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exosome and RNA sequence

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https://www.readbyqxmd.com/read/29779700/plasma-circulating-extracellular-rnas-in-left-ventricular-remodeling-post-myocardial-infarction
#1
Kirsty M Danielson, Ravi Shah, Ashish Yeri, Xiaojun Liu, Fernando Camacho Garcia, Michael Silverman, Kahraman Tanriverdi, Avash Das, Chunyang Xiao, Michael Jerosch-Herold, Bobak Heydari, Siddique Abbasi, Kendall Van Keuren-Jensen, Jane E Freedman, Yaoyu E Wang, Anthony Rosenzweig, Raymond Y Kwong, Saumya Das
Despite substantial declines in mortality following myocardial infarction (MI), subsequent left ventricular remodeling (LVRm) remains a significant long-term complication. Extracellular small non-coding RNAs (exRNAs) have been associated with cardiac inflammation and fibrosis and we hypothesized that they are associated with post-MI LVRm phenotypes. RNA sequencing of exRNAs was performed on plasma samples from patients with "beneficial" (decrease LVESVI ≥ 20%, n = 11) and "adverse" (increase LVESVI ≥ 15%, n = 11) LVRm...
May 17, 2018: EBioMedicine
https://www.readbyqxmd.com/read/29738525/optimizing-exosomal-rna-isolation-for-rna-seq-analyses-of-archival-sera-specimens
#2
Emily N Prendergast, Marcos Abraão de Souza Fonseca, Felipe Segato Dezem, Jenny Lester, Beth Y Karlan, Houtan Noushmehr, Xianzhi Lin, Kate Lawrenson
Exosomes are endosome-derived membrane vesicles that contain proteins, lipids, and nucleic acids. The exosomal transcriptome mediates intercellular communication, and represents an understudied reservoir of novel biomarkers for human diseases. Next-generation sequencing enables complex quantitative characterization of exosomal RNAs from diverse sources. However, detailed protocols describing exosome purification for preparation of exosomal RNA-sequence (RNA-Seq) libraries are lacking. Here we compared methods for isolation of exosomes and extraction of exosomal RNA from human cell-free serum, as well as strategies for attaining equal representation of samples within pooled RNA-Seq libraries...
2018: PloS One
https://www.readbyqxmd.com/read/29727687/variants-in-exosc9-disrupt-the-rna-exosome-and-result-in-cerebellar-atrophy-with-spinal-motor-neuronopathy
#3
David T Burns, Sandra Donkervoort, Juliane S Müller, Ellen Knierim, Diana Bharucha-Goebel, Eissa Ali Faqeih, Stephanie K Bell, Abdullah Y AlFaifi, Dorota Monies, Francisca Millan, Kyle Retterer, Sarah Dyack, Sara MacKay, Susanne Morales-Gonzalez, Michele Giunta, Benjamin Munro, Gavin Hudson, Mena Scavina, Laura Baker, Tara C Massini, Monkol Lek, Ying Hu, Daniel Ezzo, Fowzan S AlKuraya, Peter B Kang, Helen Griffin, A Reghan Foley, Markus Schuelke, Rita Horvath, Carsten G Bönnemann
The exosome is a conserved multi-protein complex that is essential for correct RNA processing. Recessive variants in exosome components EXOSC3, EXOSC8, and RBM7 cause various constellations of pontocerebellar hypoplasia (PCH), spinal muscular atrophy (SMA), and central nervous system demyelination. Here, we report on four unrelated affected individuals with recessive variants in EXOSC9 and the effect of the variants on the function of the RNA exosome in vitro in affected individuals' fibroblasts and skeletal muscle and in vivo in zebrafish...
May 3, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29702004/human-trna-derived-small-rnas-modulate-host-oral-microbial-interactions
#4
X He, F Li, B Bor, K Koyano, L Cen, X Xiao, W Shi, D T W Wong
Coevolution of the human host and its associated microbiota has led to sophisticated interactions to maintain a delicate homeostasis. Emerging evidence suggests that in addition to small molecules, peptides, and proteins, small regulatory noncoding RNAs (sRNAs) might play an important role in cross-domain interactions. In this study, we revealed the presence of diverse host transfer RNA-derived small RNAs (tsRNAs) among human salivary sRNAs. We selected 2 tsRNAs (tsRNA-000794 and tsRNA-020498) for further study based on their high sequence similarity to specific tRNAs from a group of Gram-negative oral bacteria, including Fusobacterium nucleatum, a key oral commensal and opportunistic pathogen...
