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exosome and RNA sequence

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https://www.readbyqxmd.com/read/29140524/noncodev5-a-comprehensive-annotation-database-for-long-non-coding-rnas
#1
ShuangSang Fang, LiLi Zhang, JinCheng Guo, YiWei Niu, Yang Wu, Hui Li, LianHe Zhao, XiYuan Li, XueYi Teng, XianHui Sun, Liang Sun, Michael Q Zhang, RunSheng Chen, Yi Zhao
NONCODE (http://www.bioinfo.org/noncode/) is a systematic database that is dedicated to presenting the most complete collection and annotation of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs). Since NONCODE 2016 was released two years ago, the amount of novel identified ncRNAs has been enlarged by the reduced cost of next-generation sequencing, which has produced an explosion of newly identified data. The third-generation sequencing revolution has also offered longer and more accurate annotations...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29133115/structural-features-of-the-interaction-of-the-3-untranslated-region-of-mrna-containing-exosomal-rna-specific-motifs-with-yb-1-a-potential-mediator-of-mrna-sorting
#2
Darya D Yanshina, Olga A Kossinova, Alexander V Gopanenko, Olga A Krasheninina, Alexey A Malygin, Alia G Ven'yaminova, Galina G Karpova
We have previously shown that YB-1 is the only protein of the HEK293 cell cytoplasmic (S100) extract that specifically interacts with RNA hairpins each containing one of the motifs ACCAGCCU (1), CAGUGAGC (2) and UAAUCCCA (3), which had been identified as often found in exosomal RNA and proposed as potential cis-acting elements targeting RNAs into exosomes. Here we explored the interactions of YB-1 with a fragment of the 3'-untranslated region (UTR) of septin 14 mRNA (SEPT14 RNA), which contains all three motifs...
November 10, 2017: Biochimie
https://www.readbyqxmd.com/read/29112229/biobehavioral-modulation-of-the-exosome-transcriptome-in-ovarian-carcinoma
#3
Susan K Lutgendorf, Premal H Thaker, Jesusa M Arevalo, Michael J Goodheart, George M Slavich, Anil K Sood, Steve W Cole
BACKGROUND: Social factors in the patient macroenvironment have been shown to influence molecular events in the tumor microenvironment and thereby influence cancer progression. However, biomarkers providing a window into the longitudinal effects of biobehavioral factors on tumor biology over time are lacking. Exosome analysis is a novel strategy for in vivo monitoring of dynamic changes in tumor cells. This study examined exosomal profiles from patients with low or high levels of social support for epithelial-mesenchymal transition (EMT) polarization and gene expression related to inflammation and β-adrenergic signaling...
November 7, 2017: Cancer
https://www.readbyqxmd.com/read/29108237/the-circrna-interactome-innovative-hallmarks-of-the-intra-and-extracellular-radiation-response
#4
Valerie Bríd O'Leary, Jan Smida, Martina Matjanovski, Corinna Brockhaus, Klaudia Winkler, Simone Moertl, Saak Victor Ovsepian, Michael John Atkinson
Generated by Quaking (QKI), circular RNAs (circRNAs) are newly recognised non-coding RNA (ncRNA) members characterised by tissue specificity, increased stability and enrichment within exosomes. Studies have shown that ionizing radiation (IR) can influence ncRNA transcription. However, it is unknown whether circRNAs or indeed QKI are regulated by IR. Microarray circRNA profiling and next generation sequencing revealed that circRNA expression was altered by low and medium dose exposure sourced predominantly from genes influencing the p53 pathway...
October 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/29100367/plasma-exosome-mir-196a-and-mir-1246-are-potential-indicators-of-localized-pancreatic-cancer
#5
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/29099035/molecular-characterization-of-peripheral-extracellular-vesicles-in-clinically-isolated-syndrome-preliminary-suggestions-from-a-pilot-study
#6
Nicoletta Nuzziello, Maria Blonda, Flavio Licciulli, Sabino Liuni, Antonella Amoruso, Alessio Valletti, Arianna Consiglio, Carlo Avolio, Maria Liguori
Extracellular vesicles (EVs), nanoparticles originated from different cell types, seem to be implicated in several cellular activities. In the Central Nervous System (CNS), glia and neurons secrete EVs and recent studies have demonstrated that the intercellular communication mediated by EVs has versatile functional impact in the cerebral homeostasis. This essential role may be due to their proteins and RNAs cargo that possibly modify the phenotypes of the targeted cells. Despite the increasing importance of EVs, little is known about their fluctuations in physiological as well as in pathological conditions...
