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https://www.readbyqxmd.com/read/28821014/efficient-and-accurate-causal-inference-with-hidden-confounders-from-genome-transcriptome-variation-data
#1
Lingfei Wang, Tom Michoel
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for higly accurate causal inference between gene expression traits using cis-regulatory DNA variations as causal anchors, which improves current methods by taking into consideration hidden confounders and weak regulations. Findr outperformed existing methods on the DREAM5 Systems Genetics challenge and on the prediction of microRNA and transcription factor targets in human lymphoblastoid cells, while being nearly a million times faster...
August 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28820886/circulating-mirnas-in-sepsis-a-network-under-attack-an-in-silico-prediction-of-the-potential-existence-of-mirna-sponges-in-sepsis
#2
Catalin Vasilescu, Mihnea Dragomir, Mihai Tanase, Dana Giza, Raluca Purnichescu-Purtan, Meng Chen, Sai-Ching Jim Yeung, George A Calin
Biomarkers based on the molecular mechanism of sepsis are important for timely diagnosis and treatment. A large panel of small non-coding microRNAs was reported to modulate the immune response in sepsis but have not been tested in clinical practice. Large-scale identification of microRNA networks in sepsis might reveal a new biological mechanism that can be also targeted by gene therapy. Therefore, the main objective of this study is to perform a comparison of the miRNA network between septic patients and healthy controls...
2017: PloS One
https://www.readbyqxmd.com/read/28820723/a-lncrna-fine-tunes-the-dynamics-of-a-cell-state-transition-involving-lin28-let-7-and-de-novo-dna-methylation
#3
Meng Amy Li, Paulo P Amaral, Priscilla Cheung, Jan H Bergmann, Masaki Kinoshita, Tüzer Kalkan, Meryem Ralser, Sam Robson, Ferdinand von Meyenn, Maike Paramor, Fengtang Yang, Caifu Chen, Jennifer Nichols, David L Spector, Tony Kouzarides, Lin He, Austin Smith
Execution of pluripotency requires progression from the naïve status represented by mouse embryonic stem cells (ESCs) to a state capacitated for lineage specification. This transition is coordinated at multiple levels. Non-coding RNAs may contribute to this regulatory orchestra. We identified a rodent-specific long non-coding RNA (lncRNA) linc1281, hereafter Ephemeron (Eprn), that modulates the dynamics of exit from naïve pluripotency. Eprn deletion delays the extinction of ESC identity, an effect associated with perduring Nanog expression...
August 18, 2017: ELife
https://www.readbyqxmd.com/read/28820337/paper-title-circular-rnas-isolation-characterisation-and-their-potential-role-in-diseases
#4
Lumei Liu, Jian Wang, Ramin Khanabdali, Bill Kalionis, Xiantao Tai, Shijin Xia
Circular RNA (circRNA) generated by alternative splicing represents a special class of non-coding RNA molecule. CircRNAs are abundant in the eukaryotic cell cytoplasm and have a characteristic organization, timing of action and disease specificity. In contrast to linear RNA, circRNAs are resistant to RNA exonuclease. Consequently, circRNA escapes normal RNA turnover and this improves circRNA stability. CircRNAs can be degraded by microRNA (miRNA) and this results in linearization of the circRNA, which can then act as competitor to endogenous RNA...
August 18, 2017: RNA Biology
https://www.readbyqxmd.com/read/28820329/sources-to-variability-in-circulating-human-mirna-signatures
#5
Andreas Keller, Trine Rounge, Christina Backes, Nicole Ludwig, Randi Gislefoss, Petra Leidinger, Hilde Langseth, Eckart Meese
An increasing number of studies propose circulating microRNAs (miRNAs) as biomarkers for a large number of human diseases including cancer, cardiovascular diseases, neurological pathologies and others. To further validate miRNA as biomarkers it is indispensable to understand the variability of circulating miRNAs in healthy individuals. We determined the longitudinal miRNomes of 90 serum samples from the Janus Serum Bank in Norway, which have been stored between 23 and 40 years at -25 degrees Celsius. We profiled three serum samples with microarrays for 30 individuals, each...
