Evidence map›Paper›PMID 39794319›Full record

ArticleNature communications2025

Host-microbe multiomic profiling identifies distinct COVID-19 immune dysregulation in solid organ transplant recipients.

Harry Pickering, Joanna Schaenman, Hoang Van Phan, Cole Maguire, Alexandra Tsitsiklis, Nadine Rouphael, Nelson Iván Agudelo Higuita, Mark A Atkinson, Scott Brakenridge, Monica Fung and 21 more

Abstract readMulticenter Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

31 authors.

Harry Pickering *David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
Joanna Schaenman *David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
Hoang Van Phan *University of California San Francisco, San Francisco, CA, USA.
Cole Maguire *The University of Texas at Austin, Austin, TX, USA.ORCID http://orcid.org/0000-0001-8986-9762
Alexandra TsitsiklisUniversity of California San Francisco, San Francisco, CA, USA.
Nadine RouphaelEmory School of Medicine, Atlanta, GA, USA.ORCID http://orcid.org/0000-0002-2512-7919
Nelson Iván Agudelo HiguitaOklahoma University Health Sciences Center, Oklahoma City, OK, USA.
Mark A AtkinsonUniversity of Florida, Gainesville, FL, USA.
Scott BrakenridgeUniversity of Florida, Gainesville, FL, USA.
Monica FungUniversity of California San Francisco, San Francisco, CA, USA.
William MesserOregon Health Sciences University, Portland, OR, USA.ORCID http://orcid.org/0000-0002-4381-6347
IMPACC Network
Ramin Salehi-RadDavid Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
Matthew C AltmanBenaroya Research Institute, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-1784-8505
Patrice M BeckerNational Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-1170-8587
Steven E BosingerEmory School of Medicine, Atlanta, GA, USA.ORCID http://orcid.org/0000-0002-2116-5061
Walter EckalbarUniversity of California San Francisco, San Francisco, CA, USA.
Annmarie HochPrecision Vaccines Program, Boston Children's Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0003-0836-2164
Naresh Doni JayaveluBenaroya Research Institute, University of Washington, Seattle, WA, USA.
Seunghee Kim-SchulzeIcahn School of Medicine at Mount Sinai, New York, NY, USA.
Meagan JenkinsDavid Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0003-1379-9176
Steven H KleinsteinYale School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0003-4957-1544
Florian KrammerIcahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID http://orcid.org/0000-0003-4121-776X
Holden T MaeckerStanford University School of Medicine, Palo Alto, CA, USA.ORCID http://orcid.org/0000-0003-0795-9946
Al OzonoffPrecision Vaccines Program, Boston Children's Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0003-4233-5899
Joann Diray-ArcePrecision Vaccines Program, Boston Children's Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0003-2183-4269
Albert ShawYale School of Medicine, New Haven, CT, USA.
Lindsey BadenHarvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0009-0004-1752-1926
Ofer LevyPrecision Vaccines Program, Boston Children's Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0002-5859-1945
Elaine F ReedDavid Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
Charles R LangelierUniversity of California San Francisco, San Francisco, CA, USA. chaz.langelier@ucsf.edu.ORCID http://orcid.org/0000-0002-6708-4646

