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miRNA next generation sequencing

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https://www.readbyqxmd.com/read/29154802/microrna-profiling-in-mda-mb-231-human-breast-cancer-cell-exposed-to-the-phaleria-macrocarpa-boerl-fruit-ethyl-acetate-fraction-pmeaf-through-iilumina-hi-seq-technologies-and-various-in-silico-bioinformatics-tools
#1
Nowroji Kavitha, Soundararajan Vijayarathna, Shanmugapriya, Chern Ein Oon, Yeng Chen, Jagat R Kanwar, Vasu Punj, Sreenivasan Sasidharan
ETHNOPHARMACOLOGICAL RELEVANCE: Phaleria macrocarpa (Scheff) Boerl, is a famous traditional medicinal plant which exhibited cytotoxicity against various cancerous cells. Traditionally, P. macrocarpa has been used to control cancer, impotency, hemorrhoids, diabetes mellitus, allergies, liver and heart disease, kidney disorders, blood diseases, acne, stroke, migraine, and various skin diseases. AIM OF THE STUDY: Recent studies have demonstrated a potent anticancer potential of P...
November 14, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/29142263/hyaluronic-acid-35-normalizes-tlr4-signaling-in-kupffer-cells-from-ethanol-fed-rats-via-regulation-of-microrna291b-and-its-target-tollip
#2
Paramananda Saikia, Sanjoy Roychowdhury, Damien Bellos, Katherine A Pollard, Megan R McMullen, Rebecca L McCullough, Arthur J McCullough, Pierre Gholam, Carol de la Motte, Laura E Nagy
TLR4 signaling in hepatic macrophages is increased after chronic ethanol feeding. Treatment of hepatic macrophages after chronic ethanol feeding with small-specific sized hyaluronic acid 35 (HA35) normalizes TLR4 signaling; however, the mechanisms for HA35 action are not completely understood. Here we used Next Generation Sequencing of microRNAs to identify negative regulators of TLR4 signaling reciprocally modulated by ethanol and HA35 in hepatic macrophages. Eleven microRNAs were up-regulated by ethanol; only 4 microRNAs, including miR291b, were decreased by HA35...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29136092/microrpm-a-microrna-prediction-model-based-only-on-plant-small-rna-sequencing-data
#3
Kuan-Chien Tseng, Yi-Fan Chiang-Hsieh, Hsuan Pai, Chi-Nga Chow, Shu-Chuan Lee, Han-Qin Zheng, Po-Li Kuo, Guan-Zhen Li, Yu-Cheng Hung, Na-Sheng Lin, Wen-Chi Chang
Motivation: MicroRNAs (miRNAs) are endogenous non-coding small RNAs (of about 22 nucleotides), which play an important role in the post-transcriptional regulation of gene expression via either mRNA cleavage or translation inhibition. Several machine learning-based approaches have been developed to identify novel miRNAs from next generation sequencing (NGS) data. Typically, precursor/genomic sequences are required as references for most methods. However, the non-availability of genomic sequences is often a limitation in miRNA discovery in non-model plants...
November 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29133016/dynamic-transcriptional-control-of-macrophage-mirna-signature-via-inflammation-responsive-enhancers-revealed-using-a-combination-of-next-generation-sequencing-based-approaches
#4
Zsolt Czimmerer, Attila Horvath, Bence Daniel, Gergely Nagy, Ixchelt Cuaranta-Monroy, Mate Kiss, Zsuzsanna Kolostyak, Szilard Poliska, Laszlo Steiner, Nikolas Giannakis, Tamas Varga, Laszlo Nagy
MicroRNAs are important components of the post-transcriptional fine-tuning of macrophage gene expression in physiological and pathological conditions. However, the mechanistic underpinnings and the cis-acting genomic factors of how macrophage polarizing signals induce miRNA expression changes are not well characterized. Therefore, we systematically evaluated the transcriptional basis underlying the inflammation-mediated regulation of macrophage microRNome using the combination of different next generation sequencing datasets...