April 1, 2018: Journal of Dental Research
https://www.readbyqxmd.com/read/29670053/testosterone-dependent-mir-26a-5p-and-let-7g-5p-act-as-signaling-mediators-to-regulate-sperm-apoptosis-via-targeting-pten-and-pmaip1
#5
Jideng Ma, Yu Fan, Jinwei Zhang, Siyuan Feng, Zihui Hu, Wanling Qiu, Keren Long, Long Jin, Qianzi Tang, Xun Wang, Qi Zhou, Yiren Gu, Weihang Xiao, Lingyan Liu, Xuewei Li, Mingzhou Li
Recent evidence suggests that testosterone deficiency can dramatically decrease the quality of sperm. MicroRNAs (miRNAs) are conserved mediators of post-transcriptional gene regulation in eukaryotes. However, the systemic regulation and function of miRNAs in sperm quality decline induced by testosterone deficiency has not been investigated. Here, we found that the sperm apoptosis was significantly enhanced and the sperm motility was dramatically decreased in hemicastrated pigs. We then used small RNA sequencing to detect miRNA profiles of sperm from pigs with prepubertal hemicastration (HC) and compared them with control libraries...
April 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29664138/characterization-of-the-catalytic-subunits-of-the-rna-exosome-like-complex-in-plasmodium-falciparum
#6
Ning Jiang, Shengchao Yu, Na Yang, Ying Feng, Xiaoyu Sang, Yao Wang, Mats Wahlgren, Qijun Chen
The eukaryotic ribonucleic acid (RNA) exosome is a versatile multi-ribonuclease complex that mediates the processing, surveillance and degradation of virtually all classes of RNA in both the nucleus and cytoplasm. The complex, composed of ten to eleven subunits, has been widely described in many organisms. Bioinformatic analyses revealed that there may be also an exosome-like complex in Plasmodium falciparum, a parasite of great importance in public health, with eight predicted subunits having high sequence similarity to their counterparts in yeast and human...
April 17, 2018: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/29626470/exosomal-mir-675-from-metastatic-osteosarcoma-promotes-cell-migration-and-invasion-by-targeting-caln1
#7
Liangzhi Gong, Qiyuan Bao, Chuanzhen Hu, Jun Wang, Qi Zhou, Li Wei, Lei Tong, Weibin Zhang, Yuhui Shen
Exosomal microRNAs(miRNAs) transfer from tumor to stromal cells is reportedly associated with cancer progression and metastasis in various epithelial cancers. However, the role of exosomal miRNA in the metastasis of osteosarcoma(OS) -the most common bone malignancy-still largely remains unknown. In this study, we purified exosomes with a median size close to 100 nm from cell culture media as well as patient serum, and proved that exosomes derived from the metastatic, but not the non-metastatic OS cells increase the migration and invasion of non-malignant fibroblast cells (hFOB1...
April 4, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29621543/cardiac-specific-delivery-by-cardiac-tissue-targeting-peptide-expressing-exosomes
#8
Hyoeun Kim, Nuri Yun, Dasom Mun, Ji-Young Kang, Seung-Hyun Lee, Hyelim Park, Hyewon Park, Boyoung Joung
Naturally occurring RNA carriers such as exosomes might be an untapped source of effective delivery vehicles. However, if exosomes are to be exploited for therapeutic applications, they must target specific tissues or cell types to avoid off-target effects. This study evaluated whether genetic modification of exosomes could enhance exosome delivery to heart cells and heart tissue without toxicity. Exosomes expressing cardiac-targeting peptide (CTP)-Lamp2b on the exosomal membrane (CTP-Exo) were generated by introducing vectors encoding CTP-Lamp2b into HEK 293 cells...
April 2, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29614491/the-biological-effect-and-clinical-application-of-long-noncoding-rnas-in-colorectal-cancer
#9
Zhenqiang Sun, Jinbo Liu, Chen Chen, Quanbo Zhou, Shuaixi Yang, Guixian Wang, Junmin Song, Zhen Li, Zhiyong Zhang, Jizhong Xu, Xiantao Sun, Yuan Chang, Weitang Yuan
Colorectal cancer (CRC) is one of the most common malignancies in the world. Easier recurrence and metastasis is the main cause of mortality in CRC patients, and the markers applied for diagnosis and treatment of CRC is still urgently needed to early diagnose and evaluate therapeutic effect. Long noncoding RNA (lncRNA) is a class of noncoding RNA that the length is more than 200 nucleotides. With the development of sequencing technique about transcriptome, increasing lncRNAs are focused on their function and mechanism related to the nosogenesis and pathology of CRC...
