ArticleCell reports. Medicine2022
System-wide transcriptome damage and tissue identity loss in COVID-19 patients.
Open access · goldAbstract read
In one paragraph
Article in Cell reports. Medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
0numbers the graph read from it
0cells of the map it votes in
31citing papers in PubMed
8.0field-weighted citation impact, top 2% of its field
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 49 citations in OpenAlex.
- Multiorgan Molecular Landscape of Severe COVID-19 Revealed by Consensus Gene Signatures and RAB8B Targeting.Journal of medical virology · 2026Article
- Multiomic spatial atlas shows deleted in malignant brain tumors 1 (DMBT1) glycoprotein is lost in colonic dysplasia.The Journal of pathology · 2025Article
- Article
- Lethal COVID-19 associates with RAAS-induced inflammation for multiple organ damage including mediastinal lymph nodes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Integrative multi-omics analysis to gain new insights into COVID-19.Scientific reports · 2024Article
- Three modes of viral adaption by the heart.Science advances · 2024Article
- Spatial multi-omics of human skin reveals KRAS and inflammatory responses to spaceflight.Nature communications · 2024Article
- Clinical Outcomes Following SARS-CoV-2 Infection in Pediatric Cystic Fibrosis Patients.Cureus · 2024Article
- Vascular Alterations Following COVID-19 Infection: A Comprehensive Literature Review.Life (Basel, Switzerland) · 2024Review
- Single-center Outcomes After Liver Transplantation With SARS-CoV-2-Positive Donors: An Argument for Increased Utilization.Transplantation direct · 2024Article
- Three Modes of Viral Adaption by the Heart.bioRxiv : the preprint server for biology · 2024Article
- Transcriptome and machine learning analysis of the impact of COVID-19 on mitochondria and multiorgan damage.PloS one · 2024Article
- A comprehensive SARS-CoV-2 and COVID-19 review, Part 2: host extracellular to systemic effects of SARS-CoV-2 infection.European journal of human genetics : EJHG · 2024Review
- Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections.Genome biology · 2023Article
- Review
- Spatial transcriptome atlas reveals pulmonary microstructure-specific COVID-19 gene signatures in cynomolgus macaques.Communications biology · 2023Article
- Plasma miR-195-5p predicts the severity of Covid-19 in hospitalized patients.Scientific reports · 2023Article
- Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts.Science translational medicine · 2023Article
- SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics.Genome biology · 2023Article
- Interactomics: Dozens of Viruses, Co-evolving With Humans, Including the Influenza A Virus, may Actively Distort Human Aging.Molecular biology and evolution · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
48 authors at 13 institutions in 2 countries.
Jiwoon ParkDepartment of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
Jonathan FooxDepartment of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
Tyler HetherNanoString Technologies, Inc., Seattle, WA, USA.
David C DankoDepartment of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
Sarah WarrenNanoString Technologies, Inc., Seattle, WA, USA.
Youngmi KimNanoString Technologies, Inc., Seattle, WA, USA.
Jason ReevesNanoString Technologies, Inc., Seattle, WA, USA.
Daniel J ButlerDepartment of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
Christopher MozsaryDepartment of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
Joel RosieneNew York Genome Center, New York, NY, USA.
Alon ShaiberNew York Genome Center, New York, NY, USA.
Evan E AfshinDepartment of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
Matthew MacKayDepartment of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
André F RendeiroThe HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
Yaron BramDepartment of Medicine, Weill Cornell Medicine, New York, NY, USA.
Vasuretha ChandarDepartment of Medicine, Weill Cornell Medicine, New York, NY, USA.
Heather GeigerNew York Genome Center, New York, NY, USA.
Arryn CraneyDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Priya VeluDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Ari M MelnickDepartment of Medicine, Weill Cornell Medicine, New York, NY, USA.
Iman HajirasoulihaDepartment of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
Afshin BeheshtiKBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA.
Deanne TaylorDepartment of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Amanda Saravia-ButlerSpace Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA.
Urminder SinghBioinformatics and Computational Biology Program, Center for Metabolic Biology, Department of Genetics, Development and Cell Biology Iowa State University, Ames, IA, USA.
Eve Syrkin WurteleBioinformatics and Computational Biology Program, Center for Metabolic Biology, Department of Genetics, Development and Cell Biology Iowa State University, Ames, IA, USA.
Jonathan SchislerMcAllister Heart Institute at The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Samantha FennesseyNew York Genome Center, New York, NY, USA.
André CorveloNew York Genome Center, New York, NY, USA.
Michael C ZodyNew York Genome Center, New York, NY, USA.
Soren GermerNew York Genome Center, New York, NY, USA.
Steven SalvatoreDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Shawn LevyHudsonAlpha Discovery Institute, Huntsville, AL, USA.
Shixiu WuHangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China.
Nicholas P TatonettiDepartment of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, New York, NY, USA.
Sagi ShapiraDepartment of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, New York, NY, USA.
Mirella SalvatoreDepartment of Medicine, Weill Cornell Medicine, New York, NY, USA.