November 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29124009/small-rnaome-sequencing-delineates-the-small-rna-landscape-of-pluripotent-adult-stem-cells-in-the-planarian-schmidtea-mediterranea
#5
Yue Li, An Zeng, Xiao-Shuan Han, Ge Li, Yong-Qin Li, Bairong Shen, Qing Jing
Small noncoding RNAs play a pivotal role in the regulation of gene expression, and are key regulators of animal development. Freshwater planarian exhibits an extraordinary ability to regenerate any missing body parts, representing an emerging model for studying mechanism underlying stem cell regulation and tissue regeneration. Here, we utilized next-generation sequencing (NGS) to identify small RNAs that are expressed in planarian adult stem cells, and are implicated in tissue regeneration. We profiled microRNAs (miRNAs), piwi-interacting RNA (piRNAs), small rDNA-derived RNAs (srRNAs) and endogenous interfering RNAs (endo-siRNAs) population from size 18-30 nt, measured the expression of 244 conserved miRNAs, and identified 41 novel miRNAs and 64 novel endo-siRNAs...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/29106599/aspedia-a-comprehensive-encyclopedia-of-human-alternative-splicing
#6
Daejin Hyung, Jihyun Kim, Soo Young Cho, Charny Park
Alternative splicing confers the human genome complexity by increasing the diversity of expressed mRNAs. Hundreds or thousands of splicing regions have been identified through differential alternative splicing analysis of high-throughput datasets. However, it is hard to explain the functional impact of each splicing event. Protein domain formation and nonsense-mediated decay are considered the main functional features of splicing. However, other functional features such as miRNA target sites, phosphorylation sites and single-nucleotide variations are directly affected by alternative splicing and affect downstream function...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29100367/plasma-exosome-mir-196a-and-mir-1246-are-potential-indicators-of-localized-pancreatic-cancer
#7
Yi-Fan Xu, Bethany N Hannafon, Yan D Zhao, Russell G Postier, Wei-Qun Ding
Patients with localized pancreatic cancer (stage I and stage IIA) have a much higher survival rate than those presenting at later stages, yet early detection remains a challenge to this malignancy. The aim of this study was to evaluate whether exosome miRNA signatures are indicative of localized pancreatic cancer. Exosomes were collected from the conditioned media of pancreatic cancer cell lines and plasma samples of localized pancreatic cancer patients (Stage I-IIA, n=15), and healthy subjects (n=15). Cellular and exosome miRNAs from pancreatic cancer cell lines were profiled by next-generation small RNA sequencing...
September 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/29089639/placental-trophoblast-debris-mediated-feto-maternal-signalling-via-small-rna-delivery-implications-for-preeclampsia
#8
Jia Wei, Cherie Blenkiron, Peter Tsai, Joanna L James, Qi Chen, Peter R Stone, Lawrence W Chamley
To profile the small RNA cargo carried by trophoblast debris derived from the placenta during normal and preeclamptic pregnancies and to determine whether trophoblast debris can deliver its small RNAs to endothelial cells with functional consequences. We confirmed that trophoblast debris can deliver its small RNAs contents to recipient endothelial cells during the co-culture. Next generation sequencing was employed to profile the small RNA contents in both normotensive and preeclamptic trophoblast debris. We identified 1278 mature miRNAs and 2646 non-miRNA small RNA fragments contained...
October 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29089558/a-total-transcriptome-profiling-method-for-plasma-derived-extracellular-vesicles-applications-for-liquid-biopsies
#9
Maria G Amorim, Renan Valieris, Rodrigo D Drummond, Melissa P Pizzi, Vanessa M Freitas, Rita Sinigaglia-Coimbra, George A Calin, Renata Pasqualini, Wadih Arap, Israel T Silva, Emmanuel Dias-Neto, Diana N Nunes
Extracellular vesicles (EVs) are key mediators of intercellular communication. Part of their biological effects can be attributed to the transfer of cargos of diverse types of RNAs, which are promising diagnostic and prognostic biomarkers. EVs found in human biofluids are a valuable source for the development of minimally invasive assays. However, the total transcriptional landscape of EVs is still largely unknown. Here we develop a new method for total transcriptome profiling of plasma-derived EVs by next generation sequencing (NGS) from limited quantities of patient-derived clinical samples, which enables the unbiased characterization of the complete RNA cargo, including both small- and long-RNAs, in a single library preparation step...
October 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29073274/transcriptome-analysis-of-mrna-and-micrornas-in-intramuscular-fat-tissues-of-castrated-and-intact-male-chinese-qinchuan-cattle
#10
Ying-Ying Zhang, Hong-Bao Wang, Ya-Ning Wang, Hong-Cheng Wang, Song Zhang, Jie-Yun Hong, Hong-Fang Guo, Dai Chen, Yang Yang, Lin-Sen Zan
Intramuscular fat (IMF) is known to enhance beef palatability and can be markedly increased by castration. However, there is little understanding of the molecular mechanism underlying the IMF deposition after castration of beef cattle. We hypothesize that genetic regulators function differently in IMF from bulls and steers. Therefore, after detecting serum testosterone and lipid parameter, as well as the contents of IMF at 6, 12, 18 and 24 months, we have investigated differentially expressed (DE) microRNAs (miRNAs) and mRNAs in IMF of bulls and steers at 24 months of age in Qinchuan cattle using next-generation sequencing, and then explored the possible biopathways regulating IMF deposition...