August 18, 2017: RNA Biology
https://www.readbyqxmd.com/read/28820062/urokinase-type-plasminogen-activator-and-the-molecular-mechanisms-of-its-regulation-in-cancer
#6
Juan Francisco Santibanez
Urokinase type plasminogen activator (uPA) is a 53-kDa serine protease initially synthesized as a catalytically inactive single chain polypeptide. Inactive-uPA is subject to proteolytic cleavage which results in the two-chain active protein. uPA plays key roles in the enhancement of cell malignancy during tumor progression. uPA is finely regulated in normal cells, but dysregulated in tumor cells, which results in increased cellular invasion capacities reflecting changes in uPA activity and expression during tumor progression...
August 18, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28819887/can-germ-cell-neoplasia-in-situ-be-diagnosed-by-measuring-serum-levels-of-microrna371a-3p
#7
A Radtke, J-F Cremers, S Kliesch, S Riek, K Junker, S A Mohamed, P Anheuser, G Belge, K-P Dieckmann
PURPOSE: Diagnosing germ cell neoplasia in situ (GCNis) can detect germ cell tumours (GCTs) at the pre-invasive stage. To date, testicular biopsy with the potential of surgical complications is the only way of safely diagnosing GCNis. Recently, microRNAs (miRs) 371-3, and miR 367 were shown to be valuable serum biomarkers of GCTs. We explored the usefulness of these candidate miRs as a marker for GCNis. METHODS: 27 patients with GCNis and no concomitant GCT were enrolled...
August 17, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28819808/mir398-and-mir395-are-involved-in-response-to-so2-stress-in-arabidopsis-thaliana
#8
Lihong Li, Huilan Yi, Meizhao Xue, Min Yi
Sulfur dioxide (SO2) is a common air pollutant that has adverse effects on plants. MicroRNAs (miRNAs) are small noncoding RNA that play critical roles in plant development and stress response. In this study, we found that two miRNAs, miR398 and miR395, were differentially expressed in Arabidopsis shoots under SO2 stress. The expression of miR398 was down-regulated, and the transcript levels of its target genes, Cu/Zn superoxide dismutases (CSD1 and CSD2), were increased during SO2 exposure. The activity of superoxide dismutase (SOD), one of the major antioxidant enzymes, was enhanced with the increase in the CSD transcript level, suggesting an important role of miR398 in response to SO2-induced oxidative stress...
August 17, 2017: Ecotoxicology
https://www.readbyqxmd.com/read/28819748/lipoxin-a4-attenuates-bronchopulmonary-dysplasia-via-upregulation-of-let-7c-and-downregulation-of-tgf-%C3%AE-1-signaling-pathway
#9
Xiao-Qing Chen, Sheng-Hua Wu, Yan-Yan Luo, Bing-Jie Li, Shu-Jun Li, Hong-Yan Lu, Rui Jin, Zhong-Yi Sun
Transforming growth factor-β (TGF-β) superfamily members are key regulators for lung development and progress of bronchopulmonary dysplasia (BPD). The mechanisms by which lipoxin A4 (LXA4) attenuates development of BPD have not been clarified. Neonatal murine BPD models were inducted by hyperoxia treatment. Neonatal mice were exposed to room air or 85% O2 hyperoxia with or without treatment with 5S,6R-methyl-LXA4 or anti-TGF-β antibodies. Mouse lung epithelial cells (MLE-12 cells) and mouse embryonic fibroblasts (NIH/3T3 cells) were cultured in room air or 85% O2 followed by treatment of LXA4, anti-TGF-β antibodies, and let-7c mimic/anti-microRNA transfections...
August 17, 2017: Inflammation
https://www.readbyqxmd.com/read/28819446/incremental-value-of-circulating-mir-122-5p-to-predict-outcome-after-out-of-hospital-cardiac-arrest
#10
Yvan Devaux, Antonio Salgado-Somoza, Josef Dankiewicz, Adeline Boileau, Pascal Stammet, Anna Schritz, Lu Zhang, Mélanie Vausort, Patrik Gilje, David Erlinge, Christian Hassager, Matthew P Wise, Michael Kuiper, Hans Friberg, Niklas Nielsen
Rationale. The value of microRNAs (miRNAs) as biomarkers has been addressed in various clinical contexts. Initial studies suggested that miRNAs, such as the brain-enriched miR-124-3p, might improve outcome prediction after out-of-hospital cardiac arrest. The aim of this study is to determine the prognostic value of miR-122-5p in a large cohort of comatose survivors of out-of-hospital cardiac arrest. Methods. We analyzed 590 patients from the Targeted Temperature Management trial (TTM-trial). Circulating levels of miR-122-5p were measured in serum samples obtained 48 hours after return of spontaneous circulation...
