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exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.
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 T W; Galas, David J; Van Keuren-Jensen, Kendall; Patel, Tushar; Jones, Jennifer C; Das, Saumya.
Afiliação
  • Murillo OD; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Thistlethwaite W; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Rozowsky J; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
  • Subramanian SL; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Lucero R; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Shah N; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Jackson AR; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Srinivasan S; Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
  • Chung A; Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Surgical Service, San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, USA.
  • Laurent CD; Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
  • Kitchen RR; Exosome Diagnostics, Inc., Waltham, MA 02451, USA.
  • Galeev T; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
  • Warrell J; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
  • Diao JA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA.
  • Welsh JA; Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
  • Hanspers K; Gladstone Institutes, San Francisco, CA 94158, USA.
  • Riutta A; Gladstone Institutes, San Francisco, CA 94158, USA.
  • Burgstaller-Muehlbacher S; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
  • Shah RV; Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
  • Yeri A; Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
  • Jenkins LM; Laboratory of Cell Biology, Center for Cancer Research, NIH, Bethesda, MD 20892, USA.
  • Ahsen ME; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
  • Cordon-Cardo C; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
  • Dogra N; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; IBM T.J. Watson Research Center, IBM Research, Yorktown Heights, NY 10598, USA.
  • Gifford SM; IBM T.J. Watson Research Center, IBM Research, Yorktown Heights, NY 10598, USA.
  • Smith JT; IBM T.J. Watson Research Center, IBM Research, Yorktown Heights, NY 10598, USA.
  • Stolovitzky G; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; IBM T.J. Watson Research Center, IBM Research, Yorktown Heights, NY 10598, USA.
  • Tewari AK; Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
  • Wunsch BH; IBM T.J. Watson Research Center, IBM Research, Yorktown Heights, NY 10598, USA.
  • Yadav KK; Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Sema4, Stamford, CT 06902, USA.
  • Danielson KM; Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
  • Filant J; Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
  • Moeller C; Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
  • Nejad P; Department of Neurology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
  • Paul A; Department of Neurology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
  • Simonson B; Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
  • Wong DK; Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Surgical Service, San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, USA.
  • Zhang X; Exosome Diagnostics, Inc., Waltham, MA 02451, USA.
  • Balaj L; Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA.
  • Gandhi R; Department of Neurology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
  • Sood AK; Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Cancer Biology, The Unive
  • Alexander RP; Pacific Northwest Research Institute, Seattle, WA 98122, USA.
  • Wang L; Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
  • Wu C; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
  • Wong DTW; School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
  • Galas DJ; Pacific Northwest Research Institute, Seattle, WA 98122, USA.
  • Van Keuren-Jensen K; Neurogenomics, The Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA.
  • Patel T; Department of Transplantation, Mayo Clinic, Jacksonville, FL 32224, USA.
  • Jones JC; Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
  • Das S; Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
Cell ; 177(2): 463-477.e15, 2019 04 04.
Article em En | MEDLINE | ID: mdl-30951672
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.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: RNA / Comunicação Celular Tipo de estudo: Observational_studies / Prognostic_studies / Risk_factors_studies Limite: Adult / Female / Humans / Male Idioma: En Revista: Cell Ano de publicação: 2019 Tipo de documento: Article País de afiliação: Estados Unidos
Texto completo
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: RNA / Comunicação Celular Tipo de estudo: Observational_studies / Prognostic_studies / Risk_factors_studies Limite: Adult / Female / Humans / Male Idioma: En Revista: Cell Ano de publicação: 2019 Tipo de documento: Article País de afiliação: Estados Unidos