting protein that activates Wnt/β-catenin signaling, involved in chondrogenesis. However, the function of ZBED3-AS1 in SFMSCs is unclear...
April 18, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28431855/relationship-between-long-noncoding-rnas-and-physiological-risk-factors-of-cardiovascular-disease
#5
REVIEW
Moshen Mazidi, Peter Penson, Anna Gluba-Brzozka, Jacek Rysz, Maciej Banach
Long noncoding ribonucleic acids (lncRNAs) are an important category of noncoding RNAs that play crucial roles in controlling the expression of genes in health and in a range of illnesses including cardiovascular disease. A large body of genetic, experimental, and epidemiologic evidence suggests roles for an increasing number of lncRNAs in the regulation of metabolism, lipid profile, inflammation, and glucose metabolism in type II diabetes. Importantly, it has been suggested that lncRNAs can regulate chromatin alteration, messenger RNA stability, microRNA action, and can control transcription factors...
March 27, 2017: Journal of Clinical Lipidology
https://www.readbyqxmd.com/read/28430799/diagnostic-and-prognostic-value-of-long-noncoding-rnas-as-biomarkers-in-urothelial-carcinoma
#6
Johanna Droop, Tibor Szarvas, Wolfgang A Schulz, Christian Niedworok, Günter Niegisch, Kathrin Scheckenbach, Michèle J Hoffmann
Many long noncoding RNAs (lncRNAs) are deregulated in cancer and contribute to oncogenesis. In urothelial carcinoma (UC), several lncRNAs have been reported to be overexpressed and proposed as biomarkers. As most reports have not been confirmed independently in large tissue sets, we aimed to validate the diagnostic and prognostic value of lncRNA upregulation in independent cohorts of UC patients. Thus, expression of seven lncRNA candidates (GAS5, H19, linc-UBC1, MALAT1, ncRAN, TUG1, UCA1) was measured by RT-qPCR in cell lines and tissues and correlated to clinicopathological parameters including follow-up data (set 1: N n = 10; T n = 106)...
2017: PloS One
https://www.readbyqxmd.com/read/28430659/lncrna-afap1-as1-promotes-growth-and-metastasis-of-cholangiocarcinoma-cells
#7
Xiuhui Shi, Hang Zhang, Min Wang, Xiaodong Xu, Yan Zhao, Ruizhi He, Min Zhang, Min Zhou, Xu Li, Feng Peng, Chengjian Shi, Ming Shen, Xin Wang, Xingjun Guo, Renyi Qin
We investigated the role of actin filament associated protein 1 antisense RNA1 (AFAP1-AS1) lncRNA in promoting cholangiocarcinoma (CCA). qRT-PCR analysis of patient samples showed that AFAP1-AS1 expression was higher in CCA tumors than matched adjacent non-tumor tissue. AFAP1-AS1 levels were also higher in CCA cell lines (HuCCT1 and TFK-1) than a normal biliary epithelium cell line (HIBEpic). AFAP1-AS1 knockdown in CCA cell lines using shAFAP1-AS1 reduced cell proliferation and colony formation in CCK-8 and colony formation assays, respectively...
April 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430627/the-long-non-coding-rna-h19-promotes-cardiomyocyte-apoptosis-in-dilated-cardiomyopathy
#8
Yanlin Zhang, Mengyao Zhang, Weiting Xu, Jianchang Chen, Xiang Zhou
In the previous study, we generated a rat model of dilated cardiomyopathy (DCM) induced by adriamycin and found that the expression of lncRNA H19 was significantly upregulated in myocardial tissue. The present study was aimed to investigate the potential role of H19 in the pathogenesis of adriamycin-induced DCM. H19 knockdown in the myocardium of DCM rats attenuated cardiomyocyte apoptosis and improved left ventricular structure and function. Adriamycin treatment was associated with elevated H19 and miR-675 expression and increased apoptosis in neonatal cardiomyocytes...
February 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430582/lncrna-chrf-induced-mir-489-loss-promotes-metastasis-of-colorectal-cancer-via-twist1-emt-signaling-pathway
#9
Youmao Tao, Tao Han, Tao Zhang, Chong Ma, Caixia Sun
microRNA-489 (miR-489) is a novel cancer-related miRNAs and functions as a tumor suppressor in human cancers. While, the clinical significance of miR-489 and its role in colorectal cancer (CRC) remain rarely known. Here, we found that the levels of miR-489 in CRC tissues were significantly lower than those in matched tumor-adjacent tissues. Furthermore, decreased levels of miR-489 also observed in CRC cell lines compared to HIEC cells. Clinicopathological analysis revealed that miR-489 underexpression was positively correlated with advanced pT stage, pN stage and AJCC stage...