September 18, 2017: Medical Sciences: Open Access Journal
https://www.readbyqxmd.com/read/29073095/broad-role-for-ybx1-in-defining-the-small-noncoding-rna-composition-of-exosomes
#7
Matthew J Shurtleff, Jun Yao, Yidan Qin, Ryan M Nottingham, Morayma M Temoche-Diaz, Randy Schekman, Alan M Lambowitz
RNA is secreted from cells enclosed within extracellular vesicles (EVs). Defining the RNA composition of EVs is challenging due to their coisolation with contaminants, lack of knowledge of the mechanisms of RNA sorting into EVs, and limitations of conventional RNA-sequencing methods. Here we present our observations using thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) to characterize the RNA extracted from HEK293T cell EVs isolated by flotation gradient ultracentrifugation and from exosomes containing the tetraspanin CD63 further purified from the gradient fractions by immunoisolation...
October 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28969022/plasma-exosomal-mirnas-based-prognosis-in-metastatic-kidney-cancer
#8
Meijun Du, Karthik V Giridhar, Yijun Tian, Michael R Tschannen, Jing Zhu, Chiang-Ching Huang, Deepak Kilari, Manish Kohli, Liang Wang
Plasma exosomal miRNAs were evaluated for prognosis in an initial set of 44 metastatic renal cell cancer (mRCC) patients by RNA sequencing. Among ∼3.49 million mappable reads per patient, miRNAs accounted for 93.1% of the mapped RNAs. 227 miRNAs with high abundance were selected for survival analysis. Cox regression analysis identified association of 6 miRNAs with overall survival (OS) (P<0.01, False discovery rate (FDR) < 0.3). Five of the associated miRNAs were quantified in an independent follow-up cohort of 65 mRCC patients by TaqMan-based miRNA assays...
September 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28934507/a-comprehensive-cell-specific-microrna-catalogue-of-human-peripheral-blood
#9
Simonas Juzenas, Geetha Venkatesh, Matthias Hübenthal, Marc P Hoeppner, Zhipei Gracie Du, Maren Paulsen, Philip Rosenstiel, Philipp Senger, Martin Hofmann-Apitius, Andreas Keller, Limas Kupcinskas, Andre Franke, Georg Hemmrich-Stanisak
With this study, we provide a comprehensive reference dataset of detailed miRNA expression profiles from seven types of human peripheral blood cells (NK cells, B lymphocytes, cytotoxic T lymphocytes, T helper cells, monocytes, neutrophils and erythrocytes), serum, exosomes and whole blood. The peripheral blood cells from buffy coats were typed and sorted using FACS/MACS. The overall dataset was generated from 450 small RNA libraries using high-throughput sequencing. By employing a comprehensive bioinformatics and statistical analysis, we show that 3' trimming modifications as well as composition of 3' added non-templated nucleotides are distributed in a lineage-specific manner-the closer the hematopoietic progenitors are, the higher their similarities in sequence variation of the 3' end...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28918518/micro-rna-profiling-of-exosomes-from-marrow-derived-mesenchymal-stromal-cells-in-patients-with-acute-myeloid-leukemia-implications-in-leukemogenesis
#10
Juliana Barrera-Ramirez, Jessie R Lavoie, Harinad B Maganti, William L Stanford, Caryn Ito, Mitchell Sabloff, Marjorie Brand, Michael Rosu-Myles, Yevgeniya Le, David S Allan
Gene regulatory networks in AML may be influenced by microRNAs (miRs) contained in exosomes derived from bone marrow mesenchymal stromal cells (MSCs). We sequenced miRs from exosomes isolated from marrow-derived MSCs from patients with AML (n = 3) and from healthy controls (n = 3; not age-matched). Known targets of mIRs that were significantly different in AML-derived MSC exosomes compared to controls were identified. Of the five candidate miRs identified by differential packaging in exosomes, only miR-26a-5p and miR-101-3p were significantly increased in AML-derived samples while miR-23b-5p, miR-339-3p and miR-425-5p were significantly decreased...
