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exosomal RNA

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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/29139296/differential-content-of-proteins-mrnas-and-mirnas-suggests-that-mdsc-and-their-exosomes-may-mediate-distinct-immune-suppressive-functions
#2
Lucia Geis-Asteggiante, Ashton T Belew, Virginia K Clements, Nathan J Edwards, Suzanne Ostrand-Rosenberg, Nagib M El-Sayed, Catherine Fenselau
Myeloid-derived suppressor cells (MDSC) are immature myeloid cells that accumulate in the circulation and the tumor microenvironment of most cancer patients. There, MDSC suppress both adaptive and innate immunity, hindering immunotherapies. The inflammatory milieu often present in cancers facilitates MDSC suppressive activity, causing aggressive tumor progression and metastasis. MDSC from tumor-bearing mice release exosomes, which carry biologically active proteins and mediate some of the immunosuppressive functions characteristic of MDSC...
November 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29137379/diagnostic-potential-of-serum-exosomal-colorectal-neoplasia-differentially-expressed-long-non-coding-rna-crnde-p-and-microrna-217-expression-in-colorectal-carcinoma
#3
Bo Yu, Qiong Du, Huan Li, Hong-Yue Liu, Xuan Ye, Bin Zhu, Qing Zhai, Xin-Xiang Li
In this study, we investigated the diagnostic potential of serum exosomal colorectal neoplasia differentially expressed (CRNDE-p) long coding RNA and microRNA-217 in colorectal carcinoma (CRC). We detected high CRNDE-p and low miR-217 levels in exosomes released by multiple CRC cell lines into culture media as well as in sera from CRC xenograft mice and CRC patients. Conversely, we observed lower CRNDE-p and higher miR-217 levels in serum exosomes from post-chemotherapy than from pre-chemotherapy patient samples...
October 13, 2017: Oncotarget
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
#4
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/29117219/cellular-and-exosome-mediated-molecular-defense-mechanism-in-bovine-granulosa-cells-exposed-to-oxidative-stress
#5
Mohammed Saeed-Zidane, Lea Linden, Dessie Salilew-Wondim, Eva Held, Christiane Neuhoff, Ernst Tholen, Michael Hoelker, Karl Schellander, Dawit Tesfaye
Various environmental insults including diseases, heat and oxidative stress could lead to abnormal growth, functions and apoptosis in granulosa cells during ovarian follicle growth and oocyte maturation. Despite the fact that cells exposed to oxidative stress are responding transcriptionally, the potential release of transcripts associated with oxidative stress response into extracellular space through exosomes is not yet determined. Therefore, here we aimed to investigate the effect of oxidative stress in bovine granulosa cells in vitro on the cellular and exosome mediated defense mechanisms...
2017: PloS One
https://www.readbyqxmd.com/read/29112229/biobehavioral-modulation-of-the-exosome-transcriptome-in-ovarian-carcinoma
#6
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/29110768/cerebrospinal-fluid-biomarkers-of-malignancies-located-in-the-central-nervous-system
#7
Cassandra Verheul, Anne Kleijn, Martine L M Lamfers
CNS malignancies include primary tumors that originate within the CNS as well as secondary tumors that develop as a result of metastatic cancer. The delicate nature of the nervous systems makes tumors located in the CNS notoriously difficult to reach, which poses several problems during diagnosis and treatment. CSF can be acquired relatively easy through lumbar puncture and offers an important compartment for analysis of cells and molecules that carry information about the malignant process. Such techniques have opened up a new field of research focused on the identification of specific biomarkers for several types of CNS malignancies, which may help in diagnosis and monitoring of tumor progression or treatment response...
2017: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29108237/the-circrna-interactome-innovative-hallmarks-of-the-intra-and-extracellular-radiation-response
#8
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/29107693/wdr74-participates-in-an-early-cleavage-of-the-pre-rrna-processing-pathway-in-cooperation-with-the-nucleolar-aaa-atpase-nvl2
#9
Nobuhiro Hiraishi, Yo-Ichi Ishida, Haruka Sudo, Masami Nagahama
WD repeat-containing protein 74 (WDR74), a nucleolar-localized protein, is the mammalian ortholog of Nsa1, a 60S ribosome assembly factor in yeast. We previously showed that WDR74 associates with MTR4, the nuclear exosome-assisting RNA helicase, whose dissociation is prohibited by an ATPase-deficient mutant of the AAA-type chaperone NVL2. However, the functions and regulation of WDR74 during ribosome biogenesis in cooperation with NVL2 remains unknown. Here, we demonstrated that knockdown of WDR74 leads to significant defects in the pre-rRNA cleavage within the internal transcribed spacer 1 (ITS1), occurring in an early stage of the processing pathway...
