Evidence map›Paper›PMID 40532694›Full record

ArticleCell genomics2025

Temporal multi-omics analysis of COVID-19 in end-stage kidney disease.

Emily Stephenson, Erin Macdonald-Dunlop, Lisa M Dratva, Rik G H Lindeboom, Zewen Kelvin Tuong, Win Min Tun, Lorenz Kretschmer, Norzawani B Buang, Stephane Ballereau, Mia Cabantaus and 20 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 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. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

30 authors.

Emily StephensonBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK.
Erin Macdonald-DunlopDepartment of Immunology and Inflammation, Imperial College London, London, UK.
Lisa M DratvaCellular Genetics, Wellcome Sanger Institute, Hinxton, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
Rik G H LindeboomCellular Genetics, Wellcome Sanger Institute, Hinxton, UK.
Zewen Kelvin TuongDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK.
Win Min TunBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
Lorenz KretschmerCellular Genetics, Wellcome Sanger Institute, Hinxton, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
Norzawani B BuangDepartment of Immunology and Inflammation, Imperial College London, London, UK.
Stephane BallereauCellular Genetics, Wellcome Sanger Institute, Hinxton, UK.
Mia CabantausDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK.
Ana PeñalverDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK.
Elena PrigmoreCellular Genetics, Wellcome Sanger Institute, Hinxton, UK.
John R FerdinandDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK.
Benjamin J StewartCellular Genetics, Wellcome Sanger Institute, Hinxton, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK.
Jack GisbyDepartment of Immunology and Inflammation, Imperial College London, London, UK.
Talat H MalikDepartment of Immunology and Inflammation, Imperial College London, London, UK.
Candice L ClarkeDepartment of Immunology and Inflammation, Imperial College London, London, UK.
Nicholas Medjeral-ThomasDepartment of Immunology and Inflammation, Imperial College London, London, UK; Imperial College Renal and Transplant Centre, Imperial College Healthcare National Health Service (NHS) Trust, Hammersmith Hospital, London, UK.
Maria PrendeckiDepartment of Immunology and Inflammation, Imperial College London, London, UK; Imperial College Renal and Transplant Centre, Imperial College Healthcare National Health Service (NHS) Trust, Hammersmith Hospital, London, UK.
Stephen McAdooDepartment of Immunology and Inflammation, Imperial College London, London, UK; Imperial College Renal and Transplant Centre, Imperial College Healthcare National Health Service (NHS) Trust, Hammersmith Hospital, London, UK.
Anais PortetDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK.
Michelle WillicombeDepartment of Immunology and Inflammation, Imperial College London, London, UK; Imperial College Renal and Transplant Centre, Imperial College Healthcare National Health Service (NHS) Trust, Hammersmith Hospital, London, UK.
Eleanor SandhuDepartment of Immunology and Inflammation, Imperial College London, London, UK; Imperial College Renal and Transplant Centre, Imperial College Healthcare National Health Service (NHS) Trust, Hammersmith Hospital, London, UK.
Matthew C PickeringDepartment of Immunology and Inflammation, Imperial College London, London, UK.
Marina BottoDepartment of Immunology and Inflammation, Imperial College London, London, UK.
Sarah A TeichmannCellular Genetics, Wellcome Sanger Institute, Hinxton, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; CIFAR Macmillan Multiscale Human Programme, CIFAR, Toronto, Canada.
Muzlifah HaniffaBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK; Department of Dermatology and National Institute for Health and Care Research (NIHR) Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
Menna R ClatworthyCellular Genetics, Wellcome Sanger Institute, Hinxton, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK.
David C ThomasDepartment of Immunology and Inflammation, Imperial College London, London, UK; Department of Medicine, University of Cambridge, Cambridge, UK. Electronic address: tdct2@cam.ac.uk.
James E PetersDepartment of Immunology and Inflammation, Imperial College London, London, UK. Electronic address: j.peters@imperial.ac.uk.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Patients with end-stage kidney disease (ESKD) are at high risk of severe COVID-19. We performed longitudinal single-cell immune profiling of ESKD patients with COVID-19. Transcriptome, surface proteome, and immunoreceptor sequencing data were generated on 580,040 high-quality cells, derived from 187 samples from 61 patients. For a subset of individuals, we obtained samples before and during infection, allowing intra-individual comparison. Longitudinal profiling demonstrated distinct temporal gene expression trajectories in severe/critical versus mild/moderate COVID-19. We identified a population of transcriptionally distinct monocytes that emerged in peripheral blood following glucocorticoid treatment. Evaluation of clonal T cell dynamics showed that the fastest expanding clones were enriched in known SARS-CoV-2-specific sequences and shared across multiple patients. Comparison with external datasets revealed upregulation of immune cell TGF-β pathway expression in ESKD, irrespective of COVID-19 status. Our data delineate the temporal dynamics of the immune response in COVID-19 in a high-risk population.

Indexed as

COVID-19Kidney Failure, ChronicAdultAgedFemaleGene Expression ProfilingHumansLongitudinal StudiesMaleMiddle AgedMonocytesMultiomicsProteomeSARS-CoV-2Single-Cell AnalysisT-LymphocytesProteomeCITE-seqCOVID-19end-stage kidney diseaseESKDglucocorticoidsinterferonlongitudinalmonocytesSARS-CoV-2sequencingsingle-cell transcriptomicsT cell receptorTCR

Identifiers

PMID40532694
PMCPMC12366655

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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.