September 16, 2017: Stem Cell Reviews
https://www.readbyqxmd.com/read/28883156/structural-insights-into-the-interaction-of-the-nuclear-exosome-helicase-mtr4-with-the-preribosomal-protein-nop53
#11
Sebastian Falk, Jan-Niklas Tants, Jerôme Basquin, Matthias Thoms, Ed Hurt, Michael Sattler, Elena Conti
The nuclear exosome and the associated RNA helicase Mtr4 participate in the processing of several ribonucleoprotein particles (RNP), including the maturation of the large ribosomal subunit (60S). S. cerevisiae Mtr4 interacts directly with Nop53, a ribosomal biogenesis factor present in late pre-60S particles containing precursors of the 5.8S rRNA. The Mtr4-Nop53 interaction plays a pivotal role in the maturation of the 5.8S rRNA, providing a physical link between the nuclear exosome and the pre-60S RNP. An analogous interaction between Mtr4 and another ribosome biogenesis factor, Utp18, directs the exosome to an earlier preribosomal particle...
December 2017: RNA
https://www.readbyqxmd.com/read/28855728/meta-signature-of-human-endometrial-receptivity-a-meta-analysis-and-validation-study-of-transcriptomic-biomarkers
#12
Signe Altmäe, Mariann Koel, Urmo Võsa, Priit Adler, Marina Suhorutšenko, Triin Laisk-Podar, Viktorija Kukushkina, Merli Saare, Agne Velthut-Meikas, Kaarel Krjutškov, Lusine Aghajanova, Parameswaran G Lalitkumar, Kristina Gemzell-Danielsson, Linda Giudice, Carlos Simón, Andres Salumets
Previous transcriptome studies of the human endometrium have revealed hundreds of simultaneously up- and down-regulated genes that are involved in endometrial receptivity. However, the overlap between the studies is relatively small, and we are still searching for potential diagnostic biomarkers. Here we perform a meta-analysis of endometrial-receptivity associated genes on 164 endometrial samples (76 from 'pre-receptive' and 88 from mid-secretory, 'receptive' phase endometria) using a robust rank aggregation (RRA) method, followed by enrichment analysis, and regulatory microRNA prediction...
August 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28754746/tumor-derived-exosomes-modulate-pd-l1-expression-in-monocytes
#13
Franziska Haderk, Ralph Schulz, Murat Iskar, Laura Llaó Cid, Thomas Worst, Karolin V Willmund, Angela Schulz, Uwe Warnken, Jana Seiler, Axel Benner, Michelle Nessling, Thorsten Zenz, Maria Göbel, Jan Dürig, Sven Diederichs, Jérôme Paggetti, Etienne Moussay, Stephan Stilgenbauer, Marc Zapatka, Peter Lichter, Martina Seiffert
In chronic lymphocytic leukemia (CLL), monocytes and macrophages are skewed toward protumorigenic phenotypes, including the release of tumor-supportive cytokines and the expression of immunosuppressive molecules such as programmed cell death 1 ligand 1 (PD-L1). To understand the mechanism driving protumorigenic skewing in CLL, we evaluated the role of tumor cell-derived exosomes in the cross-talk with monocytes. We carried out RNA sequencing and proteome analyses of CLL-derived exosomes and identified noncoding Y RNA hY4 as a highly abundant RNA species that is enriched in exosomes from plasma of CLL patients compared with healthy donor samples...
July 28, 2017: Science Immunology
https://www.readbyqxmd.com/read/28748475/next-generation-sequencing-to-investigate-urinary-micrornas-from-macaca-fascicularis-cynomolgus-monkey
#14
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/28748221/rna-substrate-length-as-an-indicator-of-exosome-interactions-in-vivo
#15
Clémentine Delan-Forino, Claudia Schneider, David Tollervey
Background: The exosome complex plays key roles in RNA processing and degradation in Eukaryotes and Archaea. Outstanding structural studies identified multiple pathways for RNA substrates into the exosome in vitro, but identifying the pathway followed by individual RNA species in vivo remains challenging. Methods: We attempted to address this question using RNase protection. In vivo RNA-protein crosslinking (CRAC) was applied to the exosome component Rrp44/Dis3, which has both endonuclease and exonuclease activity...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28737826/comparison-of-isolation-methods-of-exosomes-and-exosomal-rna-from-cell-culture-medium-and-serum
#16
Yue-Ting Tang, Yi-Yao Huang, Lei Zheng, Si-Hua Qin, Xu-Ping Xu, Tai-Xue An, Yong Xu, Ying-Song Wu, Xiu-Mei Hu, Bao-Hong Ping, Qian Wang
Exosomes are cell-derived vesicles and are abundant in biological fluids; they contain RNA molecules which may serve as potential diagnostic biomarkers in 'precision medicine'. To promote the clinical application of exosomal RNA (exoRNA), many isolation methods must be compared and validated. Exosomes in cell culture medium (CCM) and serum may be isolated using ultracentrifugation (UC), ExoQuick or Total Exosome Isolation Reagent (TEI), and exoRNA may be extracted using TRIzol-LS, SeraMir, Total Exosome RNA Isolation (TER), HiPure Liquid RNA/miRNA kit (HLR), miRNeasy or exoRNeasy...
