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miRNA next generation sequencing

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https://www.readbyqxmd.com/read/28798252/pollen-induced-oxidative-dna-damage-response-regulates-mirnas-controlling-allergic-inflammation
#1
Leopoldo Aguilera-Aguirre, Wenjing Hao, Lang Pan, Xiaoxue Li, Alfredo Saavedra-Molina, Attila Bacsi, Zsolt Radak, Sanjiv Sur, Allan R Brasier, Xueqing Ba, Istvan Boldogh
A mucosal oxidative burst is a hallmark response to pollen exposure that promotes allergic inflammatory responses. Reactive species constituents of oxidative stress signal via the modification of cellular molecules including nucleic acids. One of the most abundant oxidative genomic base damage is 8-oxo-7,8-dihydroguanine (8-oxoG), which is removed from DNA by 8-oxoguanine DNA glycosylase1 (OGG1). OGG1 in complex with 8-oxoG acts as a GDP-GTP exchange factor and induces acute inflammation; however, the mechanism(s) by which OGG1 signaling regulates allergic airway inflammation is not known...
August 10, 2017: American Journal of Physiology. Lung Cellular and Molecular Physiology
https://www.readbyqxmd.com/read/28791028/trna-derived-smallrnas-smallrnas-repertoire-has-yet-to-be-decoded-in-plants
#2
Gaurav Sablok, Kun Yang, Rui Chen, Xiaopeng Wen
Among several smallRNAs classes, microRNAs play an important role in controlling the post-transcriptional events. Next generation sequencing has played a major role in extending the landscape of miRNAs and revealing their spatio-temporal roles in development and abiotic stress. Lateral evolution of these smallRNAs classes have widely been seen with the recently emerging knowledge on tRNA derived smallRNAs. In the present perspective, we discussed classification, identification and roles of tRNA derived smallRNAs across plants and their potential involvement in abiotic and biotic stresses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28760335/microrna-21-regulates-peroxisome-proliferator-activated-receptor-alpha-a-molecular-mechanism-of-cardiac-pathology-in-cardiorenal-syndrome-type-4
#3
Sandra Chuppa, Mingyu Liang, Pengyuan Liu, Yong Liu, Marc C Casati, Allen W Cowley, Leah Patullo, Alison J Kriegel
Cardiovascular events are the leading cause of death in patients with chronic kidney disease (CKD), although the pathological mechanisms are poorly understood. Here we longitudinally characterized left ventricle pathology in a 5/6 nephrectomy rat model of CKD and identify novel molecular mediators. Next-generation sequencing of left ventricle mRNA and microRNA (miRNA) was performed at physiologically distinct points in disease progression, identifying alterations in genes in numerous immune, lipid metabolism, and inflammatory pathways, as well as several miRNAs...
July 28, 2017: Kidney International
https://www.readbyqxmd.com/read/28748475/next-generation-sequencing-to-investigate-urinary-micrornas-from-macaca-fascicularis-cynomolgus-monkey
#4
Yaligara Veeranagouda, Jean-François Léonard, Jean-Charles Gautier, Eric Boitier
Advanced sequencing technologies like next-generation sequencing (NGS) not only detect microRNAs (miRNAs) in biological samples but also facilitate de novo identification of miRNAs. Using an Ion Torrent's Ion Proton System, here we described miRNAs sequencing of urine samples collected from Macaca fascicularis (Cynomolgus monkey) to investigate miRNAs as potential novel biomarkers of nephrotoxicity in this species. Urinary miRNA sequencing methodologies described here include (a) urinary exosomal RNA isolation, (b) sequencing library preparation, (c) sequencing template preparation, and (d) template library sequencing using Ion Proton System...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28743667/integrative-analysis-of-mrna-and-mirna-expression-profiles-in-oral-lichen-planus-preliminary-results
#5
Junjun Chen, Guanhuan Du, Yufeng Wang, Linjun Shi, Jun Mi, Guoyao Tang
OBJECTIVE: Oral lichen planus (OLP), a chronic inflammatory disease of unknown etiology, is considered a potentially malignant oral disorder. The aim of the present study was to analyze candidate microRNAs (miRNAs) and genes from patients with OLP and healthy controls (HCs). STUDY DESIGN: Biopsy specimens of the oral mucosa were collected from patients with OLP (n = 9) and from HCs (n = 4). Differentially expressed miRNAs and differentially expressed genes were screened by using next-generation sequencing with DESeq and edgeR software algorithms...