Funding

Yale Clinical and Translational Science Award (U Component)UL1TR001863 · NCATS · YALE UNIVERSITY · PI John H. Krystal, LUCILA OHNO-MACHADO · 2016 to 2026
$102.9M
Using a tonsil organoid system to probe conditions for the induction of protective antibody and T cell responses to influenza.U19AI057229 · NIAID · STANFORD UNIVERSITY · PI Mark Morris Davis · 2003 to 2026
$88.5M
Translation of immunologic technologies from basic research into pre-clinical nonU19AI062629 · NIAID · OKLAHOMA MEDICAL RESEARCH FOUNDATION · PI COGGESHALL, KENNETH MARK · 2004 to 2023
$56.2M
Systems investigation of vaccine responses in B cell depleted autoimmune patientsU19AI089992 · NIAID · YALE UNIVERSITY · PI Albert C Shaw · 2010 to 2026
$50.4M
Project 3 - Ex vivo immune profiling of dengue viruses and vaccinesU19AI118610 · NIAID · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI HARRIS, EVA · 2015 to 2021
$46.6M
Systems Biological Analysis of Innate and Adaptive Responses to VaccinationU19AI090023 · NIAID · EMORY UNIVERSITY · PI AHMED, RAFI, LI, SHUZHAO · 2010 to 2021
$45.0M
Understanding Asthma EndotypesU19AI077439 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI PRESCOTT G WOODRUFF · 2008 to 2026
$41.1M
Clinical and Translational Science Collaborative of Northern Ohio, Catalyzing Linkages to Equity in Health (CLE Health)UM1TR004528 · NCATS · CASE WESTERN RESERVE UNIVERSITY · PI GRACE A MCCOMSEY · 2023 to 2026
$32.1M
Transcriptomics to define biomarkers of neonatal vaccine immunogenicityU19AI118608 · NIAID · BOSTON CHILDREN'S HOSPITAL · PI LEVY, OFER · 2017 to 2021
$24.7M
The effects of immune-age on immune-response and the molecular mechanisms which drive itP01AI153559 · NIAID · STANFORD UNIVERSITY · PI DAVIS, MARK MORRIS · 2021 to 2025
$17.8M
Tollip inhibits IL-33 signaling during airway influenza virus infectionU19AI125357 · NIAID · UNIVERSITY OF ARIZONA · PI KRAFT, MONICA, VERCELLI, DONATA · 2016 to 2025
$14.7M
Systems Immunology profiling of respiratory viral infections in vulnerable populationsU19AI167891 · NIAID · BENAROYA RESEARCH INST AT VIRGINIA MASON · PI Erik Wambre · 2022 to 2026
$14.0M
BLRD VA I01 BX005023NCATS NIH HHS UL1 TR001863NCATS NIH HHS UM1 TR004528NHLBI NIH HHS R01 HL155418NIAID NIH HHS P01 AI153559NIAID NIH HHS R01 AI104870NIAID NIH HHS R01 AI132774NIAID NIH HHS R01 AI135803NIAID NIH HHS R01 AI145835NIAID NIH HHS U19 AI057229NIAID NIH HHS U19 AI062629NIAID NIH HHS U19 AI077439NIAID NIH HHS U19 AI089992NIAID NIH HHS U19 AI090023NIAID NIH HHS U19 AI118608NIAID NIH HHS U19 AI118610NIAID NIH HHS U19 AI125357NIAID NIH HHS U19 AI128910NIAID NIH HHS U19 AI128913NIAID NIH HHS U19 AI167891NIAID NIH HHS U54 AI142766U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI) 5R01HL155418
6 · The paper itself

Abstract

Coronavirus disease 2019 (COVID-19) poses significant risks for solid organ transplant recipients, who have atypical but poorly characterized immune responses to infection. We aim to understand the host immunologic and microbial features of COVID-19 in transplant recipients by leveraging a prospective multicenter cohort of 86 transplant recipients age- and sex-matched with 172 non-transplant controls. We find that transplant recipients have higher nasal SARS-CoV-2 viral abundance and impaired viral clearance, and lower anti-spike IgG levels. In addition, transplant recipients exhibit decreased plasmablasts and transitional B cells, and increased senescent T cells. Blood and nasal transcriptional profiling demonstrate unexpected upregulation of innate immune signaling pathways and increased levels of several proinflammatory serum chemokines. Severe disease in transplant recipients, however, is characterized by a less robust induction of pro-inflammatory genes and chemokines. Together, our study reveals distinct immune features and altered viral dynamics in solid organ transplant recipients.

Indexed as

COVID-19Host Microbial InteractionsOrgan TransplantationSARS-CoV-2Transplant RecipientsAdultAgedAntibodies, ViralChemokinesFemaleHumansImmunity, InnateImmunoglobulin GMaleMiddle AgedProspective StudiesAntibodies, ViralChemokinesImmunoglobulin G

Identifiers

PMID39794319
PMCPMC11723965

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Registered trials

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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 OpenQuestion graph.