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Large-Scale Multi-omic Analysis of COVID-19 Severity.
Overmyer, Katherine A; Shishkova, Evgenia; Miller, Ian J; Balnis, Joseph; Bernstein, Matthew N; Peters-Clarke, Trenton M; Meyer, Jesse G; Quan, Qiuwen; Muehlbauer, Laura K; Trujillo, Edna A; He, Yuchen; Chopra, Amit; Chieng, Hau C; Tiwari, Anupama; Judson, Marc A; Paulson, Brett; Brademan, Dain R; Zhu, Yunyun; Serrano, Lia R; Linke, Vanessa; Drake, Lisa A; Adam, Alejandro P; Schwartz, Bradford S; Singer, Harold A; Swanson, Scott; Mosher, Deane F; Stewart, Ron; Coon, Joshua J; Jaitovich, Ariel.
  • Overmyer KA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Morgridge Institute for Research, Madison, WI 53562, USA.
  • Shishkova E; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • Miller IJ; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • Balnis J; Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA.
  • Bernstein MN; Morgridge Institute for Research, Madison, WI 53562, USA.
  • Peters-Clarke TM; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • Meyer JG; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • Quan Q; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • Muehlbauer LK; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • Trujillo EA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • He Y; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • Chopra A; Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA.
  • Chieng HC; Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA.
  • Tiwari A; Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; Division of Sleep Medicine, Albany Medical Center, Albany, NY 12208, USA.
  • Judson MA; Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA.
  • Paulson B; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • Brademan DR; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • Zhu Y; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • Serrano LR; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • Linke V; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • Drake LA; Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA.
  • Adam AP; Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA; Department of Ophthalmology, Albany Medical College, Albany, NY 12208, USA.
  • Schwartz BS; Morgridge Institute for Research, Madison, WI 53562, USA.
  • Singer HA; Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA.
  • Swanson S; Morgridge Institute for Research, Madison, WI 53562, USA.
  • Mosher DF; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA.
  • Stewart R; Morgridge Institute for Research, Madison, WI 53562, USA.
  • Coon JJ; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Morgridge Institute for Research, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, U
  • Jaitovich A; Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA. Electronic address: jaitova@amc.edu.
Cell Syst ; 12(1): 23-40.e7, 2021 01 20.
Article in English | MEDLINE | ID: covidwho-837999
Preprint
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ABSTRACT
We performed RNA-seq and high-resolution mass spectrometry on 128 blood samples from COVID-19-positive and COVID-19-negative patients with diverse disease severities and outcomes. Quantified transcripts, proteins, metabolites, and lipids were associated with clinical outcomes in a curated relational database, uniquely enabling systems analysis and cross-ome correlations to molecules and patient prognoses. We mapped 219 molecular features with high significance to COVID-19 status and severity, many of which were involved in complement activation, dysregulated lipid transport, and neutrophil activation. We identified sets of covarying molecules, e.g., protein gelsolin and metabolite citrate or plasmalogens and apolipoproteins, offering pathophysiological insights and therapeutic suggestions. The observed dysregulation of platelet function, blood coagulation, acute phase response, and endotheliopathy further illuminated the unique COVID-19 phenotype. We present a web-based tool (covid-omics.app) enabling interactive exploration of our compendium and illustrate its utility through a machine learning approach for prediction of COVID-19 severity.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Severity of Illness Index / Sequence Analysis, RNA / Machine Learning / COVID-19 Type of study: Cohort study / Observational study / Prognostic study / Randomized controlled trials Limits: Aged / Female / Humans / Male / Middle aged Language: English Journal: Cell Syst Year: 2021 Document Type: Article Affiliation country: J.cels.2020.10.003

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Severity of Illness Index / Sequence Analysis, RNA / Machine Learning / COVID-19 Type of study: Cohort study / Observational study / Prognostic study / Randomized controlled trials Limits: Aged / Female / Humans / Male / Middle aged Language: English Journal: Cell Syst Year: 2021 Document Type: Article Affiliation country: J.cels.2020.10.003