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https://www.readbyqxmd.com/read/27929461/isolation-of-high-density-lipoproteins-for-non-coding-small-rna-quantification
#1
Danielle L Michell, Ryan M Allen, Stuart R Landstreet, Shilin Zhao, Cynthia L Toth, Quanhu Sheng, Kasey C Vickers
The diversity of small non-coding RNAs (sRNA) is rapidly expanding and their roles in biological processes, including gene regulation, are emerging. Most interestingly, sRNAs are also found outside of cells and are stably present in all biological fluids. As such, extracellular sRNAs represent a novel class of disease biomarkers and are likely involved in cell signaling and intercellular communication networks. To assess their potential as biomarkers, sRNAs can be quantified in plasma, urine, and other fluids...
November 28, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27765065/extending-gene-ontology-in-the-context-of-extracellular-rna-and-vesicle-communication
#2
Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B Gerstein, Andrew F Hill, Robert R Kitchen, Jan Lötvall, Tushar Patel, Dena C Procaccini, Peter Quesenberry, Joel Rozowsky, Robert L Raffai, Aleksandra Shypitsyna, Andrew I Su, Clotilde Théry, Kasey Vickers, Marca H M Wauben, Suresh Mathivanan, Aleksandar Milosavljevic, Louise C Laurent
BACKGROUND: To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research. METHODS: By following a consensus-building process, we have worked with several academic societies/consortia, including ERCC, ISEV, and ASEMV, to identify and approve a set of exRNA and extracellular vesicle-related terms and relationships that have been incorporated into GO...
April 12, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27687708/multi-perspective-quality-control-of-illumina-rna-sequencing-data-analysis
#3
Quanhu Sheng, Kasey Vickers, Shilin Zhao, Jing Wang, David C Samuels, Olivia Koues, Yu Shyr, Yan Guo
Quality control (QC) is a critical step in RNA sequencing (RNA-seq). Yet, it is often ignored or conducted on a limited basis. Here, we present a multi-perspective strategy for QC of RNA-seq experiments. The QC of RNA-seq can be divided into four related stages: (1) RNA quality, (2) raw read data (FASTQ), (3) alignment and (4) gene expression. We illustrate the importance of conducting QC at each stage of an RNA-seq experiment and demonstrate our recommended RNA-seq QC strategy. Furthermore, we discuss the major and often neglected quality issues associated with the three major types of RNA-seq: mRNA, total RNA and small RNA...
September 29, 2016: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/27595929/hdl-and-microrna-therapeutics-in-cardiovascular-disease
#4
REVIEW
Danielle L Michell, Kasey C Vickers
microRNAs (miRNA) are small non-coding RNAs (sRNA) that post-transcriptionally regulate gene (mRNA) expression and are implicated in many biological processes and diseases. Many miRNAs have been reported to be altered in cardiovascular disease (CVD); both cellular and extracellular miRNA levels are affected by hypercholesterolemia and atherosclerosis. We and other groups have reported that lipoproteins transport miRNAs in circulation and these lipoprotein signatures are significantly altered in hypercholesterolemia and coronary artery disease (CAD)...
December 2016: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/27383910/porous-silicon-and-polymer-nanocomposites-for-delivery-of-peptide-nucleic-acids-as-anti-microrna-therapies
#5
Kelsey R Beavers, Thomas A Werfel, Tianwei Shen, Taylor E Kavanaugh, Kameron V Kilchrist, Jeremy W Mares, Joshua S Fain, Carrie B Wiese, Kasey C Vickers, Sharon M Weiss, Craig L Duvall
Self-assembled polymer/porous silicon nanocomposites overcome intracellular and systemic barriers for in vivo application of peptide nucleic acid (PNA) anti-microRNA therapeutics. Porous silicon (PSi) is leveraged as a biodegradable scaffold with high drug-cargo-loading capacity. Functionalization with a diblock polymer improves PSi nanoparticle colloidal stability, in vivo pharmacokinetics, and intracellular bioavailability through endosomal escape, enabling PNA to inhibit miR-122 in vivo.
September 2016: Advanced Materials
https://www.readbyqxmd.com/read/27076901/extending-gene-ontology-in-the-context-of-extracellular-rna-and-vesicle-communication
#6
Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B Gerstein, Andrew F Hill, Robert R Kitchen, Jan Lötvall, Tushar Patel, Dena C Procaccini, Peter Quesenberry, Joel Rozowsky, Robert L Raffai, Aleksandra Shypitsyna, Andrew I Su, Clotilde Théry, Kasey Vickers, Marca H M Wauben, Suresh Mathivanan, Aleksandar Milosavljevic, Louise C Laurent
BACKGROUND: To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research. METHODS: By following a consensus-building process, we have worked with several academic societies/consortia, including ERCC, ISEV, and ASEMV, to identify and approve a set of exRNA and extracellular vesicle-related terms and relationships that have been incorporated into GO...