2017: Theranostics
https://www.readbyqxmd.com/read/28819440/microrna-204-5p-inhibits-invasion-and-metastasis-of-laryngeal-squamous-cell-carcinoma-by-suppressing-forkhead-box-c1
#11
Wei Gao, Yongyan Wu, Xiaoling He, Chunming Zhang, Meixia Zhu, Bo Chen, Qingqing Liu, Xukuan Qu, Weiyan Li, Shuxin Wen, Binquan Wang
Background and aim: Understanding the molecular biological mechanisms underlying laryngeal squamous cell carcinoma (LSCC) invasion and metastasis is crucial for diagnosis, treatment, and prognosis. We aimed to examine the expression of the tumor suppressor microRNA-204-5p (miR-204-5p) and its target gene, forkhead box C1 (FOXC1), in human LSCC and explore their roles in the malignant behaviors of LSCC Hep-2 and TU-177 cells. Methods: The regulatory effects of miR-204-5p on the 3' untranslated region of FOXC1 predicted by bioinformatics were tested by dual-luciferase reporter assay...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28819383/metformin-inhibits-tumorigenesis-and-tumor-growth-of-breast-cancer-cells-by-upregulating-mir-200c-but-downregulating-akt2-expression
#12
Jiali Zhang, Gefei Li, Yuan Chen, Lei Fang, Chen Guan, Fumao Bai, Mengni Ma, Jianxin Lyu, Qing H Meng
Background: Metformin has been reported to inhibit the growth of various types of cancers, including breast cancer. Yet the mechanisms underlying the anticancer effects of metformin are not fully understood. Growing evidence suggests that metformin's anticancer effects are mediated at least in part by modulating microRNAs, including miR-200c, which has a tumor suppressive role in breast cancer. We hypothesized that miR-200c has a role in the antitumorigenic effects of metformin on breast cancer cells. Methods: To delineate the role of miR-200c in the effects of metformin on breast cancer, plasmids containing pre-miR-200c or miR-200c inhibitor were transfected into breast cancer cell lines...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28819307/crispr-cas9-editing-reveals-novel-mechanisms-of-clustered-microrna-regulation-and-function
#13
Lazaros Lataniotis, Andreas Albrecht, Fatma O Kok, Clinton A L Monfries, Lorena Benedetti, Nathan D Lawson, Simon M Hughes, Kathleen Steinhofel, Manuel Mayr, Anna Zampetaki
MicroRNAs (miRNAs) are important regulators of diverse physiological and pathophysiological processes. MiRNA families and clusters are two key features in miRNA biology. Here we explore the use of CRISPR/Cas9 as a powerful tool to delineate the function and regulation of miRNA families and clusters. We focused on four miRNA clusters composed of miRNA members of the same family, homo-clusters or different families, hetero-clusters. Our results highlight different regulatory mechanisms in miRNA cluster expression...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818997/ccr2-3-utr-functions-as-a-competing-endogenous-rna-to-inhibit-breast-cancer-metastasis
#14
Jinhang Hu, Xiaoman Li, Xinwei Guo, Qianqian Guo, Chenxi Xiang, Zhiting Zhang, Yingying Xing, Tao Xi, Lufeng Zheng
Diverse RNA transcripts acting as competing endogenous RNAs (ceRNAs) can co-regulate each other's expression by competing for shared microRNAs. CCR2 protein, the receptor of CCL2, is implicated in cancer progression. However, our results showed that higher CCR2 mRNA level was remarkably associated with prolonged survival of breast cancer patients. The conflicting results prompt us to study the non-coding function of CCR2 mRNA. We indicated that CCR2 3'UTR inhibited MDA-MB-231 and MCF-7 cells metastasis by repressing EMT in vitro and suppressed breast cancer metastasis in vivo Mechanistically, CCR2 3'UTR modulated RhoGAP protein STARD13 expression via acting as a STARD13 ceRNA in a microRNA-dependent and protein coding-independent manner...
