Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris

Abstract

Candida auris is among the most important emerging fungal pathogens, yet mechanistic insights into its immune recognition and control are lacking. Here, we integrate transcriptional and functional immune-cell profiling to uncover innate defence mechanisms against C. auris. C. auris induces a specific transcriptome in human mononuclear cells, a stronger cytokine response compared with Candida albicans, but a lower macrophage lysis capacity. C. auris-induced innate immune activation is mediated through the recognition of C-type lectin receptors, mainly elicited by structurally unique C. auris mannoproteins. In in vivo experimental models of disseminated candidiasis, C. auris was less virulent than C. albicans. Collectively, these results demonstrate that C. auris is a strong inducer of innate host defence, and identify possible targets for adjuvant immunotherapy.

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Fig. 1: Comparative analysis between the general and clade-specific C. auris- and C. albicans-induced host response at 24 h.
Fig. 2: Evaluating the dynamics of C. auris phagocytosis by human and murine host immune cells, and the heat sensitivity of the cell wall component that is responsible for C. auris-induced cytokine production.
Fig. 3: Mannans are fundamental for orchestrating the C. auris-induced late host response.
Fig. 4: NMR analysis of C. auris mannans revealed unique structural features.
Fig. 5: Examination of PRR and signalling pathways that are involved in the C. auris-induced host cytokine production.
Fig. 6: C. auris is less virulent than C. albicans in an experimental model of mouse disseminated candidiasis.

Data availability

Requests for materials should be addressed to the corresponding author. The datasets generated in this study are accessible through GEO Series accession number GSE154911. Source data are provided with this paper.

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Acknowledgements

We thank T. Jansen for performing the initial pilot experiments and I. Curfs-Breuker and D. Faro for their support at the CWZ hospital; C. Kaffa for her technical assistance; V. Kumar for his input during the transcriptomic data analysis; M. Gresnigt for in vitro experimental suggestions; and A. Becker for help during the revision experiments. A.J.P.B. and N.A.R.G. thank the Medical Research Council (MRC) (MR/M026663/1) and Wellcome for support and the MRC Centre for Medical Mycology at the University of Aberdeen (MR/N006364/1). A.H. and S.K. were supported by the Radboud Institute for Molecular Life Sciences. Part of the study was supported by the Hellenic Institute for the Study of Sepsis. D.L.W. was supported by National Institutes of Health grant nos NIH GM083016, GM119197 and C06RR0306551. M.G.N. was supported by an ERC Advanced Grant (no. 833247) and a Spinoza Grant from the Netherlands Organization for Scientific Research.

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Contributions

Conceptualization: J.F.M., D.L.W. and M.G.N.; methodology: M.B., S.K., J.M.B., M.J., D.R., M.D.K., D.W.L., Z.M., Y.N.J., A.C., A.H., N.A.R.G., A.J.P.B., J.F.M., D.L.W. and M.G.N.; investigation: M.B., S.K., J.M.B., M.J, D.R., D.W.L., P.J.R., B.G., F.L.v.d.V., B.-J.K., E.J.G.-B., G.R., A.H., N.A.R.G., A.J.P.B., D.L.W. and M.G.N.; writing the original draft: M.B., S.K. and M.G.N.; review and editing the manuscript: M.B., S.K., J.M.B., M.J., M.D.K., D.W.L., Z.M., Y.N.J., A.C., F.L.v.d.V., E.J.G.-B., A.H., N.A.R.G., A.J.P.B., J.F.M., D.L.W. and M.G.N.; supervision: M.J., F.L.v.d.V., A.H., N.A.R.G., A.J.P.B. and M.G.N.

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Correspondence to Mariolina Bruno or Mihai G. Netea.

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Extended data

Extended Data Fig. 1 Transcriptomic profiling PBMCs stimulated with live C. albicans or C. auris and respective cell wall components β-glucans and mannans for 4 and 24 hours.

