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exosome and RNA sequence

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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
#1
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-pre-ribosomal-protein-nop53
#2
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 pre-ribosomal particle...
September 7, 2017: RNA
https://www.readbyqxmd.com/read/28855728/meta-signature-of-human-endometrial-receptivity-a-meta-analysis-and-validation-study-of-transcriptomic-biomarkers
#3
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
#4
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
#5
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
#6
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
#7
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
#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...
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28659881/rna-profiling-analysis-of-the-serum-exosomes-derived-from-patients-with-active-and-latent-mycobacterium-tuberculosis-infection
#12
Lingna Lv, Cuidan Li, Xiuli Zhang, Nan Ding, Tianshu Cao, Xinmiao Jia, Jinghui Wang, Liping Pan, Hongyan Jia, Zihui Li, Ju Zhang, Fei Chen, Zongde Zhang
Tuberculosis (TB) has exceeded HIV as the most lethal infectious disease globally for two consecutive years. Moreover, one third of the world's population is estimated to have latent tuberculosis infection (LTBI). This is mainly because of difficulties associated with diagnosis and treatment for both TB and LTBI patients. Exosomes provide a promising research tool for TB diagnosis and treatment because they are released from various cells containing valuable biochemical information related to disease. In this study, we performed RNA-sequencing analysis on exosomes derived from clinical specimens of healthy controls (HC), active tuberculosis (ATB), and LTBI patients...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28646161/circulating-exosomal-mir-125a-3p-as-a-novel-biomarker-for-early-stage-colon-cancer
#13
Jing Wang, Feihu Yan, Qi Zhao, Fei Zhan, Ruitao Wang, Liang Wang, Yanqiao Zhang, Xiaoyi Huang
Circulating exosome holds great potentials as biomarker for diagnosis and prognosis of human cancers. Previously, we have applied small RNA sequencing to identify aberrantly expressed exosomal miRNAs as candidates for diagnostic markers in colon cancer patients. In this validation cohort, plasma derived exosomal miRNA was isolated from 50 early-stage colon cancer patients and 50 matched healthy volunteers. Real-time qRT-PCR revealed that miR-125a-3p, miR-320c were significantly up-regulated in plasma exosomes of the patients with early stage colon cancer...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28643872/circulating-microrna-as-candidates-for-early-embryonic-viability-in-cattle
#14
Ky G Pohler, Jonathan A Green, Laura A Moley, Sumedha Gunewardena, Wei-Ting Hung, Rebecca R Payton, Xiaoman Hong, Lane K Christenson, Tom W Geary, Michael F Smith
Blood-borne extracellular vesicles (i.e., exosomes and microvesicles) carrying microRNAs (miRNAs) could make excellent biomarkers of disease and different physiologic states, including pregnancy status. We tested the hypothesis that circulating extracellular vesicle-derived miRNAs might differentiate the pregnancy status of cows that had maintained pregnancy to Day 30 from non-pregnant cows or from those that exhibited embryonic mortality between Days 17 and 30 of gestation. Cows were randomly assigned for artificial insemination with fertile semen (n = 36) or dead semen (n = 8; control group) on Day 0 (day of estrus)...
August 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/28536328/-microrna-in-various-aspects-of-cancer-development
#15
Sho Nambara, Koshi Mimori
MicroRNAs(miRNAs)are small(18-25 nucleotides)noncoding RNA molecules that bind to partially complementary mRNA sequences, resulting in target degradation or translation inhibition. A single miRNA can influence the expression of hundreds of target genes, and miRNAs have been implicated as key molecules in various diseases, including cancer. Many studies have shown that the miRNAs play an important role in cancer cells and tumor microenvironment and may be biomarkers for early detection and therapeutic targets for various cancers...
May 2017: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/28514744/characterization-of-mouse-serum-exosomal-small-rna-content-the-origins-and-their-roles-in-modulating-inflammatory-response
#16
Xin Zhou, Zinan Jiao, Juling Ji, Shuyuan Li, Xiaodi Huang, Xiaoshuang Lu, Heng Zhao, Jingwen Peng, Xinya Chen, Qiuhong Ji, Yuhua Ji
In the last decade, although studies on exosomal microRNAs (miRNAs) derived from serum and other body fluids have increased dramatically; the contents and biological significance of serum exosomes under normal conditions remain unclear. In the present study, we profiled the small RNA content of mouse serum exosomes (mSEs) using small RNAseq and found that fragments of transfer RNAs (tRNAs) and miRNAs were the two predominant exosomal RNA species, accounting for approximately 60% and 10% of mapped reads, respectively...
June 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28499455/bovis-bacillus-calmette-guerin-bcg-infection-induces-exosomal-mirna-release-by-human-macrophages
#17
Shamila D Alipoor, Esmaeil Mortaz, Payam Tabarsi, Parissa Farnia, Mehdi Mirsaeidi, Johan Garssen, Masoud Movassaghi, Ian M Adcock
BACKGROUND: Tuberculosis (TB) remains a significant global health concern and its diagnosis is challenging due to the limitations in the specificity and sensitivity of the current diagnostic tests. Exosomes are bioactive 30-100 nm vesicles produced by most cell types and are found in almost all human body fluids. Exosomal microRNAs (miRNAs) can transfer biological information between cells and tissues and may act as potential biomarkers in many diseases. In this pilot study, we assessed the miRNA profile of exosomes released from human monocyte-derived macrophages upon infection with Mycobacterium bovis Bacillus Calmette-Guerin (BCG)...
May 12, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28490497/protein-composition-of-the-hepatitis-a-virus-quasi-envelope
#18
Kevin L McKnight, Ling Xie, Olga González-López, Efraín E Rivera-Serrano, Xian Chen, Stanley M Lemon
The Picornaviridae are a diverse family of RNA viruses including many pathogens of medical and veterinary importance. Classically considered "nonenveloped," recent studies show that some picornaviruses, notably hepatitis A virus (HAV; genus Hepatovirus) and some members of the Enterovirus genus, are released from cells nonlytically in membranous vesicles. To better understand the biogenesis of quasi-enveloped HAV (eHAV) virions, we conducted a quantitative proteomics analysis of eHAV purified from cell-culture supernatant fluids by isopycnic ultracentrifugation...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28471299/interleukin-10-deficiency-impairs-reparative-properties-of-bone-marrow-derived-endothelial-progenitor-cell-exosomes
#19
Yujia Yue, Venkata Naga Srikanth Garikipati, Suresh Kumar Verma, David A Goukassian, Raj Kishore
Endothelial progenitor cell (EPC)-based therapy has immense potential to promote cardiac neovascularization and attenuate ischemic injury. Functional benefits of EPCs and other adult stem cell therapies largely involve paracrine mechanisms and exosomes secreted by stem cells are emerging as pivotal paracrine entity of stem/progenitor cells. However, modest outcomes after EPC-/stem cell-based clinical trials suggest that stem cell/exosome function might be modulated by stimuli they encounter in ischemic tissues, including systemic inflammation...
June 15, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28469418/pisma-a-visual-representation-of-motif-distribution-in-dna-sequences
#20
Rogelio Alcántara-Silva, Moisés Alvarado-Hermida, Gibrán Díaz-Contreras, Martha Sánchez-Barrios, Samantha Carrera, Silvia Carolina Galván
BACKGROUND: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code-like, as a gene-map-like, and as a transcript scheme. RESULTS: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes...
2017: Bioinformatics and Biology Insights
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