August 17, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28818587/phenanthrene-responsive-micrornas-and-their-targets-in-wheat-roots
#15
Jinfeng Li, Le Yue, Yu Shen, Yu Sheng, Xinhua Zhan, Guohua Xu, Baoshan Xing
MicroRNAs (miRNAs) play key roles in plant growth, development and responses to abiotic stress. Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants. However, it is yet unknown how miRNAs work during PAH uptake by plant roots. Thus, in this study we ascertain phenanthrene (a model PAH)-responsive miRNAs using small RNA high-throughput deep sequencing and their target genes in wheat roots. We identified 108 conserved and non-conserved miRNA members belonging to 82 miRNA families and found 11 differentially expressed miRNAs, among which four miRNAs (miR156, miR164, miR171a and miR9678-3p) were up-regulated and the other seven miRNAs (miR398, miR531, miR1121, miR5048-5p, miR9653b, miR9773 and miR9778) were down-regulated...
August 8, 2017: Chemosphere
https://www.readbyqxmd.com/read/28818515/integrative-analysis-of-hepatic-microrna-and-mrna-to-identify-potential-biological-pathways-associated-with-monocrotaline-induced-liver-injury-in-mice
#16
Zhenlin Huang, Minwei Chen, Jiaqi Zhang, Yuchen Sheng, Lili Ji
Pyrrolizidine alkaloids (PAs) are a type of natural hepatotoxic compounds. Monocrotaline (MCT), belongs to PAs, is a main compound distributed in medicinal herb Crotalaria ferruginea Grah. ex Benth. This study aims to identify the potential biological signaling pathway associated with MCT-induced liver injury by analyzing the integrative altered hepatic microRNA (miRNA) and mRNA expression profile. C57BL/6 mice were orally given with MCT (270, 330mg/kg). Serum alanine/aspartate aminotransferase (ALT/AST) activity, total bilirubin (TBil) amount and liver histological evaluation showed the liver injury induced by MCT...
August 14, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28818266/microrna-93-elevation-after-myocardial-infarction-is-cardiac-protective
#17
Kai Li, Tao Lin, Lingdan Chen, Neng Wang
Coronary Artery Disease (CAD) is one of the most serious diseases that endangers human health worldwide, myocardial infarction (MI) is an acute form of CAD. Recent developments in MI therapies have resulted in significant reductions in mortality. However, subsequent chronic congestive heart failure and ventricle remodeling plagues an increasing number of MI patients. MicroRNAs (miR) have been reported to be involved in the process of cardiac remodeling, a recent study shows that miR-93 is elevated in the blood of CAD patients...
September 2017: Medical Hypotheses
https://www.readbyqxmd.com/read/28818100/mir-140-5p-suppresses-the-proliferation-migration-and-invasion-of-gastric-cancer-by-regulating-yes1
#18
Zheng Fang, Shuai Yin, Ruochuan Sun, Shangxin Zhang, Min Fu, Youliang Wu, Tao Zhang, Junaid Khaliq, Yongxiang Li
BACKGROUND: The aberrant expression of microRNA-140-5p (miR-140-5p) has been described in gastric cancer (GC). However, the role of miR-140-5p in GC remains unclear. In this study, the prognostic relevance of miR-140-5p in GC was investigated and YES1 was identified as a novel target of miR-140-5p in regulating tumor progression. METHODS: miR-140-5p level was determined in 20 paired frozen specimens through quantitative real-time PCR, and analyzed in tissue microarrays through in situ hybridization...
August 17, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28817918/re-microrna-141-suppresses-prostate-cancer-stem-cells-and-metastasis-by-targeting-a-cohort-of-pro-metastasis-genes
#19
Anthony Atala
No abstract text is available yet for this article.
September 2017: Journal of Urology
https://www.readbyqxmd.com/read/28817830/microrna-200a-inhibits-transforming-growth-factor-%C3%AE-1-induced-proximal-tubular-epithelial-mesenchymal-transition-by-targeting-%C3%AE-catenin
#20
Yi Gong, Zhexue Qin, Baoshang Zhou, Hua Chen, Zhengmin Shi, Jing Zhang
BACKGROUND: The epithelial-mesenchymal transition (EMT) is a crucial event in the development of renal interstitial fibrosis (RIF). A growing body of evidence indicates that β-catenin plays an important role in various types of fibrosis. Although members of the microRNA (miRNA)-200 family have been suggested to suppress EMT in cancer and fibrosis, the function of miRNA-200a in regulating the progression of RIF is unknown. We speculate that miRNA-200a may hinder this progression through the suppression of β-catenin...
August 18, 2017: Nephron
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