a, Principal component analysis (PCA) performed on normalized count data (normTransform, DESeq2) demonstrates the main component introducing variance in the dataset is time (40%), as indicated by a clear split between the early 4-hour host induced response (left, triangle) and the late 24-hour response (right, circle). To a lower extent (15%), the second component introducing variance appears to be inherent to the stimulus (color). b, At 4 h, PCA reveals a clear donor clustering (shape) irrespective of stimulus (color), indicating the main variance in the early host response reflects inter-individual differences (left). PCA on the late response, 24 h, is predominantly influenced by the respective stimulus (38%, color), and to a lower extent by the donors (19%, shape), indicated by the scattering of stimuli together with a rough clustering amongst donors. c, Pathway enrichment plot displaying the top 20 enriched pathways for both C. albicans live and C. auris live (color) at 24 h. Enrichment determined using Consensus PathDB, including pathways as defined by KEGG and Reactome (shape), considering a p-adjusted value < 0.01 (indicated as ‘q-value’) significant. Size of the geometric points indicates the amount of DEG in relation to the pathways’ size. The exact q values and the data used to make this figure can be found in Source Data Extended Data Fig. 1. Source data

Extended Data Fig. 2 Comparative LDH secretion, LDH cytokine gene expression and phagocytosis dynamics between C. albicans and C. auris.

a, Assessment of Candida induced cell death of PBMCs after 24 h stimulation without (RPMI; negative control) or with C. albicans, several C. auris strains originating from all five geographical clades or a positive control (dead cells). Lactate dehydrogenase (LDH) was detected as measure of cell death (Mean ± SEM, n = 6, pooled from two independent experiments). b, Log2Fold Change (Log2FC) of IL-6, IL-1β, and IL-1RN (encoding for IL-1Ra) gene expression in PBMCs from 3 donors stimulated for 24 h with C. albicans (1006110) and C. auris (KCTC17810, clade II) and their respective cell wall components, β-glucans (left) and mannans (right). Graphs represent Log2FC from DEG analysis. * p < 0.05, ** p < 0.01, *** p < 0.001, 1-way ANOVA with correction for multiple comparison. c, The BMDM phagocytic capacity of Thimerosal-fixed C. albicans or C. auris strains in the course of 3-hours. BMDM engulfment depicted as the percentage of macrophages having phagocytosed at least one fungal cell (left), and the phagocytic index, here considered as the number of fungal cells engulfed per 100 macrophages (right); graphs represent mean, n = 9, pooled from at least two independent experiments. d, BMDM phagocytic capacity of Thimerosal-fixed C. albicans or C. auris strains after 1 h. Engulfment is depicted as the percentage of macrophages having phagocytosed at least one fungal cell; graphs represent mean ± SEM, n = 9, pooled from at least two independent experiments. e, BMDM phagocytic capacity of live C. albicans or C. auris strains after 1 h. Engulfment is depicted as the percentage of macrophages having phagocytosed at least one fungal cell. Graphs represent mean ± SEM, n = 9 (n = 7 for C. auris 10051893), pooled from at least two independent experiments. * p < 0.05, ** p < 0.01, *** p < 0.001, d 1-way ANOVA with a Holm-Sidak’s multiple comparison test, e Kruskal Wallis test with two-sided Dunn’s multiple comparison. f, Distribution of phagocytosed Thimerosal-fixed fungal cells per macrophage in a 3-hour period, n ≥ 100 observations per condition. Data used to make this figure can be found in Source Data Extended Data Fig. 2. Source data

Extended Data Fig. 3 Relative C. auris induced ROS production and heat-sensitivity of the cell wall components responsible for the C. auris induced cytokine production.

a, Neutrophil ROS release after 1-hour stimulation without (RPMI; negative control) or with heat-killed C. albicans, C. auris strains or zymosan (positive control), depicted in relative light units (RLU) either as time-course (left) or as area under the curve (AUC, right), n = 9. b, PBMC ROS release after 1-hour stimulation without (RPMI; negative control) or with heat-killed C. albicans, C. auris strains or zymosan (positive control), depicted in RLU either as time-course (left) or as AUC (right), n = 6. c, TNF-α, IL-6, IL-1β, and IL-1Ra levels in the supernatant of PBMCs after stimulation without (RPMI; negative control) or with heat-killed C. albicans and C. auris from all five geographical clades for 24 h, n = 8. d, PBMC production of cytokines IFN-γ (n = 10; n = 7 for C. auris 10051895), IL-10 (n = 6), IL-17 (n = 6), and IL-22 (n = 14; n = 6 for C. auris 10051893; n = 11 for C. auris 10051895) after stimulation without (RPMI; negative control) or with heat-killed C. albicans and C. auris for 7 days. Graphs represent mean ± SEM, data are pooled from at least two independent experiments. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p = 0.001, a, b Time curves (left panels) were assessed for statistical differences between C. auris strains and C. albicans by a two-way ANOVA, Area Under curve (AUC) means (right panels) were compared using the two-sided Wilcoxon signed rank test, c, d two-sided Wilcoxon matched pairs signed-rank test comparing respective C. auris strains with C. albicans as control or reference species. Data used to make this figure can be found in Source Data Extended Data Fig. 3. Source data