2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/26991245/effect-of-drug-therapy-on-net-cholesterol-efflux-capacity-of-high-density-lipoprotein-enriched-serum-in-rheumatoid-arthritis
#7
Michelle J Ormseth, Patricia G Yancey, Joseph F Solus, S Louis Bridges, Jeffrey R Curtis, MacRae F Linton, Sergio Fazio, Sean S Davies, L Jackson Roberts, Kasey C Vickers, Valentina Kon, C Michael Stein
OBJECTIVE: Patients with rheumatoid arthritis (RA) have an increased risk of coronary heart disease (CHD). Some RA therapies may modify this risk, but the underlying mechanisms are unclear. The cholesterol efflux capacity of high-density lipoprotein (HDL) is associated with a reduced CHD risk in non-RA populations; however, inflammation may impair the function of HDL. The aim of this study was to evaluate whether reduced inflammation resulting from treatment with methotrexate (MTX), adalimumab (ADA), or tocilizumab (TCZ) would increase the net cholesterol efflux capacity of HDL in patients with RA...
September 2016: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/26646011/transcriptomic-analysis-of-chronic-hepatitis-b-and-c-and-liver-cancer-reveals-microrna-mediated-control-of-cholesterol-synthesis-programs
#8
Sara R Selitsky, Timothy A Dinh, Cynthia L Toth, C Lisa Kurtz, Masao Honda, Benjamin R Struck, Shuichi Kaneko, Kasey C Vickers, Stanley M Lemon, Praveen Sethupathy
UNLABELLED: Chronic hepatitis B (CHB), chronic hepatitis C (CHC), and associated hepatocellular carcinoma (HCC) are characterized by cholesterol imbalance and dyslipidemia; however, the key regulatory drivers of these phenotypes are incompletely understood. Using gene expression microarrays and high-throughput sequencing of small RNAs, we performed integrative analysis of microRNA (miRNA) and gene expression in nonmalignant and matched cancer tissue samples from human subjects with CHB or CHC and HCC...
December 8, 2015: MBio
https://www.readbyqxmd.com/read/26400237/transfer-rna-detection-by-small-rna-deep-sequencing-and-disease-association-with-myelodysplastic-syndromes
#9
Yan Guo, Amma Bosompem, Sanjay Mohan, Begum Erdogan, Fei Ye, Kasey C Vickers, Quanhu Sheng, Shilin Zhao, Chung-I Li, Pei-Fang Su, Madan Jagasia, Stephen A Strickland, Elizabeth A Griffiths, Annette S Kim
BACKGROUND: Although advances in sequencing technologies have popularized the use of microRNA (miRNA) sequencing (miRNA-seq) for the quantification of miRNA expression, questions remain concerning the optimal methodologies for analysis and utilization of the data. The construction of a miRNA sequencing library selects RNA by length rather than type. However, as we have previously described, miRNAs represent only a subset of the species obtained by size selection. Consequently, the libraries obtained for miRNA sequencing also contain a variety of additional species of small RNAs...
September 24, 2015: BMC Genomics
https://www.readbyqxmd.com/read/26320939/biogenesis-delivery-and-function-of-extracellular-rna
#10
James G Patton, Jeffrey L Franklin, Alissa M Weaver, Kasey Vickers, Bing Zhang, Robert J Coffey, K Mark Ansel, Robert Blelloch, Andrei Goga, Bo Huang, Noelle L'Etoille, Robert L Raffai, Charles P Lai, Anna M Krichevsky, Bogdan Mateescu, Vanille J Greiner, Craig Hunter, Olivier Voinnet, Michael T McManus
The Extracellular RNA (exRNA) Communication Consortium was launched by the National Institutes of Health to focus on the extent to which RNA might function in a non-cell-autonomous manner. With the availability of increasingly sensitive tools, small amounts of RNA can be detected in serum, plasma, and other bodily fluids. The exact mechanism(s) by which RNA can be secreted from cells and the mechanisms for the delivery and uptake by recipient cells remain to be determined. This review will summarize current knowledge about the biogenesis and delivery of exRNA and outline projects seeking to understand the functional impact of exRNA...
