Pneumonia recovery reprograms the alveolar macrophage pool
Antoine Guillon, Emad I. Arafa, Kimberly A. Barker, Anna C. Belkina, Ian Martin, Anukul T. Shenoy, Alicia K. Wooten, Carolina Lyon De Ana, Anqi Dai, Adam Labadorf, Jaileene Hernandez Escalante, Hans Dooms, Hélène Blasco, Katrina E. Traber, Matthew R. Jones, Lee J. Quinton, Joseph P. Mizgerd
Antoine Guillon, Emad I. Arafa, Kimberly A. Barker, Anna C. Belkina, Ian Martin, Anukul T. Shenoy, Alicia K. Wooten, Carolina Lyon De Ana, Anqi Dai, Adam Labadorf, Jaileene Hernandez Escalante, Hans Dooms, Hélène Blasco, Katrina E. Traber, Matthew R. Jones, Lee J. Quinton, Joseph P. Mizgerd
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Research Article Pulmonology

Pneumonia recovery reprograms the alveolar macrophage pool

Abstract

Community-acquired pneumonia is a widespread disease with significant morbidity and mortality. Alveolar macrophages are tissue-resident lung cells that play a crucial role in innate immunity against bacteria that cause pneumonia. We hypothesized that alveolar macrophages display adaptive characteristics after resolution of bacterial pneumonia. We studied mice 1 to 6 months after self-limiting lung infections with Streptococcus pneumoniae, the most common cause of bacterial pneumonia. Alveolar macrophages, but not other myeloid cells, recovered from the lung showed long-term modifications of their surface marker phenotype. The remodeling of alveolar macrophages was (a) long-lasting (still observed 6 months after infection), (b) regionally localized (observed only in the affected lobe after lobar pneumonia), and (c) associated with macrophage-dependent enhanced protection against another pneumococcal serotype. Metabolomic and transcriptomic profiling revealed that alveolar macrophages of mice that recovered from pneumonia had new baseline activities and altered responses to infection that better resembled those of adult humans. The enhanced lung protection after mild and self-limiting bacterial respiratory infections includes a profound remodeling of the alveolar macrophage pool that is long-lasting; compartmentalized; and manifest across surface receptors, metabolites, and both resting and stimulated transcriptomes.

Authors

Antoine Guillon, Emad I. Arafa, Kimberly A. Barker, Anna C. Belkina, Ian Martin, Anukul T. Shenoy, Alicia K. Wooten, Carolina Lyon De Ana, Anqi Dai, Adam Labadorf, Jaileene Hernandez Escalante, Hans Dooms, Hélène Blasco, Katrina E. Traber, Matthew R. Jones, Lee J. Quinton, Joseph P. Mizgerd

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Figure 3

Myeloid cell subsets differentiating experienced mice from naive mice.

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Myeloid cell subsets differentiating experienced mice from naive mice. F...
For A–C, a flow cytometry data set containing equal numbers of live single-cell CD45+ events from left lung lobes of n = 6 mice in each of the 2 groups (naive or experienced) was phenotyped for relative surface expression of myeloid cell markers CD11c, CD64, Ly6C, Ly6G, MHC II, and SiglecF. (A) Leukocyte subsets in the lungs of naive and experienced mice. Unsupervised clustering of 24 cell subsets (numbered according to cell quantity) was generated using the PhenoGraph algorithm, with heatmap color intensity representing median surface expression for each marker across the entire data set including all cells from all mice. The Wilcoxon rank-sum test with Benjamini-Hochberg multiple-comparisons adjustments was used to compare relative numbers of events (cells) within each cluster between naive and experienced mice, with the FDR-adjusted P value shown for each cluster. (B) Distributions of leukocyte phenotypes in the lungs of naive and experienced mice. The 20 most abundant PhenoGraph clusters based on multidimensional single-cell data (A) were color-coded and plotted on a 2-dimensional (2D) graph using the opt-SNE algorithm for naive and experienced mice. Opt-SNE 2D coordinates are shown on x and y axes. (C) Distributions of manually gated myeloid cells on the opt-SNE map. Myeloid cell-types were binned as in Figure 2 based on expression levels of the surface markers of interest. (D) Expression of surface markers across alveolar macrophages from the lungs of naive or experienced mice, depicted as a representative histogram from a single naive (red) or experienced (blue) mouse. Orange histogram represents matched fluorescence minus one negative control. (E) Comparisons of individual surface markers on alveolar macrophages between naive and experienced mice. MFI values per mouse were plotted for each surface marker, with data collected over 2–3 independent experiments and each data point representing an individual animal and horizontal lines representing group means. Asterisks (*) indicate comparisons reaching statistical significance (P < 0.05) using unpaired 2-tailed Student’s t tests.