June 8, 2017: Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology
https://www.readbyqxmd.com/read/28740838/a-rare-case-of-centronuclear-myopathy-with-dnm2-mutation-genotype-phenotype-correlation
#6
REVIEW
Amir Ghorbani Aghbolaghi, Mirna Lechpammer
Centronuclear myopathy (CNM) is a group of rare genetic muscle disorders characterized by muscle fibers with centrally located nuclei. The most common forms of CNM have been attributed to X-linked recessive mutations in the MTM1 gene; autosomal-dominant mutations in the DNM2 gene-encoding dynamin-2, the BIN1 gene; and autosomal-recessive mutations in BIN1, RYR1, and TTN genes. Dominant CNM due to DNM2 mutations usually follows a mild clinical course with the onset in adolescence. Currently, around 35 mutations of the DNM2 gene have been identified in CNM; however, the underlying molecular mechanism of DNM2 mutation in the pathology of CNM remains elusive, and the standard clinical characteristics have not yet been defined...
April 2017: Autopsy & case reports
https://www.readbyqxmd.com/read/28722430/multi-amplified-sensing-of-microrna-by-a-small-dna-fragment-driven-enzymatic-cascade-reaction
#7
Eunjung Kim, Philip D Howes, Spencer W Crowder, Molly M Stevens
Combining technological developments such as nanomaterials, DNA nanotechnology, and functional enzymes has great potential to facilitate next generation high performance molecular diagnostic systems. In this work, we describe a microRNA (miRNA) detection assay that combines target recycling and isothermal amplification in an elegantly designed enzyme-mediated cascade reaction. Target recycling is driven by the action of duplex-specific nuclease (DSN), resulting in highly amplified translation of input miRNA to short output DNA fragments...
January 27, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28710117/genetic-and-epigenetic-drivers-of-neuroendocrine-tumors-net
#8
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/28704519/e2f1-somatic-mutation-within-mirna-target-site-impairs-gene-regulation-in-colorectal-cancer
#9
Camila M Lopes-Ramos, Bruna P Barros, Fernanda C Koyama, Paola A Carpinetti, Julia Pezuk, Nayara T S Doimo, Angelita Habr-Gama, Rodrigo O Perez, Raphael B Parmigiani
BACKGROUND: Genetic studies have largely concentrated on the impact of somatic mutations found in coding regions, and have neglected mutations outside of these. However, 3' untranslated regions (3' UTR) mutations can also disrupt or create miRNA target sites, and trigger oncogene activation or tumor suppressor inactivation. METHODS: We used next-generation sequencing to widely screen for genetic alterations within predicted miRNA target sites of oncogenes associated with colorectal cancer, and evaluated the functional impact of a new somatic mutation...
2017: PloS One
https://www.readbyqxmd.com/read/28704127/retinal-mirnas-variations-in-a-large-cohort-of-inherited-retinal-disease
#10
Xiu-Feng Huang, Zhi-Qin Huang, Xiao-Long Fang, Zhen-Ji Chen, Wan Cheng, Zi-Bing Jin
BACKGROUND: Although great efforts have been paid on identification of genetic predisposition in the inherited retinal disease (IRD), genetic causes of a large proportion of patients remain a mystery. This dilemma makes us attempt to speculate that genetic components other than coding genes might be an additional pool predisposing IRD. In this study, we aim to perform a mutational screening in a large cohort of IRD patients with a particular focus on retina-specific or abundant microRNAs (miRs)...
July 13, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28703747/the-prostate-cancer-cells-resistant-to-docetaxel-as-in-vitro-model-for-discovering-micrornas-predictive-of-the-onset-of-docetaxel-resistance
#11
Lorenzo Bascetta, Arianna Oliviero, Romina D'Aurizio, Monica Evangelista, Alberto Mercatanti, Marco Pellegrini, Francesca Marrocolo, Sergio Bracarda, Milena Rizzo
On the grounds that miRNAs present in the blood of prostate cancer (PCa) patients are released in the growth medium by PCa cells, it is conceivable that PCa cells resistant to docetaxel (DCT) (DCT(R)) will release miRNAs that may be found in PCa patients under DCT therapy if resistant PCa cells appear. We isolated DCT(R) clones respectively from 22Rv1 and DU-145 PCa cell lines and performed through next-generation sequencing (NGS) the miRNAs profiles of the released miRNAs. The analysis of the NGS data identified 105 and 1 miRNAs which were differentially released in the growth medium of the 22Rv1/DCT(R) and DU-145/DCT(R) clones, respectively...