March 26, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29557993/mirna-profiling-of-exosomes-from-spontaneous-hypertensive-rats-using-next-generation-sequencing
#10
Xiaoyan Liu, Wen Yuan, Lei Yang, Jing Li, Jun Cai
The role and miRNA expression profile of exosomes in hypertension remain largely unknown. Therefore, next-generation sequencing was used to define the miRNA expression profile of plasma exosomes in spontaneously hypertensive rats (SHRs), the most widely used animal model of human essential hypertension, and their controls, normotensive Wistar-Kyoto rats (WKYs). Results revealed that percentages of miRNA in the total small RNA isolated from SHRs and WKYs were not significantly different. Twenty-seven miRNAs were significantly differentially expressed (DE) between SHR and WKY exosomes, including 23 up-regulated and four down-regulated in SHR exosomes as compared to WKY exosomes...
March 20, 2018: Journal of Cardiovascular Translational Research
https://www.readbyqxmd.com/read/29546715/purification-of-exosomes-from-primary-schwann-cells-rna-extraction-and-next-generation-sequencing-of-exosomal-rnas
#11
Cristian De Gregorio, Paula Díaz, Rodrigo López-Leal, Patricio Manque, Felipe A Court
Exosomes are small (30-150 nm) vesicles of endosomal origin secreted by most cell types. Exosomes contain proteins, lipids, and RNA species including microRNA, mRNA, rRNA, and long noncoding RNAs. The mechanisms associated with exosome synthesis and cargo loading are still poorly understood. A role for exosomes in intercellular communication has been reported in physiological and pathological conditions both in vitro and in vivo. Previous studies have suggested that Schwann cell-derived exosomes regulate neuronal functions, but the mechanisms are still unclear...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29498242/cell-based-and-exosome-therapy-in-diabetic-stroke
#12
Poornima Venkat, Michael Chopp, Jieli Chen
Stroke is a global health concern and it is imperative that therapeutic strategies with wide treatment time frames be developed to improve neurological outcome in patients. Patients with diabetes mellitus who suffer a stroke have worse neurological outcomes and long-term functional recovery than nondiabetic stroke patients. Diabetes induced vascular damage and enhanced inflammatory milieu likely contributes to worse post stroke outcomes. Diabetic stroke patients have an aggravated pathological cascade, and treatments that benefit nondiabetic stroke patients do not necessarily translate to diabetic stroke patients...
March 2, 2018: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/29483512/a-cryptic-rna-binding-domain-mediates-syncrip-recognition-and-exosomal-partitioning-of-mirna-targets
#13
Fruzsina Hobor, Andre Dallmann, Neil J Ball, Carla Cicchini, Cecilia Battistelli, Roksana W Ogrodowicz, Evangelos Christodoulou, Stephen R Martin, Alfredo Castello, Marco Tripodi, Ian A Taylor, Andres Ramos
Exosomal miRNA transfer is a mechanism for cell-cell communication that is important in the immune response, in the functioning of the nervous system and in cancer. Syncrip/hnRNPQ is a highly conserved RNA-binding protein that mediates the exosomal partition of a set of miRNAs. Here, we report that Syncrip's amino-terminal domain, which was previously thought to mediate protein-protein interactions, is a cryptic, conserved and sequence-specific RNA-binding domain, designated NURR (N-terminal unit for RNA recognition)...
February 26, 2018: Nature Communications
https://www.readbyqxmd.com/read/29481617/turnover-of-aberrant-pre-40s-pre-ribosomal-particles-is-initiated-by-a-novel-endonucleolytic-decay-pathway
#14
Elodie Choque, Claudia Schneider, Olivier Gadal, Christophe Dez
Ribosome biogenesis requires more than 200 trans-acting factors to achieve the correct production of the two mature ribosomal subunits. Here, we have identified Efg1 as a novel, nucleolar ribosome biogenesis factor in Saccharomyces cerevisiae that is directly linked to the surveillance of pre-40S particles. Depletion of Efg1 impairs early pre-rRNA processing, leading to a strong decrease in 18S rRNA and 40S subunit levels and an accumulation of the aberrant 23S rRNA. Using Efg1 as bait, we revealed a novel degradation pathway of the 23S rRNA...
