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Inflammatory monocytes promote granuloma control of Yersinia infection

Nature Microbiology volume 8, pages 666–678 (2023)Cite this article

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Abstract

Granulomas are organized immune cell aggregates formed in response to chronic infection or antigen persistence. The bacterial pathogen Yersinia pseudotuberculosis (Yp) blocks innate inflammatory signalling and immune defence, inducing neutrophil-rich pyogranulomas (PGs) within lymphoid tissues. Here we uncover that Yp also triggers PG formation within the murine intestinal mucosa. Mice lacking circulating monocytes fail to form defined PGs, have defects in neutrophil activation and succumb to Yp infection. Yersinia lacking virulence factors that target actin polymerization to block phagocytosis and reactive oxygen burst do not induce PGs, indicating that intestinal PGs form in response to Yp disruption of cytoskeletal dynamics. Notably, mutation of the virulence factor YopH restores PG formation and control of Yp in mice lacking circulating monocytes, demonstrating that monocytes override YopH-dependent blockade of innate immune defence. This work reveals an unappreciated site of Yersinia intestinal invasion and defines host and pathogen drivers of intestinal granuloma formation.

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Fig. 1: Intestinal PGs form upon oral Yersinia infection.
Fig. 2: Intestinal inflammation is spatially restricted to PGs.
Fig. 3: Inflammatory monocytes maintain PGs to restrict infection.
Fig. 4: Inflammatory monocytes control systemic Yersinia.
Fig. 5: Yersinia virulence factors induce intestinal PGs.
Fig. 6: Neutrophils control YopH-deficient Yersinia in absence of monocytes.

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Data availability

Raw RNA sequencing data are available on the Gene Expression Omnibus (accession no. GSE194334). All other raw data are available upon request to the corresponding author.

Code availability

Code for RNA sequencing analysis is available in the Supplementary Code File.

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Acknowledgements

We thank J. Bliska for generously providing plasmids for Yop mutant Yp strains, as well as K. Davis for generously providing the mCherry+ Yp plasmid. We thank the staff at the PennVet Comparative Pathology Core for their help in preparing the histological samples. We thank D. Christian and A. Stout for key advice on confocal microscopy methods, and S. Shin for constructive editorial comments and scientific discussion. This work was supported by NIH Awards R01AI128530 (I.E.B.), R0AI1139102A1 (I.E.B.), R01DK123528 (I.E.B.) and a BWF Investigator in the Pathogenesis of Infectious Disease Award (I.E.B.); the Foundation Blanceflor Postdoctoral Scholarship (D.S.), the Swedish Society for Medical Research postdoctoral fellowship (D.S.) and the Sweden-America Foundation J. Sigfrid Edström award (D.S.); NIH NRSA F31AI160741-01 (R.M.); NIH T32 AI141393-2 in Microbial Pathogenesis and Genomics (R.M.); Mark Foundation Grant 19-011MIA (I.E.B.), F32 AI164655 (J.P.G.); and NSF GRFP Award (S.P.). We thank members of the Brodsky laboratory for scientific discussion and D. Grubaugh for comments on the manuscript. We thank R. Kratofil for scientific discussion and advice on assays to measure neutrophil activation.

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  1. These authors contributed equally: Daniel Sorobetea, Rina Matsuda.

Authors and Affiliations

  1. Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA

    Daniel Sorobetea, Rina Matsuda, Stefan T. Peterson, James P. Grayczyk, Indira Rao, Elise Krespan, Matthew Lanza, Charles-Antoine Assenmacher, Daniel P. Beiting, Enrico Radaelli & Igor E. Brodsky

  2. Department of Nephrology, University Hospital Regensburg, Regensburg, Germany

    Matthias Mack

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Contributions

D.S. established the initial findings of intestinal granulomas. D.S., R.M. and I.E.B. conceptualized the study and devised experiments. D.S. and R.M. devised the methodology and performed experiments. S.T.P., J.P.G. and I.R. performed experiments. C.-A.A., E.R. and M.L. performed the histology and histopathological scoring. E.K. prepared the RNA sequencing libraries. M.M. provided the anti-CCR2 antibody. R.M. and D.B. analysed the RNA sequencing data. I.E.B. acquired the funding and supervised the study. D.S., R.M. and I.E.B. wrote the original draft. All authors reviewed and edited the manuscript.

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Correspondence to Igor E. Brodsky.

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Extended data

Extended Data Fig. 1 Intestinal pyogranulomas form upon oral Yersinia infection.