April 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28429752/lncrna-hit-promotes-cell-proliferation-of-non-small-cell-lung-cancer-by-association-with-e2f1
#10
L Yu, F Fang, S Lu, X Li, Y Yang, Z Wang
Lung cancer is the leading cause of cancer-related death around the world. Long noncoding RNA (lncRNA) has pivotal roles in cancer occurrence and development. However, only a few lncRNAs have been functionally characterized. In the present study, we investigated the effects of lncRNA-HIT (HOXA transcript induced by TGFβ) expression on non-small cell lung cancer (NSCLC) cell phenotype with the gain-of-function and loss-of-function assays. We found that ectopic expression or knockdown of lncRNA-HIT markedly increased or decreased NSCLC cell proliferation, respectively...
April 21, 2017: Cancer Gene Therapy
https://www.readbyqxmd.com/read/28428987/microarray-profiling-and-co-expression-network-analysis-of-the-lncrnas-and-mrnas-associated-with-acute-leukemia-in-adults
#11
Hui Cheng, Chong Mei Huang, Yang Wang, Xiao Xia Hu, Xiao Qian Xu, Xian Min Song, Gu Sheng Tang, Li Chen, Jian Min Yang
Acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) are common types of acute leukemia in adults and cause low survival rate and poor outcome after 5 years despite high rates of complete remission (CR) with modern chemotherapeutic regimens. To understand the distinct mechanisms in leukemogenesis for ALL and AML and to identify markers for diagnosis and treatment, lncRNA and mRNA expression profiles of AML and ALL patients and healthy controls were generated using microarray analysis. For comparison, the differentially expressed mRNA functions were annotated using gene ontology (GO) and pathway analysis...
April 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28428004/long-noncoding-rna-awpph-promotes-hepatocellular-carcinoma-progression-through-ybx1-and-serves-as-a-prognostic-biomarker
#12
Xiaodong Zhao, Yanbo Liu, Shuo Yu
Long noncoding RNAs (lncRNAs) have been shown to play important roles in various cancers. However, the clinical significances and biological roles of lncRNAs in hepatocellular carcinoma (HCC) remain largely unknown. In this study, using online-available data sets and quantitative real-time PCR, we identified a novel lncRNA termed lncRNA-AWPPH, which is highly expressed in HCC tissues. Its upregulation is correlated with encapsulation incomplete, microvascular invasion, advanced TNM stage and BCLC stage. Cox proportional hazards regression analysis revealed that high lncRNA-AWPPH expression is an independent prognostic factor for poor recurrence-free and overall survival...
April 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28427943/high-density-lipoprotein-from-coronary-artery-disease-patients-cause-abnormal-expression-of-long-non-coding-rnas-in-vascular-endothelial-cells
#13
Xiang Liu, Tian-Tian Wang, Yan Li, Mao-Mao Shi, Hua-Ming Li, Hao-Xiang Yuan, Zhi-Wei Mo, Jing Chen, Bin Zhang, Yang-Xin Chen, Jing-Feng Wang, Wei-Ping Dai, Ying-Qi Xu, Zhi-Ping Wang, Xi Zhang, Zhi-Jun Ou, Jing-Song Ou
Increased evidence showed that normal high density lipoprotein (HDL) can convert to dysfunction HDL in diseases states including coronary artery disease (CAD), which regulates vascular endothelial cell function differently. Long non-coding RNAs (lncRNAs) play an extensive role in various important biological processes including endothelial cell function. However, whether lncRNAs involved in the regulation of HDL metabolism and HDL-induced changes of vascular endothelial function remains unclear. Cultured human umbilical vein endothelial cells (HUVECs) were treated with HDL from healthy subjects and patients with CAD and hypercholesterolemia for 24 h, then the cells were collected for lncRNA-Seq and the expressions of lncRNAs, genes and mRNAs were identified...
April 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28427208/identification-of-differentially-expressed-lncrnas-involved-in-transient-regeneration-of-the-neonatal-c57bl-6j-mouse-heart-by-next-generation-high-throughput-rna-sequencing
#14
Yu-Mei Chen, Hua Li, Yi Fan, Qi-Jun Zhang, Xing Li, Li-Jie Wu, Zi-Jie Chen, Chun Zhu, Ling-Mei Qian
Previous studies have shown that mammalian cardiac tissue has a regenerative capacity. Remarkably, neonatal mice can regenerate their cardiac tissue for up to 6 days after birth, but this capacity is lost by day 7. In this study, we aimed to explore the expression pattern of long noncoding RNA (lncRNA) during this period and examine the mechanisms underlying this process. We found that 685 lncRNAs and 1833 mRNAs were differentially expressed at P1 and P7 by the next-generation high-throughput RNA sequencing...
March 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28427159/genome-wide-analysis-of-long-noncoding-rna-and-mrna-co-expression-profile-in-intrahepatic-cholangiocarcinoma-tissue-by-rna-sequencing
#15
Wenhui Yang, Yuan Li, Xia Song, Jun Xu, Jun Xie
Long noncoding RNAs (lncRNAs), which are pervasively transcribed in the genome, are emerging in molecular biology as crucial regulators of cancer. RNA-seq data were downloaded from GEO of NCBI and further analyzed to identify novel targets in intrahepatic cholangiocarcinoma (iCCA).We investigated differences in lncRNA and mRNA profiles between 7 pairs of iCCA and adjacent normal tissues. 230 lncRNAs were differentially expressed more than four-fold change in iCCA tissues. Among these, 97 were upregulated and 133 downregulated relatively to normal tissues...