July 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28702194/elevation-of-brain-enriched-mirnas-in-cerebrospinal-fluid-of-patients-with-acute-ischemic-stroke
#12
Sofie Sølvsten Sørensen, Ann-Britt Nygaard, Anting Liu Carlsen, Niels H H Heegaard, Mads Bak, Thomas Christensen
BACKGROUND: The purpose of this study was to investigate the potential of cerebrospinal fluid miRNAs as diagnostic biomarkers of acute ischemic stroke using three different profiling techniques in order to identify and bypass any influence from technical variation. METHODS: Cerebrospinal fluid (CSF) from patients with acute ischemic stroke (n = 21) and controls (n = 21) was collected by lumbar puncture. miRNA analysis was performed with three different methods: 1) Trizol RNA extraction followed by Illumina Next Generation Sequencing (NGS) on all small RNAs, 2) Exiqon RNA extraction protocol and miRNA qPCR assays, and 3) validation of 24 selected miRNAs with Norgen Biotek RNA extraction protocol and Applied Biosystems qPCR assays...
2017: Biomarker Research
https://www.readbyqxmd.com/read/28685435/hypoxia-related-tumor-acidosis-affects-microrna-expression-pattern-in-prostate-and-breast-tumor-cells
#13
A Riemann, S Reime, O Thews
MicroRNAs (miRNAs) are small non-coding RNA sequences which are able to modulate the expression of many functional proteins. The expression level of miRNAs can be modulated by parameters of the tumor microenvironment like hypoxia, nutrient deprivation or oxidative stress. Since miRNAs can act either as oncogenes or tumor suppressors, this may affect malignant progression or therapy resistance. In the present study it was analyzed whether extracellular acidosis can impact on miRNA expression. Therefore, tumor cells (R3327-AT-1 prostate and Walker-256 mammary carcinoma cells) were incubated at pH 6...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28678424/the-metabolic-syndrome-alters-the-mirna-signature-of-porcine-adipose-tissue-derived-mesenchymal-stem-cells
#14
Yu Meng, Alfonso Eirin, Xiang-Yang Zhu, Hui Tang, Pritha Chanana, Amir Lerman, Andre J Van Wijnen, Lilach O Lerman
Autologous transplantation of mesenchymal stem cells (MSCs) is a viable option for the treatment of several diseases. Evidence indicates that MSCs release extracellular vesicles (EVs) and that EVs shuttle miRNAs to damaged parenchymal cells to activate an endogenous repair program. We hypothesize that comorbidities may interfere with the packaging of cargo in MSC-derived EVs. Therefore, we examined whether metabolic syndrome (MetS) modulates the miRNA content packed within MSC-derived EVs. MSCs were collected from swine abdominal adipose tissue after 16 weeks of lean or obese diet (n = 7 each)...
July 5, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28666407/small-rna-fragments-derived-from-multiple-rna-classes-the-missing-element-of-multi-omics-characteristics-of-the-hepatitis-c-virus-cell-culture-model
#15
Paulina Jackowiak, Anna Hojka-Osinska, Anna Philips, Agnieszka Zmienko, Lucyna Budzko, Patrick Maillard, Agata Budkowska, Marek Figlerowicz
BACKGROUND: A pool of small RNA fragments (RFs) derived from diverse cellular RNAs has recently emerged as a rich source of functionally relevant molecules. Although their formation and accumulation has been connected to various stress conditions, the knowledge on RFs produced upon viral infections is very limited. Here, we applied the next generation sequencing (NGS) to characterize RFs generated in the hepatitis C virus (HCV) cell culture model (HCV-permissive Huh-7.5 cell line). RESULTS: We found that both infected and non-infected cells contained a wide spectrum of RFs derived from virtually all RNA classes...
