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/ Support:Base by Base is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming:❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 More at basebybase.com On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/base-by-base-54-corrupted-pdf 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...