February 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28425476/lncrnas2pathways-identifying-the-pathways-influenced-by-a-set-of-lncrnas-of-interest-based-on-a-global-network-propagation-method
#16
Junwei Han, Siyao Liu, Zeguo Sun, Yunpeng Zhang, Fan Zhang, Chunlong Zhang, Desi Shang, Haixiu Yang, Fei Su, Yanjun Xu, Chunquan Li, Huan Ren, Xia Li
Long non-coding RNAs (lncRNAs) have been demonstrated to play essential roles in diverse cellular processes and biological functions. Exploring the functions associated with lncRNAs may help provide insight into their underlying biological mechanisms. The current methods primarily focus on investigating the functions of individual lncRNAs; however, essential biological functions may be affected by the combinatorial effects of multiple lncRNAs. Here, we have developed a novel computational method, LncRNAs2Pathways, to identify the functional pathways influenced by the combinatorial effects of a set of lncRNAs of interest based on a global network propagation algorithm...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424740/essential-role-of-long-non-coding-rnas-in-de-novo-chromatin-modifications-the-genomic-address-code-hypothesis
#17
Ken Nishikawa, Akira R Kinjo
The epigenome, i.e., the whole of chromatin modifications, is transferred from mother to daughter cells during cell differentiation. When de novo chromatin modifications (establishment or erasure of, respectively, new or pre-existing DNA methylations and/or histone modifications) are made in a daughter cell, however, it has a different epigenome than its mother cell. Although de novo chromatin modification is an important event that comprises elementary processes of cell differentiation, its molecular mechanism remains poorly understood...
April 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28424495/significance-of-genetic-polymorphisms-in-long-non-coding-rna-ac079767-4-in-tuberculosis-susceptibility-and-clinical-phenotype-in-western-chinese-han-population
#18
Zhenzhen Zhao, Mei Zhang, Jun Ying, Xuejiao Hu, Jingya Zhang, Yanhong Zhou, Yi Zhou, Xingbo Song, Binwu Ying
Recent studies have implicated long non-coding RNA, AC079767.4, as a highly susceptible gene in tuberculosis. The aim of the study was to preliminarily explore the possible association of single nucleotide polymorphisms (SNPs) in AC079767.4 gene with clinical phenotypes and TB susceptibility in Western Chinese Han population. The improved multiplex ligation detection reaction (iMLDR) method was employed to genotype 4 SNPs in AC079767.4 in 554 tuberculosis patients and 561 healthy individuals. In subgroup analysis, only the C allele for rs12477677 was associated with the decreased susceptibility to pulmonary TB with a p-value of 0...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28423738/lncrna-snhg1-a-non-degradable-sponge-for-mir-338-promotes-expression-of-proto-oncogene-cst3-in-primary-esophageal-cancer-cells
#19
Yan Yan, Qingxia Fan, Liping Wang, Yue Zhou, Jianhua Li, Kun Zhou
Competing endogenous RNA (ceRNA) is a newly proposed mechanism that describes a crosstalk among lncRNAs, mRNAs and their shared miRNAs. In this study, the role of miR-338-3p (miR-338) in the progression of esophageal cancer and its involve in the ceRNA regulatory circuit lncRNA-Snhg1/CST3 were explored. MiR-338 displayed a 30% decreased expression in esophageal squamous cell carcinoma tissues compared with the adjacent. Then, proto-oncogene CST3 was predicted and validated as a target gene of miR-338. Gain-and-loss-function experiments indicated that miR-338 suppressed expression of CST3 protein (also Cystatin C, CysC), promoted expression of apoptotic proteins caspase-8/3, attenuated esophageal carcinoma cell growth and induced its apoptosis...
March 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423704/prognostic-and-clinicopathological-role-of-long-non-coding-rna-uca1-in-various-carcinomas
#20
Xiaoxiong Wang, Fei Peng, Liang Cheng, Guang Yang, Daming Zhang, Jiaqi Liu, Xin Chen, Shiguang Zhao
Urothelial cancer associated 1 (UCA1) as an oncogenic long non-coding RNA (LncRNA) was aberrantly upregulated in various solid tumors. Numerous studies have demonstrated overexpression of UCA1 is an unfavorable prognostic indicator in cancer patients. This study aimed to further explore the prognosis role and clinical significance of UCA1 in cancer. Eligible studies were recruited by a systematic search in PubMed, Embase, Cochrane Library and Web of Science databases. A total of 19/16 studies with 1587/1291 cancer patients were included to evaluate the association between UCA1 expression and overall survival (OS) and clinicopathological factors of malignancies by computing hazard ratio (HR), odds ratios (OR) and confidence interval (CI)...
March 9, 2017: Oncotarget
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