October 28, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29107112/the-emerging-role-of-exosome-derived-non-coding-rnas-in-cancer-biology
#10
Qing Fan, Shibo Wei, Liang Yang, Xiaodong Zhang, Xueqiang Peng, Dongming Su, Zhenhua Zhai, Xiangdong Hua, Hangyu Li
Exosomes are a new means of intercellular information exchange that have aroused great research interest. Long neglected in research, exosomes were deemed nonfunctional cellular components to be discarded. However, it has been gradually revealed that exosomes are an important tool for the exchange of intercellular information and material. Exosomes contain specific repertoires of non-coding RNAs (ncRNAs, including microRNA and lncRNA), indicating that a specific RNA sorting mechanism may exist. Correspondingly, intracellular multivesicular bodies (MVBs) are produced after fusion with the cell membrane to release exosomes rather than inducing autophagy, which reveals that there may be a specific regulatory mechanism for MVB secretion...
October 26, 2017: Cancer Letters
https://www.readbyqxmd.com/read/29106545/extracellular-vesicles-in-diagnostics-and-therapy-of-the-ischaemic-heart-position-paper-from-the-working-group-on-cellular-biology-of-the-heart-of-the-european-society-of-cardiology
#11
Joost Petrus Gerardus Sluijter, Sean Michael Davidson, Chantal Marthe Boulanger, Edit Iren Buzás, Dominique Paschalis Victor de Kleijn, Felix Benedikt Engel, Zoltán Giricz, Derek J Hausenloy, Raj Kishore, Sandrine Lecour, Jonathan Leor, Rosalinda Madonna, Cinzia Perrino, Fabrice Prunier, Susmita Sahoo, Ray Michel Schiffelers, Rainer Schulz, Linda Wilhelmina Van Laake, Kirsti Ytrehus, Péter Ferdinandy
Extracellular vesicles (EVs) - particularly exosomes and microvesicles - are attracting considerable interest in the cardiovascular field as the wide range of their functions is recognized. These capabilities include transporting regulatory molecules including different RNA species, lipids, and proteins through the extracellular space including blood and delivering these cargos to recipient cells to modify cellular activity. EVs powerfully stimulate angiogenesis, and can protect the heart against myocardial infarction...
November 2, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/29100367/plasma-exosome-mir-196a-and-mir-1246-are-potential-indicators-of-localized-pancreatic-cancer
#12
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/29100284/exosomes-containing-differential-expression-of-microrna-and-mrna-in-osteosarcoma-that-can-predict-response-to-chemotherapy
#13
Ji-Feng Xu, Ya-Ping Wang, Shui-Jun Zhang, Yu Chen, Hai-Feng Gu, Xiao-Fan Dou, Bing Xia, Qing Bi, Shun-Wu Fan
A major challenge in osteosarcoma (OS) is the selection of the most effective chemotherapeutic agents for individual patients, while the administration of ineffective chemotherapy increases mortality and decreases quality of life in patients. This emphasizes the need to evaluate every patient's probability of responding to each chemotherapeutic agent. We developed a profiling strategy for serum exosomal microRNAs and mRNAs in OS patients with differential chemotherapeutic responses. Twelve miRNAs were up regulated and 18 miRNAs were under regulated significantly in OS patient with poor chemotherapeutic response when compared with those in good chemotherapeutic response (p<0...
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
#14
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/29093021/the-rna-exosome-and-rna-exosome-linked-disease
#15
Derrick J Morton, Emily G Kuiper, Stephanie K Jones, Sara W Leung, Anita H Corbett, Milo B Fasken
The RNA exosome is an evolutionarily conserved, ribonuclease complex that is critical for both processing and degradation of a variety of RNAs. Cofactors that associate with the RNA exosome likely dictate substrate specificity for this complex. Recently, mutations in genes encoding both structural subunits of the RNA exosome and its cofactors have been linked to human disease. Mutations in the RNA exosome genes EXOSC3 and EXOSC8 cause pontocerebellar hypoplasia type 1b (PCH1b) and type 1c (PCH1c), respectively, which are similar autosomal recessive, neurodegenerative diseases...