(a) Flow cytometry plots displaying the gating strategy employed to identify eosinophils, dendritic cells, B cells and T cells in small-intestinal tissue at day 5 post-Yp infection. Representative of four independent experiments. (b) Frequency and total number of eosinophils, dendritic cells, B cells, CD4+ T cells and CD8+ T cells in small-intestinal tissue at day 5 post Yp-infection. Each data point represents one mouse (n = 15-20). Lines represent median. Pooled from four independent experiments. Wilcoxon test (two-tailed) was performed for paired analyses (PG- vs PG + ). Mann-Whitney U test (two-tailed) was performed for all remaining statistical analyses. * (p < 0.05), ** (p < 0.01), *** (p < 0.001), **** (p < 0.0001), NS (not significant, p > 0.05).

Extended Data Fig. 2 Non-pyogranuloma tissue does not undergo inflammation.

(a) Heat map of top 30 significantly upregulated genes in PG- compared to uninfected samples in descending order by fold change. False discovery rate < 0.05 using Benjamini–Hochberg procedure. (b) Gene ontology analysis of top 30 upregulated genes by fold change only in PG- compared to uninfected samples. Dotted line denotes p = 0.05.

Extended Data Fig. 3 CCR2-deficient mice cannot control intestinal Yersinia.

(a) Quantification of total number of intestinal lesions at day 3 post infection. Each data point indicates one mouse (n = 9-11). Line represents median. Pooled from two independent experiments. (b) H&E-stained paraffin-embedded small-intestinal sections containing Peyer’s patches from WT and Ccr2gfp/gfp mice at day 5 post infection. Dashed circle denotes area containing pyogranuloma or necrosuppurative lesion. Scale bars = 500 μm. Representative images from two independent experiments. (c) Bacterial burdens in small intestinal PG- and PG + tissue at day 3 post infection. Each data point represents mean CFU of 3-5 pooled punch biopsies from one mouse (n = 15-25). Lines represent geometric mean. Pooled data from four independent experiments. (d) Frequency of monocytes in blood at day 5 post infection. Each data point represents one mouse (n = 29-30). Lines indicate median. Pooled data from four independent experiments. (e) Bacterial burdens in small intestinal PG- and PG + tissue at day 5 post infection. Each data point represents the mean CFU of 3-5 pooled punch biopsies from one mouse (n = 21-30). Lines indicate geometric mean. Data pooled from four independent experiments. (f) Bacterial burdens in small intestinal PG- and PG + tissue at day 3 post infection. Each data point represents the mean CFU of 3-5 pooled punch biopsies from one mouse (n = 10-13). Lines indicate geometric mean. Pooled data from two independent experiments. (g) H&E-stained paraffin-embedded sections containing pyogranulomas from WT and Ccr2gfp/gfp mice at day 3 post-infection. Dashed circle denotes area containing pyogranuloma. Scale bars = 100 μm. Representative images of one experiment. All statistical analyses by Mann-Whitney U test (two-tailed). * (p < 0.05), ** (p < 0.01), *** (p < 0.001), **** (p < 0.0001), NS (not significant, p > 0.05).

Extended Data Fig. 4 Effects of monocyte deficiency on other cell types.

(a) Total numbers and frequencies of CD4+ T cells, CD8+ T cells, B cells, and DCs in small intestinal PG + tissue. Each data point indicates the mean of 3-10 pooled punch biopsies from one mouse (n = 20-22). Lines represent median. Pooled data from three to five independent experiments. (b) Frequency of neutrophils in MLN and spleen at day 5 post infection. Each data point represents one mouse (n = 8-12). Lines represent median. Pooled data from two independent experiments. (c) Neutrophil surface CD11b expression in MLN at day 5 post-infection was measured by flow cytometry. Each data point represents one mouse (n = 6). Lines represent median. Representative of two independent experiments. (d) Intracellular levels of CD11b in neutrophils in small intestinal PG + tissue at day 5 post-infection were measured by flow cytometry. Each data point represents the mean of 3-10 pooled punch biopsies from one mouse (n = 6-7). Lines represent median. Representative of four independent experiments. (e) Cytokine levels in homogenates of tissue punch biopsies at day 5 post infection were measured by cytometric bead array. Each data point represents the mean of 3-10 pooled punch biopsies from one mouse (n = 18-22). Lines represent median. Pooled data from three independent experiments. (f) Intracellular levels of cytokines and lipocalin in neutrophils in small intestinal PG + tissue at day 5 post-infection were measured by flow cytometry. Each data point represents the mean of 3-10 pooled punch biopsies from one mouse (n = 18-19). Lines represent median. Pooled data from three independent experiments. All statistical analyses by Mann-Whitney U test (two-tailed). * (p < 0.05), ** (p < 0.01), *** (p < 0.001), **** (p < 0.0001), NS (not significant, p > 0.05).

