Prolonged exposure to lung-derived cytokines is associated with activation of microglia in patients with COVID-19
Rogan A. Grant, Taylor A. Poor, Lango Sichizya, Estefani Diaz, Joseph I. Bailey, Sahil Soni, Karolina J. Senkow, Xóchitl G. Pérez-Leonor, Hiam Abdala-Valencia, Ziyan Lu, Helen K. Donnelly, Lacy M. Simons, Egon A. Ozer, Robert M. Tighe, Jon W. Lomasney, Richard G. Wunderink, Benjamin D. Singer, Alexander V. Misharin, G.R. Scott Budinger, for The Northwestern University Successful Clinical Response In Pneumonia Therapy (NU SCRIPT) Investigators
Rogan A. Grant, Taylor A. Poor, Lango Sichizya, Estefani Diaz, Joseph I. Bailey, Sahil Soni, Karolina J. Senkow, Xóchitl G. Pérez-Leonor, Hiam Abdala-Valencia, Ziyan Lu, Helen K. Donnelly, Lacy M. Simons, Egon A. Ozer, Robert M. Tighe, Jon W. Lomasney, Richard G. Wunderink, Benjamin D. Singer, Alexander V. Misharin, G.R. Scott Budinger, for The Northwestern University Successful Clinical Response In Pneumonia Therapy (NU SCRIPT) Investigators
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Clinical Research and Public Health COVID-19 Immunology

Prolonged exposure to lung-derived cytokines is associated with activation of microglia in patients with COVID-19

Abstract

BACKGROUND Survivors of pneumonia, including SARS-CoV-2 pneumonia, are at increased risk for cognitive dysfunction and dementia. In rodent models, cognitive dysfunction following pneumonia has been linked to the systemic release of lung-derived pro-inflammatory cytokines. Microglia are poised to respond to inflammatory signals from the circulation, and their dysfunction has been linked to cognitive impairment in murine models of dementia and in humans.METHODS We measured levels of 55 cytokines and chemokines in bronchoalveolar lavage fluid and plasma from 341 patients with respiratory failure and 13 healthy controls, including 93 unvaccinated patients with COVID-19 and 203 patients with other causes of pneumonia. We used flow cytometry to sort neuroimmune cells from postmortem brain tissue from 5 patients who died from COVID-19 and 3 patients who died from other causes for single-cell RNA-sequencing.RESULTS Microglia from patients with COVID-19 exhibited a transcriptomic signature suggestive of their activation by circulating pro-inflammatory cytokines. Peak levels of pro-inflammatory cytokines were similar in patients with pneumonia irrespective of etiology, but cumulative cytokine exposure was higher in patients with COVID-19. Treatment with corticosteroids reduced expression of COVID-19–specific cytokines.CONCLUSION Prolonged lung inflammation results in sustained elevations in circulating cytokines in patients with SARS-CoV-2 pneumonia compared with those with pneumonia secondary to other pathogens. Microglia from patients with COVID-19 exhibit transcriptional responses to inflammatory cytokines. These findings support data from rodent models causally linking systemic inflammation with cognitive dysfunction in pneumonia and support further investigation into the role of microglia in pneumonia-related cognitive dysfunction.FUNDING SCRIPT U19AI135964, UL1TR001422, P01AG049665, P01HL154998, R01HL149883, R01LM013337, R01HL153122, R01HL147290, R01HL147575, R01HL158139, R01ES034350, R01ES027574, I01CX001777, U01TR003528, R21AG075423, T32AG020506, F31AG071225, T32HL076139.

Authors

Rogan A. Grant, Taylor A. Poor, Lango Sichizya, Estefani Diaz, Joseph I. Bailey, Sahil Soni, Karolina J. Senkow, Xóchitl G. Pérez-Leonor, Hiam Abdala-Valencia, Ziyan Lu, Helen K. Donnelly, Lacy M. Simons, Egon A. Ozer, Robert M. Tighe, Jon W. Lomasney, Richard G. Wunderink, Benjamin D. Singer, Alexander V. Misharin, G.R. Scott Budinger, for The Northwestern University Successful Clinical Response In Pneumonia Therapy (NU SCRIPT) Investigators

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Figure 1

Microglia exhibit distinct transcriptional responses in patients with COVID-19.

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Microglia exhibit distinct transcriptional responses in patients with CO...
(A) Uniform manifold approximation and projection (UMAP) of 65,767 cells isolated from the frontal lobes of 8 patients postmortem. HSR, heat shock response; TCM, T central memory; TEM, T effector memory. (B) Relative abundance of microglial cell states as a percentage of total microglia. No significant differences are observed by diagnosis (q ≤ 0.05, Mann-Whitney). (C) Hierarchical clustering of mean marker gene expression by cell type and cell state by diagnosis. (D) MA plot of differentially expressed genes in total microglia in COVID-19 versus controls by pseudobulk differential expression analysis. Significantly upregulated genes are shown in red, and significantly downregulated genes are shown in blue (q < 0.05, Wald test). Genes shown in gray are not significantly differentially expressed. (E) Callouts of key markers of cell division and cell cycle arrest from D. All genes shown are significantly differentially expressed (q < 0.05, Wald test). (F) Gene set enrichment of Hallmark TNF-α Signaling Via NF-κB (M5890) from pseudobulk differential expression analysis (q = 5.96 × 10–16, multilevel splitting Monte Carlo). (G) Median modular expression of Hallmark TNF-α Signaling Via NF-κB (M5890) by diagnosis. Points represent median expression in total microglia from each patient (q = 2.6 × 10–2, Mann-Whitney). (H) Representative images of combined immunofluorescence and smFISH (RNAScope) from human frontal lobe tissue sections showing cell cycle–arrested, pro-inflammatory microglia in patients with COVID-19 relative to controls. Images are pseudocolored by channel as follows: DAPI: blue, IBA1: green, IL1B: red, CCL2: cyan, CDKN1A: magenta.