November 1, 2017: RNA
https://www.readbyqxmd.com/read/29081510/isolation-and-characterization-of-urinary-extracellular-vesicles-implications-for-biomarker-discovery
#16
REVIEW
Michael L Merchant, Ilse M Rood, Jeroen K J Deegens, Jon B Klein
Urine is a valuable diagnostic medium and, with the discovery of urinary extracellular vesicles, is viewed as a dynamic bioactive fluid. Extracellular vesicles are lipid-enclosed structures that can be classified into three categories: exosomes, microvesicles (or ectosomes) and apoptotic bodies. This classification is based on the mechanisms by which membrane vesicles are formed: fusion of multivesicular bodies with the plasma membranes (exosomes), budding of vesicles directly from the plasma membrane (microvesicles) or those shed from dying cells (apoptotic bodies)...
October 30, 2017: Nature Reviews. Nephrology
https://www.readbyqxmd.com/read/29078295/intercellular-mrna-trafficking-via-membrane-nanotube-like-extensions-in-mammalian-cells
#17
Gal Haimovich, Christopher M Ecker, Margaret C Dunagin, Elliott Eggan, Arjun Raj, Jeffrey E Gerst, Robert H Singer
RNAs have been shown to undergo transfer between mammalian cells, although the mechanism behind this phenomenon and its overall importance to cell physiology is not well understood. Numerous publications have suggested that RNAs (microRNAs and incomplete mRNAs) undergo transfer via extracellular vesicles (e.g., exosomes). However, in contrast to a diffusion-based transfer mechanism, we find that full-length mRNAs undergo direct cell-cell transfer via cytoplasmic extensions characteristic of membrane nanotubes (mNTs), which connect donor and acceptor cells...
October 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29074968/coding-and-noncoding-landscape-of-extracellular-rna-released-by-human-glioma-stem-cells
#18
Zhiyun Wei, Arsen O Batagov, Sergio Schinelli, Jintu Wang, Yang Wang, Rachid El Fatimy, Rosalia Rabinovsky, Leonora Balaj, Clark C Chen, Fred Hochberg, Bob Carter, Xandra O Breakefield, Anna M Krichevsky
Tumor-released RNA may mediate intercellular communication and serve as biomarkers. Here we develop a protocol enabling quantitative, minimally biased analysis of extracellular RNAs (exRNAs) associated with microvesicles, exosomes (collectively called EVs), and ribonucleoproteins (RNPs). The exRNA complexes isolated from patient-derived glioma stem-like cultures exhibit distinct compositions, with microvesicles most closely reflecting cellular transcriptome. exRNA is enriched in small ncRNAs, such as miRNAs in exosomes, and precisely processed tRNA and Y RNA fragments in EVs and exRNPs...
October 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/29073095/broad-role-for-ybx1-in-defining-the-small-noncoding-rna-composition-of-exosomes
#19
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/29063370/pathways-of-production-and-delivery-of-hepatocyte-exosomes
#20
Li Chen, Ruju Chen, Sherri Kemper, David R Brigstock
Hepatocyte exosomes (Exo(Hep)) are proposed to mediate physiological or pathophysiological signaling in a variety of hepatic target cells. Exo(Hep) were purified from the medium of primary mouse hepatocytes or AML12 cells and characterized as ~100 nm nanovesicles that were positive for proteins commonly found in exosomes (CD9, CD81, flotillin) or hepatocytes (asialoglycoprotein receptor). Ethanol treatment of hepatocytes caused increased Exo(Hep) release and increased cellular mRNA expression of components involved in intracellular vesicle trafficking (Rab 5a,b,c, Rab 7a, Rab 27a,b) or exosome biogenesis via the ESCRT (HGS, Alix, STAM1, TSG101, VTA1, YKT6) or ceramide (nSmase2) pathways...
October 23, 2017: Journal of Cell Communication and Signaling
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