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Start Over "David K. Wong" Topic humans Publisher escholarship, university of california
2 results on '"David K. Wong"'

1. exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids

Author

Oscar Murillo, David J. Galas, Andrew I. Su, Liang Wang, Saumya Das, Parham Nejad, Srimeenakshi Srinivasan, Aleksandar Milosavljevic, Andrew R. Jackson, Bridget Simonson, Xuan Zhang, Ashish Yeri, Navneet Dogra, Anil K. Sood, Alexander R. Pico, Stacey M. Gifford, Anders Riutta, Roopali Gandhi, Louise C. Laurent, Jennifer Jones, Neethu Shah, Carlos Cordon-Cardo, Kirsty Danielson, Timur R. Galeev, Matthew E. Roth, Kendall Van Keuren-Jensen, Robert R. Kitchen, Courtney Moeller, William Thistlethwaite, Allen Chung, Roger P. Alexander, David T.W. Wong, Jonathan Warrell, Tushar Patel, Justyna Filant, Kristina Hanspers, Gustavo Stolovitzky, Sai Lakshmi Subramanian, Leonora Balaj, David K. Wong, Mark Gerstein, Kei-Hoi Cheung, Sebastian Burgstaller-Muehlbacher, Ashutosh K. Tewari, Robert L. Raffai, Kamlesh K Yadav, Anu Paul, Benjamin H. Wunsch, Joel Rozowsky, Rocco Lucero, Lisa M. Miller Jenkins, Joshua T. Smith, Joshua A. Welsh, Ravi V. Shah, James A. Diao, Clara D. Laurent, Chunlei Wu, and Mehmet Eren Ahsen

Subjects
Adult, Male, Cell Communication, Computational biology, exosomes, Biology, deconvolution, Extracellular vesicles, Medical and Health Sciences, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Genetics, ribonucleoproteins, Humans, Circulating MicroRNA, 030304 developmental biology, Ribonucleoprotein, 0303 health sciences, Atlas (topology), ERCC, Human Genome, Reproducibility of Results, Biological Sciences, extracellular RNA, Body Fluids, lipoproteins, RNA, Female, exRNA, extracellular vesicles, Sequence Analysis, Cell-Free Nucleic Acids, Software, 030217 neurology & neurosurgery, Biotechnology, Extracellular RNA, Developmental Biology
Abstract

To develop a map of cell-cell communication mediated by extracellular RNA (exRNA), the NIH Extracellular RNA Communication Consortium created the exRNA Atlas resource (https://exrna-atlas.org). The Atlas version 4P1 hosts 5,309 exRNA-seq and exRNA qPCR profiles from 19 studies and a suite of analysis and visualization tools. To analyze variation between profiles, we apply computational deconvolution. The analysis leads to a model with six exRNA cargo types (CT1, CT2, CT3A, CT3B, CT3C, CT4), each detectable in multiple biofluids (serum, plasma, CSF, saliva, urine). Five of the cargo types associate with known vesicular and non-vesicular (lipoprotein and ribonucleoprotein) exRNA carriers. To validate utility of this model, we re-analyze an exercise response study bydeconvolution to identify physiologically relevant response pathways that were not detected previously. To enable wide application of this model, as part of theexRNA Atlas resource, we provide tools for deconvolution and analysis of user-provided case-control studies.

Published
2019
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2. Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

Author

Pike See Cheah, George G. Daaboul, Srimeenakshi Srinivasan, Xandra O. Breakefield, Ravi V. Shah, Anil K. Sood, Eric Londin, Lucie D. Laurent, Bridget Simonson, Louise C. Laurent, Xuan Zhang, Rogan Magee, Isidore Rigoutsos, Parham Nejad, Justyna Filant, Anu Paul, Rodosthenis S. Rodosthenous, Venkatesh L. Murthy, Allen Chung, Tushar Patel, Leonora Balaj, Saumya Das, Ashish Yeri, Cuong To, Peter De Hoff, Irene K. Yan, Clara D. Laurent, David K. Wong, Roopali Gandhi, Robert L. Raffai, Kirsty Danielson, Roger P. Alexander, Jodi Lapidus, and Courtney Moeller

Subjects
Adult, Male, Small RNA, Computational biology, Biology, Extracellular vesicles, Medical and Health Sciences, Article, General Biochemistry, Genetics and Molecular Biology, ribonucleoprotein, Cell Line, Extracellular Vesicles, 03 medical and health sciences, 0302 clinical medicine, Genetics, Humans, Lack of knowledge, Circulating MicroRNA, Isolation (database systems), 030304 developmental biology, 0303 health sciences, Sequence Analysis, RNA, Human Genome, lipoprotein, Reproducibility of Results, Extracellular vesicle, Biological Sciences, Healthy Volunteers, extracellular RNA, Body Fluids, Biomarker (cell), MicroRNAs, RNA, Female, Optimal methods, extracellular vesicles, Sequence Analysis, Cell-Free Nucleic Acids, 030217 neurology & neurosurgery, Biotechnology, Extracellular RNA, Developmental Biology
Abstract

Poor reproducibility within and across studies arising from lack of knowledge regarding the performance of extracellular RNA (exRNA) isolation methods has hindered progress in the exRNA field. A systematic comparison of ten exRNA isolation methods across five biofluids revealed marked differences in the complexity and reproducibility of the resulting small RNAseq profiles. The relative efficiency with which each method accessed different exRNA carrier subclasses was determined by estimating the proportions of extracellular vesicle- (EV), ribonucleoprotein-(RNP)-, and high-density lipoprotein- (HDL) specific miRNA signatures in each profile. An interactive web-based application (miRDaR) was developed to help investigators select the optimal exRNA isolation method for their studies. miRDar provides comparative statistics for all expressed miRNAs or a selected subset of miRNAs in the desired biofluid for each exRNA isolation method, and returns a ranked list of exRNA isolation methods prioritized by complexity, expression level and reproducibility. These results will improve reproducibility and stimulate further progress in exRNA biomarker development.

Published
2019
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