Extended Data Fig. 4 Transcriptional changes induced by purified cell wall components and their respective exposure on C. albicans and C. auris surface.

a, Heatmap displaying the Log2Fold change (color scale) of the top 50 DEG of C. albicans live, for both Candida species and their cell wall components, β-glucan and mannan, at 4 h (left panel) and 24 h (right panel). b, Flow cytometry plot based on forward scatter component (FSC) and side scatter component (SSC), demonstrating C. auris strains are slightly smaller and of higher complexity than C. albicans. c, Flow cytometry-based comparison of cell wall components of C. albicans and C. auris strains. Mean fluorescent intensity (MFI) of thimerosal-fixed Candida cells stained for Fc-Dectin-1, a marker for β-glucan (left), and ConA, a marker for mannans (right). Graphs represent mean ± SEM of the 3 means, each performed with three replicates in three independent measurements, * p < 0.05, Kruskall Wallis test with two-sided Dunn’s multiple comparison test was performed comparing the respective C. auris strains with the two C. albicans reference strains. Data used to make this figure can be found in Source Data Extended Data Fig. 4. Source data

Extended Data Fig. 5 Evaluation of cytokine production upon C. albicans and C. auris mannan stimulation.

a, PBMC production of cytokines TNF-α, IL-6, IL-1β, and IL-1Ra after 24 h stimulation without (RPMI; negative control) or with purified mannans from C. albicans and C. auris strains in the presence of 10% heat-inactivated human serum, n = 7. b, PBMC production of cytokines IFN-γ (n = 6), IL-17 (n = 9), and IL-22 (n = 9) after 7 days hours stimulation without (RPMI; negative control) or with purified mannans from C. albicans and C. auris strains in the presence of 10% human serum. Graphs represent mean ± SEM, data pooled from at least two independent experiments. * p < 0.05, two-sided Wilcoxon matched pairs signed-rank test, comparing respective C. auris strains with C. albicans as control or reference species. Data used to make this figure can be found in Source Data Extended Data Fig. 5. Source data

Extended Data Fig. 6 Cytokine levels in plasma and organ homogenates from C.albicans and C. auris-infected mice.

a, IL-6 production in plasma and supernatants from liver homogenates. b, IFN-γ production in supernatants from kidney and spleen homogenates. c–e, IL-1β (c), IL-17 (d), and IL-10 (e) production in plasma and supernatants from liver, kidney, and spleen homogenates. Mice have been infected i.v. with 1×106 c.f.u. of C. albicans or C. auris. Graphs represent mean ± SEM, n = 6 per group per time-point pooled from two independent experiments. Data used to make this figure can be found in Source Data Extended Data Fig. 6. Source data

Extended Data Fig. 7 Applied gating strategies across flow cytometry experiments.

a, Gating strategy for FITC-labelled Candida in PBMCs (linked to Fig. 2b). All events were plotted based on forward scatter (FS) and side scatter (SS) characteristics. In the upper plot (2.1) the region of cells positive for FITC-Candida was highlighted (green gate) while in the bottom plot (2.2) CD14 positive cells are represented (red gate) gated within the total PBMCs population (1). Within the CD14 + cells selection, the amount of phagocytosed FITC positive Candida was examined by plotting (3) the FITC signal against the CD14-PB450 signal (blue gate) and the percentage of cells and mean fluorescent intensity (MFI) were used for analysis. b, Gating strategy for Thimerosal-fixed Candida cells stained for either β-glucan using Fc-Dectin-1 or ConA as marker for mannans (Extended Data Fig. 4c).

Supplementary information

Supplementary Information

Supplementary Tables 1–8.

Reporting Summary

Supplementary Video 1

C. auris is able to multiply within phagosomes.

Supplementary Video 2

C. auris accumulates in high numbers within macrophages and does not induce macrophage lysis.

Supplementary Video 3

C. auriscells are taken up extensively into a subpopulation of macrophages.

Supplementary Video 4

Phagocytosis of C. albicans SC5314 and macrophage lysis after 3 h.

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Bruno, M., Kersten, S., Bain, J.M. et al. Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris. Nat Microbiol (2020). https://doi.org/10.1038/s41564-020-0780-3

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