February 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29479137/micrornas-associated-with-the-development-of-kidney-diseases-in-humans-and-animals
#15
REVIEW
Osamu Ichii, Taro Horino
Mature microRNAs (miRNAs) are single-stranded RNAs with approximately 18-25 bases, and their sequences are highly conserved among animals. miRNAs act as posttranscriptional regulators by binding mRNAs, and their main function involves the degradation of their target mRNAs. Recent studies revealed altered expression of miRNAs in the kidneys during the progression of acute kidney injury (AKI) and chronic kidney disease (CKD) in humans and experimental rodent models by using high-throughput screening techniques including microarray and small RNA sequencing...
January 2018: Journal of Toxicologic Pathology
https://www.readbyqxmd.com/read/29478310/isolation-of-exosome-like-nanoparticles-and-analysis-of-micrornas-derived-from-coconut-water-based-on-small-rna-high-throughput-sequencing
#16
Zhehao Zhao, Siran Yu, Min Li, Xin Gui, Ping Li
In this study, the presence of microRNAs in coconut water was identified by real-time polymerase chain reaction (PCR) based on the results of high-throughput small RNA sequencing. In addition, the differences in microRNA content between immature and mature coconut water were compared. A total of 47 known microRNAs belonging to 25 families and 14 new microRNAs were identified in coconut endosperm. Through analysis using a target gene prediction software, potential microRNA target genes were identified in the human genome...
March 21, 2018: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29463374/nano-vesicles-are-a-potential-tool-to-monitor-therapeutic-efficacy-of-carbon-ion-radiotherapy-in-prostate-cancer
#17
Qi Yu, Ping Li, Meilin Weng, Shuang Wu, Yafang Zhang, Xue Chen, Qing Zhang, Guangxia Shen, Xianting Ding, Shen Fu
Exosomes are nano-vesicles that contribute to the effectiveness of many treatments. The aim of this study was to identify profiles of microRNA (miRNA) contained in serum exosomes that are differentially regulated in patients with prostate cancer undergoing carbon ion radiotherapy (CIRT). RNA was extracted from serum exosomes of eight patients with localized prostate cancer before and after CIRT, and miRNA was analyzed by the next generation sequencing. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the major signaling pathways associated with the proliferation of prostate cancer cells, such as MAPK, PI3K-AKT, mTOR, and AMPK may be implicated in the mechanism of CIRT action...
January 1, 2018: Journal of Biomedical Nanotechnology
https://www.readbyqxmd.com/read/29462250/the-lnclocator-a-subcellular-localization-predictor-for-long-non-coding-rnas-based-on-a-stacked-ensemble-classifier
#18
Cao Zhen, Xiaoyong Pan, Yang Yang, Yan Huang, Hong-Bin Shen
Motivation: The long non-coding RNA (lncRNA) studies have been hot topics in the field of RNA biology. Recent studies have shown that their subcellular localizations carry important information for understanding their complex biological functions. Considering the costly and time-consuming experiments for identifying subcellular localization of lncRNAs, computational methods are urgently desired. However, to the best of our knowledge, there are no computational tools for predicting the lncRNA subcellular locations to date...
February 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29444662/a-systematic-approach-to-rna-associated-motif-discovery
#19
Tian Gao, Jiang Shu, Juan Cui
BACKGROUND: Sequencing-based large screening of RNA-protein and RNA-RNA interactions has enabled the mechanistic study of post-transcriptional RNA processing and sorting, including exosome-mediated RNA secretion. The downstream analysis of RNA binding sites has encouraged the investigation of novel sequence motifs, which resulted in exceptional new challenges for identifying motifs from very short sequences (e.g., small non-coding RNAs or truncated messenger RNAs), where conventional methods tend to be ineffective...
February 14, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29430178/engineered-exosome-mediated-delivery-of-functionally-active-mir-26a-and-its-enhanced-suppression-effect-in-hepg2-cells
#20
Gaofeng Liang, Shu Kan, Yanliang Zhu, Shuying Feng, Wenpo Feng, Shegan Gao
Introduction: Exosomes are closed-membrane nanovesicles that are secreted by a variety of cells and exist in most body fluids. Recent studies have demonstrated the potential of exosomes as natural vehicles that target delivery of functional small RNA and chemotherapeutics to diseased cells. Methods: In this study, we introduce a new approach for the targeted delivery of exosomes loaded with functional miR-26a to scavenger receptor class B type 1-expressing liver cancer cells...
2018: International Journal of Nanomedicine
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