2015: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/26320937/meeting-report-discussions-and-preliminary-findings-on-extracellular-rna-measurement-methods-from-laboratories-in-the-nih-extracellular-rna-communication-consortium
#11
Louise C Laurent, Asim B Abdel-Mageed, P David Adelson, Jorge Arango, Leonora Balaj, Xandra Breakefield, Elizabeth Carlson, Bob S Carter, Blanca Majem, Clark C Chen, Emanuele Cocucci, Kirsty Danielson, Amanda Courtright, Saumya Das, Zakaria Y Abd Elmageed, Daniel Enderle, Alan Ezrin, Marc Ferrer, Jane Freedman, David Galas, Roopali Gandhi, Matthew J Huentelman, Kendall Van Keuren-Jensen, Yashar Kalani, Yong Kim, Anna M Krichevsky, Charles Lai, Madhu Lal-Nag, Clara D Laurent, Trevor Leonardo, Feng Li, Ivana Malenica, Debasis Mondal, Parham Nejad, Tushar Patel, Robert L Raffai, Renee Rubio, Johan Skog, Robert Spetzler, Jie Sun, Kahraman Tanriverdi, Kasey Vickers, Liang Wang, Yaoyu Wang, Zhiyun Wei, Howard L Weiner, David Wong, Irene K Yan, Ashish Yeri, Stephen Gould
Extracellular RNAs (exRNAs) have been identified in all tested biofluids and have been associated with a variety of extracellular vesicles, ribonucleoprotein complexes and lipoprotein complexes. Much of the interest in exRNAs lies in the fact that they may serve as signalling molecules between cells, their potential to serve as biomarkers for prediction and diagnosis of disease and the possibility that exRNAs or the extracellular particles that carry them might be used for therapeutic purposes. Among the most significant bottlenecks to progress in this field is the lack of robust and standardized methods for collection and processing of biofluids, separation of different types of exRNA-containing particles and isolation and analysis of exRNAs...
2015: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/26246194/inhibition-of-mir-29-has-a-significant-lipid-lowering-benefit-through-suppression-of-lipogenic-programs-in-liver
#12
C Lisa Kurtz, Emily E Fannin, Cynthia L Toth, Daniel S Pearson, Kasey C Vickers, Praveen Sethupathy
MicroRNAs (miRNAs) are important regulators and potential therapeutic targets of metabolic disease. In this study we show by in vivo administration of locked nucleic acid (LNA) inhibitors that suppression of endogenous miR-29 lowers plasma cholesterol levels by ~40%, commensurate with the effect of statins, and reduces fatty acid content in the liver by ~20%. Whole transcriptome sequencing of the liver reveals 883 genes dysregulated (612 down, 271 up) by inhibition of miR-29. The set of 612 down-regulated genes are most significantly over-represented in lipid synthesis pathways...
August 6, 2015: Scientific Reports
https://www.readbyqxmd.com/read/26233505/utility-of-select-plasma-microrna-for-disease-and-cardiovascular-risk-assessment-in-patients-with-rheumatoid-arthritis
#13
COMPARATIVE STUDY
Michelle J Ormseth, Joseph F Solus, Kasey C Vickers, Annette M Oeser, Paolo Raggi, C Michael Stein
OBJECTIVE: MicroRNA (miRNA) are small noncoding RNA that posttranscriptionally regulate gene expression and serve as potential mediators and markers of disease. Recently, plasma miR-24-3p and miR-125a-5p concentrations were shown to be elevated in rheumatoid arthritis (RA) and useful for RA diagnosis. We assessed the utility of 7 candidate plasma miRNA, selected for biological relevance, for RA diagnosis and use as markers of disease activity and subclinical atherosclerosis in RA. METHODS: The cross-sectional study included 168 patients with RA and 91 control subjects of similar age, race, and sex...
October 2015: Journal of Rheumatology
https://www.readbyqxmd.com/read/26132860/kras-dependent-sorting-of-mirna-to-exosomes
#14
Diana J Cha, Jeffrey L Franklin, Yongchao Dou, Qi Liu, James N Higginbotham, Michelle Demory Beckler, Alissa M Weaver, Kasey Vickers, Nirpesh Prasad, Shawn Levy, Bing Zhang, Robert J Coffey, James G Patton
Mutant KRAS colorectal cancer (CRC) cells release protein-laden exosomes that can alter the tumor microenvironment. To test whether exosomal RNAs also contribute to changes in gene expression in recipient cells, and whether mutant KRAS might regulate the composition of secreted microRNAs (miRNAs), we compared small RNAs of cells and matched exosomes from isogenic CRC cell lines differing only in KRAS status. We show that exosomal profiles are distinct from cellular profiles, and mutant exosomes cluster separately from wild-type KRAS exosomes...