2017: PloS One
https://www.readbyqxmd.com/read/29067470/multiple-micrornas-function-as-self-protective-modules-in-acetaminophen-induced-hepatotoxicity-in-humans
#11
Dianke Yu, Leihong Wu, Pritmohinder Gill, William H Tolleson, Si Chen, Jinchun Sun, Bridgett Knox, Yaqiong Jin, Wenming Xiao, Huixiao Hong, Yong Wang, Zhen Ren, Lei Guo, Nan Mei, Yongli Guo, Xi Yang, Leming Shi, Yinting Chen, Linjuan Zeng, Kostiantyn Dreval, Volodymyr Tryndyak, Igor Pogribny, Hong Fang, Tieliu Shi, Sandra McCullough, Sudeepa Bhattacharyya, Laura Schnackenberg, William Mattes, Richard D Beger, Laura James, Weida Tong, Baitang Ning
Acetaminophen (APAP) overdose is the leading cause of acute liver failure. Yet the mechanisms underlying adaptive tolerance toward APAP-induced liver injury are not fully understood. To better understand molecular mechanisms contributing to adaptive tolerance to APAP is an underpinning foundation for APAP-related precision medicine. In the current study, the mRNA and microRNA (miRNA) expression profiles derived from next generation sequencing data for APAP-treated (5 and 10 mM) HepaRG cells and controls were analyzed systematically...
October 24, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/29056573/noncoding-rna-expression-and-targeted-next-generation-sequencing-distinguish-tubulocystic-renal-cell-carcinoma-tc-rcc-from-other-renal-neoplasms
#12
Charles H Lawrie, María Armesto, Marta Fernandez-Mercado, María Arestín, Lorea Manterola, Ibai Goicoechea, Erika Larrea, María M Caffarel, Angela M Araujo, Carla Sole, Maris Sperga, Isabel Alvarado-Cabrero, Michal Michal, Ondrej Hes, José I López
Tubulocystic renal cell carcinoma (TC-RCC) is a rare recently described renal neoplasm characterized by gross, microscopic, and immunohistochemical differences from other renal tumor types and was recently classified as a distinct entity. However, this distinction remains controversial particularly because some genetic studies suggest a close relationship with papillary RCC (PRCC). The molecular basis of this disease remains largely unexplored. We therefore performed noncoding (nc) RNA/miRNA expression analysis and targeted next-generation sequencing mutational profiling on 13 TC-RCC cases (11 pure, two mixed TC-RCC/PRCC) and compared with other renal neoplasms...
October 19, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29049316/genomic-comparison-of-early-passage-conditionally-reprogrammed-breast-cancer-cells-to-their-corresponding-primary-tumors
#13
Akanksha S Mahajan, Bruna M Sugita, Anju N Duttargi, Francisco Saenz, Ewa Krawczyk, Justine N McCutcheon, Aline S Fonseca, Bhaskar Kallakury, Paula Pohlmann, Yuriy Gusev, Luciane R Cavalli
Conditionally reprogrammed cells (CRCs) are epithelial cells that are directly isolated from patients' specimens and propagated in vitro with feeder cells and a Rho kinase inhibitor. A number of these cells have been generated from biopsies of breast cancer patients, including ductal carcinoma in situ and invasive carcinomas. The characterization of their genomic signatures is essential to determine their ability to reflect the natural biology of their tumors of origin. In this study, we performed the genomic characterization of six newly established invasive breast cancer CRC cultures in comparison to the original patients' primary breast tumors (PBT) from which they derived...
2017: PloS One
https://www.readbyqxmd.com/read/29046635/mirna-in-circulating-microvesicles-as-biomarkers-for-age-related-cognitive-decline
#14
Asha Rani, Andrew O'Shea, Lara Ianov, Ronald A Cohen, Adam J Woods, Thomas C Foster
Community dwelling older individuals from the North Florida region were examined for health status and a comprehensive neuropsychological battery, including the Montreal Cognitive Assessment (MoCA), was performed on each participant. A subpopulation (58 females and 39 males) met the criteria for age (60-89) and no evidence of mild cognitive impairment, with a MoCA score ≥23. Despite the stringent criteria for participation, MoCA scores were negatively correlated within the limited age range. Extracellular microvesicles were isolated from the plasma and samples were found to be positive for the exosome marker CD63, with an enrichment of particles within the size range for exosomes...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/29043608/limitations-of-high-throughput-methods-for-mirna-expression-profiles-in-non-functioning-pituitary-adenomas
#15
O Darvasi, P M Szabo, K Nemeth, K Szabo, S Spisak, I Liko, S Czirjak, K Racz, P Igaz, A Patocs, Henriett Butz
Microarray, RT-qPCR based arrays and next-generation-sequencing (NGS) are available high-throughput methods for miRNA profiling (miRNome). Analytical and biological performance of these methods were tested in identification of biologically relevant miRNAs in non-functioning pituitary adenomas (NFPA). miRNome of 4 normal pituitary (NP) and 8 NFPA samples was determined by these platforms and expression of 21 individual miRNAs was measured on 30 (20 NFPA and 10 NP) independent samples. Complex bioinformatics was used...
