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Key patient demographics shape innate immune topography in noncritical hypoxic COVID-19 pneumonia
Allison C. Billi, Rachael Wasikowski, Feiyang Ma, Srilakshmi Yalavarthi, Claire K. Hoy, Yu Zuo, Matthew T. Patrick, Neha Shah, Christine Parker, Chad Aaronson, Alyssa Harbaugh, Matthew F. Lucido, Kerby Shedden, Krishna Rao, Heidi B. IglayReger, Charles F. Burant, J. Michelle Kahlenberg, Lam C. Tsoi, Johann E. Gudjonsson, Jason S. Knight, Yogendra Kanthi
Allison C. Billi, Rachael Wasikowski, Feiyang Ma, Srilakshmi Yalavarthi, Claire K. Hoy, Yu Zuo, Matthew T. Patrick, Neha Shah, Christine Parker, Chad Aaronson, Alyssa Harbaugh, Matthew F. Lucido, Kerby Shedden, Krishna Rao, Heidi B. IglayReger, Charles F. Burant, J. Michelle Kahlenberg, Lam C. Tsoi, Johann E. Gudjonsson, Jason S. Knight, Yogendra Kanthi
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Research Article COVID-19 Immunology

Key patient demographics shape innate immune topography in noncritical hypoxic COVID-19 pneumonia

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Abstract

Risk of severe disease and death due to COVID-19 is increased in certain patient demographic groups, including those of advanced age, male sex, and obese body mass index. Investigations of the biological variations that contribute to this risk have been hampered by heterogeneous severity, with immunologic features of critical disease potentially obscuring differences between risk groups. To examine immune heterogeneity related to demographic risk factors, we enrolled 38 patients hospitalized with clinically homogeneous COVID-19 pneumonia — defined as oxygen saturation less than 94% on room air without respiratory failure, septic shock, or multiple organ dysfunction — and performed single-cell RNA-Seq of leukocytes collected at admission. Examination of individual risk factors identified strong shifts within neutrophil and monocyte/dendritic cell (Mo/DC) compartments, revealing altered immune cell type–specific responses in higher risk COVID-19 patient subgroups. Specifically, we found transcriptional evidence of altered neutrophil maturation in aged versus young patients and enhanced cytokine responses in Mo/DCs of male versus female patients. Such innate immune cell alterations may contribute to outcome differences linked to these risk factors. They also highlight the importance of diverse patient cohorts in studies of therapies targeting the immune response in COVID-19.

Authors

Allison C. Billi, Rachael Wasikowski, Feiyang Ma, Srilakshmi Yalavarthi, Claire K. Hoy, Yu Zuo, Matthew T. Patrick, Neha Shah, Christine Parker, Chad Aaronson, Alyssa Harbaugh, Matthew F. Lucido, Kerby Shedden, Krishna Rao, Heidi B. IglayReger, Charles F. Burant, J. Michelle Kahlenberg, Lam C. Tsoi, Johann E. Gudjonsson, Jason S. Knight, Yogendra Kanthi

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Figure 3

Effects of risk factors on Mo/DC shifts in COVID-19.

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Effects of risk factors on Mo/DC shifts in COVID-19.
(A) UMAP plot of 8,...
(A) UMAP plot of 8,420 Mo/DCs colored by cell type. (B) Dot plot of representative marker genes for each Mo/DC type. Color scale, average marker gene expression. Dot size, percentage of cells expressing marker gene. (C) Heatmap of relative expansion or contraction of each Mo/DC type in comparison of patients with COVID-19 versus controls (disease column) and in each risk factor subgroup comparison (excluding control patients). Blue, increased in the higher risk subgroup (aged, male sex, obese). Red, increased in the lower risk subgroup (young, female sex, normal BMI). Value shows log2 ([number of cells in higher risk subgroup]/[total number of cells in both subgroups]). (D) UMAP plot of Mo/DCs split by disease state. Bar plot, proportion of Mo/DCs in each subcluster split by disease state. (E) UMAP plot of Mo/DCs of patients with COVID-19 split by sex. Bar plot, proportion of Mo/DCs in each subcluster split by sex. (F) UMAP plot of Mo/DCs of patients with COVID-19 split by BMI group. Bar plot, proportion of Mo/DCs in each subcluster split by BMI group.

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