54: Immune trajectories in COVID-19 among patients with end-stage kidney disease

Stephenson E et al., Cell Genomics - Longitudinal single-cell multi-omics profiling of PBMCs from 61 end-stage kidney disease (ESKD) patients with COVID-19 (580,040 cells) reveals distinct temporal immune trajectories in severe versus mild disease, emergence of a dexamethasone-associated monocyte population, and expanding T cell clones enriched for SARS-CoV-2 specificity. Key terms: COVID-19, end-stage kidney disease, single-cell multi-omics, T cell receptors, glucocorticoids.

Study Highlights:
Longitudinal single-cell CITE-seq and paired TCR/BCR sequencing of PBMCs from ESKD patients show divergent temporal gene-expression trajectories in severe/critical versus mild/moderate COVID-19. An early and stronger interferon response is seen in severe disease with a steeper decline over time, and HLA class II expression falls over time in severe cases. The fastest-expanding T cell clones are enriched for known SARS-CoV-2-specific TCRα sequences and form public motifs with inferred MHC class II restriction. Glucocorticoid treatment (dexamethasone) is associated with the rapid emergence of a distinct CD163-high, dexamethasone-related monocyte population.

Conclusion:
This multi-omics longitudinal study delineates time-dependent immune differences between mild and severe COVID-19 in a high-risk ESKD population, identifies steroid-associated monocytes, and documents shared SARS-CoV-2-directed T cell clonotypes; findings are observational and do not prove causality.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Temporal multi-omics analysis of COVID-19 in end-stage kidney disease

First author:
Stephenson E

Journal:
Cell Genomics

DOI:
10.1016/j.xgen.2025.100918

Reference:
Stephenson E, Macdonald-Dunlop E, Dratva LM, et al. Temporal multi-omics analysis of COVID-19 in end-stage kidney disease. Cell Genomics. 2025;5:100918. doi:10.1016/j.xgen.2025.100918

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

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QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-06-24.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited transcript sections describing time-resolved multi-omics methodology, interferon dynamics, TNF expression vs protein uncoupling, dexamethasone-induced monocytes, expanding SARS-CoV-2–specific T cell clones and public TCR motifs, baseline TGF-β signaling in ESKD, HLA class II changes with severity, and Mendelian
- transcript topics: Time-resolved multi-omics methodology (CITE-seq, VDJ, Olink); Interferon response dynamics in COVID-19; TNF gene expression vs TNF-α protein uncoupling; Dexamethasone-associated monocytes (dex. monos); Public SARS-CoV-2–specific T cell clones and TCR motifs; Baseline TGF-β signaling across immune cells in ESKD

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Met...