Lars F WestbladeDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Melissa CushingDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Hanna RennertDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Alison J KriegelDepartment of Physiology, Cardiovascular Center, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.
Olivier ElementoDepartment of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
Marcin ImielinskiNew York Genome Center, New York, NY, USA.
Charles M RiceLaboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
Alain C BorczukDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Cem MeydanDepartment of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
Robert E SchwartzDepartment of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
Christopher E MasonDepartment of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
Cornell University · USNew York Genome Center · USNanostring Technologies (United States) · USColumbia University · USIowa State University · USAmes Research Center · USBroad Institute · USChildren's Hospital of Philadelphia · USDiscovery Institute · USHangzhou Cancer Hospital · CNMedical College of Wisconsin · USRockefeller University · USUniversity of North Carolina at Chapel Hill · US
Funding
Project 3: Targeting PRMT5 in Mantle Cell LymphomaP01CA214274 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI BALLMAN, KARLA V. · 2018 to 2022
$8.9MGenetic Viral and Host Adaptations to Breach Species Barriers of HCVR01AI107301 · NIAID · PRINCETON UNIVERSITY · PI Thomas Pietschmann, Alexander Ploss · 2013 to 2026
$6.0MSupplement for MINI point-of-use deviceU01DA053941 · NIDA · UNIVERSITY OF MIAMI CORAL GABLES · PI MASON, CHRISTOPHER EDWARD, SCHURER, STEPHAN C · 2021 to 2022
$5.2MClinical and Molecular Heterogeneity in the Myelodysplastic SyndromesR01CA249054 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI MASON, CHRISTOPHER EDWARD, PARK, CHRISTOPHER Y · 2020 to 2024
$3.5MMetagenomic profiling of urinary cell-free DNA to monitor urinary tract infection after kidney transplantationR01AI151059 · NIAID · CORNELL UNIVERSITY · PI DADHANIA, DARSHANA, DE VLAMINCK, IWIJN · 2020 to 2024
$3.4MThe Spatiotemporal Landscape of the Human Brain EpitranscriptomeR01MH117406 · NIMH · WEILL MEDICAL COLL OF CORNELL UNIV · PI MASON, CHRISTOPHER EDWARD · 2018 to 2022
$3.3MOptimization of the engineered 3D hepatic microenvironment enhances pluripotent stem cell derived hepatocyteR01DK121072 · NIDDK · WEILL MEDICAL COLL OF CORNELL UNIV · PI SCHWARTZ, ROBERT E · 2020 to 2024
$2.6MModeling Hepatoblastoma using pluripotent stem cell derived hepatocyte-like cellsR01CA234614 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI SCHWARTZ, ROBERT E · 2019 to 2023
$1.9MMolecular and Translational Oncology ResearchT32CA203702 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI BLENIS, JOHN, GIANNAKAKOU, PARASKEVI · 2017 to 2021
$1.4MMapping the RNA modification N6-methyladenosine during Zika virus infectionR21AI129851 · NIAID · WEILL MEDICAL COLL OF CORNELL UNIV · PI HORNER, STACY MICHELLE, MASON, CHRISTOPHER EDWARD · 2017 to 2018
$469kIdentification of Hepatitis B Virus permissiveness factorsR03DK117252 · NIDDK · WEILL MEDICAL COLL OF CORNELL UNIV · PI SCHWARTZ, ROBERT E · 2018 to 2019
$254kNCI NIH HHS P01 CA214274NCI NIH HHS R01 CA234614NCI NIH HHS R01 CA249054NCI NIH HHS T32 CA203702NIAID NIH HHS R01 AI107301NIAID NIH HHS R01 AI151059NIAID NIH HHS R21 AI129851NIDA NIH HHS U01 DA053941NIDDK NIH HHS R01 DK121072NIDDK NIH HHS R03 DK117252NIMH NIH HHS R01 MH117406
Abstract
The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and other lung injury states such as acute respiratory distress syndrome, remain poorly understood. To address these challenges, we combine transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues to define body-wide transcriptome changes in response to COVID-19. We then match these data with spatial protein and expression profiling across 357 tissue sections from 16 representative patient lung samples and identify tissue-compartment-specific damage wrought by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, evident as a function of varying viral loads during the clinical course of infection and tissue-type-specific expression states. Overall, our findings reveal a systemic disruption of canonical cellular and transcriptional pathways across all tissues, which can inform subsequent studies to combat the mortality of COVID-19 and to better understand the molecular dynamics of lethal SARS-CoV-2 and other respiratory infections.
Indexed as
SARS-CoV-2AdultAgedAged, 80 and overCase-Control StudiesCohort StudiesCOVID-19FemaleGene Expression RegulationHumansInfluenza, HumanLungMaleMiddle AgedOrthomyxoviridaeRespiratory Distress Syndromecoronaviruscoronavirus disease 2019COVID-19evere acute respiratory syndrome coronavirus 2host responsenext-generation sequencingNGSRNA-seqSARS-CoV-2spatial transcriptomics
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.