June 30, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28655866/microrna-profiling-associated-with-non-small-cell-lung-cancer-next-generation-sequencing-detection-experimental-validation-and-prognostic-value
#16
Sandra Gallach, Eloisa Jantus-Lewintre, Silvia Calabuig-Fariñas, David Montaner, Sergio Alonso, Rafael Sirera, Ana Blasco, Marta Usó, Ricardo Guijarro, Miguel Martorell, Carlos Camps
BACKGROUND: The average five-year survival index for non-small cell lung cancer (NSCLC) patients is approximately 15%. Emerging evidence indicates that microRNAs constitute a new class of gene regulators in humans that may play an important role in tumorigenesis. Hence, there is growing interest in studying their role as possible new biomarkers whose expression is aberrant in cancer. Therefore, in this study we identified deregulated miRNAs by next generation sequencing (NGS) and analyzed their prognostic value...
June 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28649807/microrna-196-regulates-hox-gene-expression-in-human-gluteal-adipose-tissue
#17
Adeline Divoux, Hui Xie, Jian-Liang Li, Kalypso Karastergiou, Ranjan J Perera, R Jeffrey Chang, Susan K Fried, Steven R Smith
OBJECTIVE: Lower body fat is associated with diminishing cardiometabolic risk. Physiological differences between gluteofemoral and abdominal subcutaneous adipocyte functions are known, but the molecular basis for depot differences in adipocyte function is poorly understood. The objective of this study was to identify depot differences in microRNA (miRNA) expression in human abdominal and gluteofemoral subcutaneous adipose tissues and their implication in gene regulation. METHODS: Abdominal and gluteofemoral adipose tissue aspirates obtained from 18 participants (9 male and 9 female, age 30 ± 1...
August 2017: Obesity
https://www.readbyqxmd.com/read/28643865/characterization-and-biological-function-of-milk-derived-mirnas
#18
Regina Golan-Gerstl, Yaffa Elbaum Shiff, Vardit Lavi-Moshayoff, Daniel Schecter Dena Leshkowitz, Shimon Reif
SCOPE: Breastfeeding is associated with reduced risk of infection, immune mediated disorders, obesity and even cancer. Recently it was found that breast milk contains a variety of microRNAs (miRNAs) in the skim and fat layer that can be transferred to infants, and appear to play important roles in those biological functions. METHODS AND RESULTS: This study applied Next Generation Sequencing and quantitative real time PCR analysis to determine the miRNA expression profile of the skim and fat fraction of human, goat, and bovine milk as well as infant formulas...
June 23, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28641312/impact-of-novel-mir-145-3p-regulatory-networks-on-survival-in-patients-with-castration-resistant-prostate-cancer
#19
Yusuke Goto, Akira Kurozumi, Takayuki Arai, Nijiro Nohata, Satoko Kojima, Atsushi Okato, Mayuko Kato, Kazuto Yamazaki, Yasuo Ishida, Yukio Naya, Tomohiko Ichikawa, Naohiko Seki
BACKGROUND: Despite recent advancements, metastatic castration-resistant prostate cancer (CRPC) is not considered curative. Novel approaches for identification of therapeutic targets of CRPC are needed. METHODS: Next-generation sequencing revealed 945-1248 miRNAs from each lethal mCRPC sample. We constructed miRNA expression signatures of CRPC by comparing the expression of miRNAs between CRPC and normal prostate tissue or hormone-sensitive prostate cancer (HSPC)...
July 25, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28626163/lower-serum-levels-of-mir-29c-3p-and-mir-19b-3p-as-biomarkers-for-alzheimer-s-disease
#20
Yuquan Wu, Juan Xu, Jing Xu, Jun Cheng, Demin Jiao, Chun Zhou, Yi Dai, Qingyong Chen
MicroRNAs (miRNAs) are short noncoding RNA that participate in posttranscriptional gene regulation. However, little is understood about the roles of miRNAs in Alzheimer's disease (AD). In this study, we used next-generation sequencing on RNA extracted from the serum samples of 20 AD patients and 20 controls, yielding a total of 72 miRNAs with significantly changed expression levels. Among these candidates, we selected 9 miRNAs with most significant alteration in disease, and validated their expression levels using RT-qPCR analysis on serum samples from 45 AD patients and 40 control subjects...
June 2017: Tohoku Journal of Experimental Medicine
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