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3 results on '"Das, Saumya"'

1. Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

Author

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

Subjects
Biological Sciences, Genetics, Human Genome, Biotechnology, Adult, Body Fluids, Cell Line, Cell-Free Nucleic Acids, Circulating MicroRNA, Extracellular Vesicles, Female, Healthy Volunteers, Humans, Male, MicroRNAs, RNA, Reproducibility of Results, Sequence Analysis, RNA, extracellular RNA, extracellular vesicles, lipoprotein, ribonucleoprotein, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
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 10 exRNA isolation methods across 5 biofluids revealed marked differences in the complexity and reproducibility of the resulting small RNA-seq 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

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

Author

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

Subjects
Biological Sciences, Genetics, Human Genome, Biotechnology, Adult, Body Fluids, Cell Communication, Cell-Free Nucleic Acids, Circulating MicroRNA, Extracellular Vesicles, Female, Humans, Male, RNA, Reproducibility of Results, Sequence Analysis, RNA, Software, ERCC, deconvolution, exRNA, exosomes, extracellular RNA, extracellular vesicles, lipoproteins, ribonucleoproteins, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
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 by deconvolution to identify physiologically relevant response pathways that were not detected previously. To enable wide application of this model, as part of the exRNA Atlas resource, we provide tools for deconvolution and analysis of user-provided case-control studies.

Published
2019

3. The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research

Author

Das, Saumya, Consortium, The Extracellular RNA Communication, Abdel-Mageed, Asim B, Adamidi, Catherine, Adelson, P David, Akat, Kemal M, Alsop, Eric, Ansel, K Mark, Arango, Jorge, Aronin, Neil, Avsaroglu, Seda Kilinc, Azizian, Azadeh, Balaj, Leonora, Ben-Dov, Iddo Z, Bertram, Karl, Bitzer, Markus, Blelloch, Robert, Bogardus, Kimberly A, Breakefield, Xandra Owens, Calin, George A, Carter, Bob S, Charest, Al, Chen, Clark C, Chitnis, Tanuja, Coffey, Robert J, Courtright-Lim, Amanda, Datta, Amrita, DeHoff, Peter, Diacovo, Thomas G, Erle, David J, Etheridge, Alton, Ferrer, Marc, Franklin, Jeffrey L, Freedman, Jane E, Galas, David J, Galeev, Timur, Gandhi, Roopali, Garcia, Aitor, Gerstein, Mark Bender, Ghai, Vikas, Ghiran, Ionita Calin, Giraldez, Maria D, Goga, Andrei, Gogakos, Tasos, Goilav, Beatrice, Gould, Stephen J, Guo, Peixuan, Gupta, Mihir, Hochberg, Fred, Huang, Bo, Huentelman, Matt, Hunter, Craig, Hutchins, Elizabeth, Jackson, Andrew R, Kalani, M Yashar S, Kanlikilicer, Pinar, Karaszti, Reka Agnes, Van Keuren-Jensen, Kendall, Khvorova, Anastasia, Kim, Yong, Kim, Hogyoung, Kim, Taek Kyun, Kitchen, Robert, Kraig, Richard P, Krichevsky, Anna M, Kwong, Raymond Y, Laurent, Louise C, Lee, Minyoung, L’Etoile, Noelle, Levy, Shawn E, Li, Feng, Li, Jenny, Li, Xin, Lopez-Berestein, Gabriel, Lucero, Rocco, Mateescu, Bogdan, Matin, AC, Max, Klaas EA, McManus, Michael T, Mempel, Thorsten R, Meyer, Cindy, Milosavljevic, Aleksandar, Mondal, Debasis, Mukamal, Kenneth Jay, Murillo, Oscar D, Muthukumar, Thangamani, Nickerson, Deborah A, O’Donnell, Christopher J, Patel, Dinshaw J, Patel, Tushar, Patton, James G, Paul, Anu, Peskind, Elaine R, Phelps, Mitch A, Putterman, Chaim, Quesenberry, Peter J, Quinn, Joseph F, Raffai, Robert L, and Ranabothu, Saritha

Subjects
Genetics, Biomarkers, Cell-Free Nucleic Acids, Extracellular Vesicles, Humans, Knowledge Bases, MicroRNAs, RNA, Extracellular RNA Communication Consortium, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The Extracellular RNA Communication Consortium (ERCC) was launched to accelerate progress in the new field of extracellular RNA (exRNA) biology and to establish whether exRNAs and their carriers, including extracellular vesicles (EVs), can mediate intercellular communication and be utilized for clinical applications. Phase 1 of the ERCC focused on exRNA/EV biogenesis and function, discovery of exRNA biomarkers, development of exRNA/EV-based therapeutics, and construction of a robust set of reference exRNA profiles for a variety of biofluids. Here, we present progress by ERCC investigators in these areas, and we discuss collaborative projects directed at development of robust methods for EV/exRNA isolation and analysis and tools for sharing and computational analysis of exRNA profiling data.

Published
2019

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