September 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28732356/the-circrna-interactome-innovative-hallmarks-of-the-intra-and-extracellular-radiation-response
#17
Valerie Bríd O'Leary, Jan Smida, Martina Matjanovski, Corinna Brockhaus, Klaudia Winkler, Simone Moertl, Saak Victor Ovsepian, Michael John Atkinson
Generated by Quaking (QKI), circular RNAs (circRNAs) are newly recognised non-coding RNA (ncRNA) members characterised by tissue specificity, increased stability and enrichment within exosomes. Studies have shown that ionizing radiation (IR) can influence ncRNA transcription. However, it is unknown whether circRNAs or indeed QKI are regulated by IR. Microarray circRNA profiling and next generation sequencing revealed that circRNA expression was altered by low and medium dose exposure sourced predominantly from genes influencing the p53 pathway...
July 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28727754/dysregulation-of-endothelial-colony-forming-cell-function-by-a-negative-feedback-loop-of-circulating-mir-146a-and-146b-in-cardiovascular-disease-patients
#18
Ting-Yu Chang, Wei-Chi Tsai, Tse-Shun Huang, Shu-Han Su, Chih-Young Chang, Hsiu-Yen Ma, Chun-Hsien Wu, Chih-Yung Yang, Chi-Hung Lin, Po-Hsun Huang, Cheng-Chung Cheng, Shu-Meng Cheng, Hsei-Wei Wang
Functional impairment of endothelial colony-forming cells (ECFCs), a specific cell lineage of endothelial progenitor cells (EPCs) is highly associated with the severity of coronary artery disease (CAD), the most common type of cardiovascular disease (CVD). Emerging evidence show that circulating microRNAs (miRNAs) in CAD patients' body fluid hold a great potential as biomarkers. However, our knowledge of the role of circulating miRNA in regulating the function of ECFCs and the progression of CAD is still in its infancy...
2017: PloS One
https://www.readbyqxmd.com/read/28687512/recessive-mutation-in-exosc3-associates-with-mitochondrial-dysfunction-and-pontocerebellar-hypoplasia
#19
Gudrun Schottmann, Sylvie Picker-Minh, Jana Marie Schwarz, Esther Gill, Richard J T Rodenburg, Werner Stenzel, Angela M Kaindl, Markus Schuelke
Recessive mutations in EXOSC3, encoding a subunit of the human RNA exosome complex, cause pontocerebellar hypoplasia type 1b (PCH1B). We report a boy with severe muscular hypotonia, psychomotor retardation, progressive microcephaly, and cerebellar atrophy. Biochemical abnormalities comprised mitochondrial complex I and pyruvate dehydrogenase complex (PDHc) deficiency. Whole exome sequencing uncovered a known EXOSC3 mutation p.(D132A) as the underlying cause. In patient fibroblasts, a large portion of the EXOSC3 protein was trapped in the cytosol...
July 4, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28684402/braf-v600-inhibition-alters-the-microrna-cargo-in-the-vesicular-secretome-of-malignant-melanoma-cells
#20
Taral R Lunavat, Lesley Cheng, Berglind O Einarsdottir, Roger Olofsson Bagge, Somsundar Veppil Muralidharan, Robyn A Sharples, Cecilia Lässer, Yong Song Gho, Andrew F Hill, Jonas A Nilsson, Jan Lötvall
The BRAF inhibitors vemurafenib and dabrafenib can be used to treat patients with metastatic melanomas harboring BRAF(V600) mutations. Initial antitumoral responses are often seen, but drug-resistant clones with reactivation of the MEK-ERK pathway soon appear. Recently, the secretome of tumor-derived extracellular vesicles (EVs) has been ascribed important functions in cancers. To elucidate the possible functions of EVs in BRAF-mutant melanoma, we determined the RNA content of the EVs, including apoptotic bodies, microvesicles, and exosomes, released from such cancer cells after vemurafenib treatment...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
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