2015: ELife
https://www.readbyqxmd.com/read/25652088/robust-passive-and-active-efflux-of-cellular-cholesterol-to-a-designer-functional-mimic-of-high-density-lipoprotein
#15
Andrea J Luthi, Nicholas N Lyssenko, Duyen Quach, Kaylin M McMahon, John S Millar, Kasey C Vickers, Daniel J Rader, Michael C Phillips, Chad A Mirkin, C Shad Thaxton
The ability of HDL to support macrophage cholesterol efflux is an integral part of its atheroprotective action. Augmenting this ability, especially when HDL cholesterol efflux capacity from macrophages is poor, represents a promising therapeutic strategy. One approach to enhancing macrophage cholesterol efflux is infusing blood with HDL mimics. Previously, we reported the synthesis of a functional mimic of HDL (fmHDL) that consists of a gold nanoparticle template, a phospholipid bilayer, and apo A-I. In this work, we characterize the ability of fmHDL to support the well-established pathways of cellular cholesterol efflux from model cell lines and primary macrophages...
May 2015: Journal of Lipid Research
https://www.readbyqxmd.com/read/25516621/human-scavenger-receptor-class-b-type-i-variants-lipid-traits-and-cardiovascular-disease
#16
EDITORIAL
Kasey C Vickers, Annabelle Rodriguez
No abstract text is available yet for this article.
December 2014: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/25467845/dysfunctional-high-density-lipoproteins-in-children-with-chronic-kidney-disease
#17
Ryohei Kaseda, Kathy Jabs, Tracy E Hunley, Deborah Jones, Aihua Bian, Ryan M Allen, Kasey C Vickers, Patricia G Yancey, MacRae F Linton, Sergio Fazio, Valentina Kon
OBJECTIVES: Our aim was to determine if chronic kidney disease (CKD) occurring in childhood impairs the normally vasoprotective functions of high-density lipoproteins (HDLs). MATERIALS AND METHODS: HDLs were isolated from children with end-stage renal disease on dialysis (ESRD), children with moderate CKD and controls with normal kidney function. Macrophage response to HDLs was studied as expression of inflammatory markers (MCP-1, TNF-α, IL-1β) and chemotaxis...
February 2015: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/25435401/mining-diverse-small-rna-species-in-the-deep-transcriptome
#18
Kasey C Vickers, Leslie A Roteta, Holli Hucheson-Dilks, Leng Han, Yan Guo
Transcriptomes of many species are proving to be exquisitely diverse, and many investigators are now using high-throughput sequencing to quantify non-protein-coding RNAs, namely small RNAs (sRNA). Unfortunately, most studies are focused solely on microRNA changes, and many investigators are not analyzing the full compendium of sRNA species present in their large datasets. We provide here a rationale to include all types of sRNAs in sRNA sequencing analyses, which will aid in the discovery of their biological functions and physiological relevance...
January 2015: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/25246565/microrna-223-coordinates-cholesterol-homeostasis
#19
Kasey C Vickers, Stuart R Landstreet, Michael G Levin, Bassem M Shoucri, Cynthia L Toth, Robert C Taylor, Brian T Palmisano, Fatiha Tabet, Huanhuan L Cui, Kerry-Anne Rye, Praveen Sethupathy, Alan T Remaley
MicroRNAs (miRNAs) regulate a wide variety of biological processes and contribute to metabolic homeostasis. Here, we demonstrate that microRNA-223 (miR-223), an miRNA previously associated with inflammation, also controls multiple mechanisms associated with cholesterol metabolism. miR-223 promoter activity and mature levels were found to be linked to cellular cholesterol states in hepatoma cells. Moreover, hypercholesterolemia was associated with increased hepatic miR-223 levels in athero-prone mice. miR-223 was found to regulate high-density lipoprotein-cholesterol (HDL-C) uptake, through direct targeting and repression of scavenger receptor BI, and to inhibit cholesterol biosynthesis through the direct repression of sterol enzymes 3-hydroxy-3-methylglutaryl-CoA synthase 1 and methylsterol monooxygenase 1 in humans...
October 7, 2014: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/25246237/alternative-applications-for-distinct-rna-sequencing-strategies
#20
Leng Han, Kasey C Vickers, David C Samuels, Yan Guo
Recent advances in RNA library preparation methods, platform accessibility and cost efficiency have allowed high-throughput RNA sequencing (RNAseq) to replace conventional hybridization microarray platforms as the method of choice for mRNA profiling and transcriptome analyses. RNAseq is a powerful technique to profile both long and short RNA expression, and the depth of information gained from distinct RNAseq methods is striking and facilitates discovery. In addition to expression analysis, distinct RNAseq approaches also allow investigators the ability to assess transcriptional elongation, DNA variance and exogenous RNA content...
July 2015: Briefings in Bioinformatics
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