October 18, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/29042072/mir-200b-downregulates-kruppel-like-factor-2-klf2-during-acute-hypoxia-in-human-endothelial-cells
#16
Rafal Bartoszewski, Marcin Serocki, Anna Janaszak-Jasiecka, Sylwia Bartoszewska, Kinga Kochan-Jamrozy, Arkadiusz Piotrowski, Jarosław Króliczewski, James F Collawn
The role of microRNAs in controlling angiogenesis is recognized as a promising therapeutic target in both cancer and cardiovascular disorders. However, understanding a miRNA's pleiotropic effects on angiogenesis is a limiting factor for these types of therapeutic approaches. Using genome-wide next-generation sequencing, we examined the role of an antiangiogenic miRNA, miR-200b, in primary human endothelial cells. The results indicate that miR-200b has complex effects on hypoxia-induced angiogenesis in human endothelia and importantly, that many of the reported miR-200b effects using miRNA overexpression may not be representative of the physiological role of this miRNA...
December 2017: European Journal of Cell Biology
https://www.readbyqxmd.com/read/29036818/a-9-microrna-signature-in-serum-serves-as-a-noninvasive-biomarker-in-early-diagnosis-of-alzheimer-s-disease
#17
Rui Guo, Gang Fan, Jian Zhang, Chunxiao Wu, Yifeng Du, Hui Ye, Zhang Li, Lili Wang, Zhihui Zhang, Lu Zhang, Yueran Zhao, Zhiming Lu
Alzheimer's disease (AD) is the most common type of age-related neurodegenerative disorder; nevertheless, nowadays there are no reliable biomarkers or non-invasive techniques available for its early detection. Recent studies have indicated that the circulating level profiles of microRNAs (miRNAs) have the potential to be used as valuable biomarkers for diagnosis, staging, and progress monitoring of various diseases. Here we report a novel 9-miRNA signature (hsa-miR-26a-5p, hsa-miR-181c-3p, hsa-miR-126-5p, hsa-miR-22-3p, hsa-miR-148b-5p, hsa-miR-106b-3p, hsa-miR-6119-5p, hsa-miR-1246, and hsa-miR-660-5p) that can be utilized as biomarker for detecting AD...
October 12, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/29036653/mircarta-a-central-repository-for-collecting-mirna-candidates
#18
Christina Backes, Tobias Fehlmann, Fabian Kern, Tim Kehl, Hans-Peter Lenhof, Eckart Meese, Andreas Keller
The continuous increase of available biological data as consequence of modern high-throughput technologies poses new challenges for analysis techniques and database applications. Especially for miRNAs, one class of small non-coding RNAs, many algorithms have been developed to predict new candidates from next-generation sequencing data. While the amount of publications describing novel miRNA candidates keeps steadily increasing, the current gold standard database for miRNAs - miRBase - has not been updated since June 2014...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036601/arrhythmogenic-right-ventricular-cardiomyopathy-implications-of-next-generation-sequencing-and-of-mirnas-regulation-in-appropriate-understanding-and-treatment
#19
Salvatore Patanè, Francesco Patanè
No abstract text is available yet for this article.
October 4, 2017: Europace: European Pacing, Arrhythmias, and Cardiac Electrophysiology
https://www.readbyqxmd.com/read/29020847/sphingolipids-and-microrna-changes-in-blood-following-blast-traumatic-brain-injury-an-exploratory-study
#20
Venkata Siva Sai Sujith Sajja, Anna Jablonska, Norman Haughey, Jeff W M Bulte, Robert D Stevens, Joseph B Long, Piotr Walczak, Miroslaw Janowski
At present, accurate and reliable biomarkers to ascertain the presence, severity, or prognosis of blast traumatic brain injury (bTBI) are lacking. There is an urgent need to establish accurate and reliable biomarkers capable of mbTBI detection. Currently, there are no studies that identify changes in miRNA and lipids at varied severities of bTBI. Various biological components such as lipids, circulating mRNA, and miRNA, could potentially be detected using advanced techniques such as next-generation sequencing and mass spectroscopy...
November 17, 2017: Journal of Neurotrauma
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