Extended Data Fig. 5 CCR2-deficient mice cannot control systemic Yersinia.

(a) Bacterial burdens in indicated organs at day 3 post infection. Each data point represents one mouse (n = 10-14 for PP, MLN, lung; 21-25 for spleen, liver). Lines represent geometric mean. Pooled data from two to four independent experiments. (b) Bacterial burdens in indicated organs at day 5 post infection. Each data point represents one mouse (n = 29-30). Lines represent geometric mean. Pooled data from four independent experiments. (c) Bacterial burdens in indicated organs at day 3 post infection. Each data point represents one mouse (n = 10-13). Lines represent geometric mean. Pooled data from two independent experiments. (d) Survival of infected mice. Pooled data from two independent experiments. Statistical analyses by (a-c) Mann-Whitney U test (two-tailed) or (d) Mantel-Cox test. * (p < 0.05), ** (p < 0.01), *** (p < 0.001), **** (p < 0.0001), NS (not significant, p > 0.05).

Extended Data Fig. 6 Yersinia virulence factors induce intestinal pyogranulomas.

(a) Cumulative bacterial burdens in PG- tissue at day 5 post infection. Each symbol represents one mouse (n = 9-11). Lines represent geometric mean. Dotted line represents limit of detection. Pooled from two independent experiments. (b) Frequency of monocytes in small-intestinal tissue and MLN. Each symbol represents one mouse (n = 3-9). Lines represent median. Pooled and representative data from two independent experiments. (c) Frequency of neutrophils in small-intestinal tissue and MLN. Each symbol represents one mouse (n = 3-9). Lines represent median. Pooled and representative data from two independent experiments. (d) Bacterial burdens in indicated organs at day 5 post-infection. Each symbol represents one mouse (n = 10-43). Lines represent geometric mean. Pooled from 2-6 independent experiments. (e) Total number of intestinal lesions at day 5 post infection. Each symbol represents one mouse (n = 8-10). Lines represent median. Pooled from two independent experiments. (f) Total number of intestinal lesions at day 5 post infection. Each symbol represents one mouse (n = 11). Lines represent median. Pooled from three independent experiments. (g) Frequency and total number of monocytes in small-intestinal PG + tissue at day 5 post WT or YopHR409A Yp infection. Each data point represents one mouse (n = 8-10). Lines represent median. Pooled from two independent experiments. (h) Bacterial burdens in indicated organs at day 3 post WT or YopHR409A Yp infection. Each symbol represents one mouse (n = 10-13). Lines represent geometric mean. Pooled from two independent experiments. Statistical analyses by (a, d, e) Kruskal–Wallis test with Dunn’s post-test and (b, c, f, g, h) Mann-Whitney U test (two-tailed). * (p < 0.05), ** (p < 0.01), *** (p < 0.001), **** (p < 0.0001), NS (not significant, p > 0.05).

Extended Data Fig. 7 Anti-Gr-1 effectively depletes neutrophils during infection.

(a) Flow cytometry plots displaying the gating strategy employed to identify neutrophils and monocytes upon anti-Gr-1 administration. Due to masking of Ly-6G and Ly-6C epitopes by anti-Gr-1, monocytes were identified as CCR2-GFP+ cells (green box) and neutrophils were identified as SSC high cells (pink boxes). Representative images of three independent experiments. (b) Frequency of monocytes in blood at day 5 post infection was determined by flow cytometry. Each symbol represents one mouse (n = 10-11). Lines represent median. Data from three independent experiments. Statistical analyses by Kruskal-Wallis test with Dunn’s post-test. * (p < 0.05), ** (p < 0.01), *** (p < 0.001), **** (p < 0.0001), NS (not significant, p > 0.05).

Supplementary information

Reporting Summary

Supplementary Tables 1 and 2

Table 1. Gene Ontology analysis of PG+ versus PG− samples. Table 2. Gene Ontology analysis of PG− versus uninfected samples.

Supplementary Code File 1

Code for RNA sequencing analysis.

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Sorobetea, D., Matsuda, R., Peterson, S.T. et al. Inflammatory monocytes promote granuloma control of Yersinia infection. Nat Microbiol 8, 666–678 (2023). https://doi.org/10.1038/s41564-023-01338-6

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