Abstract
Dendritic cells (DCs) that orchestrate mucosal immunity have been studied in mice. Here we characterized human gut DC populations and defined their relationship to previously studied human and mouse DCs. CD103+Sirpα− DCs were related to human blood CD141+ DCs and to mouse intestinal CD103+CD11b− DCs and expressed markers of cross-presenting DCs. CD103+Sirpα+ DCs aligned with human blood CD1c+ DCs and mouse intestinal CD103+CD11b+ DCs and supported the induction of regulatory T cells. Both CD103+ DC subsets induced the TH17 subset of helper T cells, while CD103−Sirpα+ DCs induced the TH1 subset of helper T cells. Comparative analysis of transcriptomes revealed conserved transcriptional programs among CD103+ DC subsets and identified a selective role for the transcriptional repressors Bcl-6 and Blimp-1 in the specification of CD103+CD11b− DCs and intestinal CD103+CD11b+ DCs, respectively. Our results highlight evolutionarily conserved and divergent programming of intestinal DCs.
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Acknowledgements
We thank T. Okada (RIKEN, Japan) for YFP–Bcl-6 mice52; E. Meffre (Yale University) for Blimp-1–YFP mice53; J. Sweere and H. Kiefel for critical reading of the manuscript; L. Rott for assistance with flow cytometry and cell sorting; E. Resurreccion for assistance with immunohistochemistry; K. Bhat for writing Python scripts; all members of the Butcher laboratory for discussions; and the Immunological Genome Project and the Merad laboratory (Mount Sinai School of Medicine) for generating the publicly available microarray data of sorted mouse intestinal DC. Supported by the US National Institutes of Health (R01 AI093981, R01 DK084647 and R37 AI047822 to E.C.B.; 5T32AI007290-25 to M.L.; K01 AR59378 to S.J.K.; and AI07290 to H.H.), the US Department of Veterans Affairs (E.C.B.), the Digestive Disease Center of Stanford University (under P30 DK056339), the German Research Foundation (K.L.), the Crohn's and Colitis Foundation of America (K.L. and M.L.), The Stanford Institute for Immunity, Transplantation and Infection (K.L.), the Agency for Science, Technology And Research of Singapore (R.Z.), the Swiss National Science Foundation (PBBEP3-133516 to D.B.), the Swiss Foundation for Grants in Biology and Medicine (PASMP3-142725 to D.B.), the Leukemia & Lymphoma Society (K.M.A.), the California Institute for Regenerative Medicine (H.H.) and the Arthritis Foundation (H.H.).
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P.B.W. designed and did human DC experiments, including microarrays, analyzed gene expression and wrote the manuscript; K.L. designed and did all mouse experiments, analyzed gene expression and wrote the manuscript; M.L. prepared RNA and did quality control for microarray studies; D.B. provided YFP–Bcl-6 and Blimp-1–YFP mice and helped to design and to do the experiments; J.M. provided human tissue; S.J.K. designed and did experiments with mice with DC-specific Blimp-1 deficiency; R.Z. helped with YFP–Bcl-6 experiments; A.D. provided Bcl6−/− mice and feedback; K.M.A. provided feedback and YFP–Bcl-6 and Blimp-1–YFP mice; B.D. provided mice with DC-specific Blimp-1 deficiency; H.H. drove the initial interest and provided advice; and E.C.B. analyzed gene expression, guided the study and wrote the manuscript.
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Integrated supplementary information
Supplementary Figure 1 Gating strategy for human intestinal DC subsets.
Lamina propria mononuclear cells obtained from jejunal tissue sections were stained for live/dead viability marker, CD45, lineage markers (CD3, CD14, CD16, CD56, CD19), HLADR, CD11c, CD123. Phenotypic Analysis of CD11c+ DC was done by successive gating on live CD45+ population and then the HLADR+ lineage− population.
Supplementary Figure 2 Absence of canonical macrophage marker expression on CD103−Sirpα+ DCs.
a) Expression of CD64 and on CD14+ lamina propria macrophages (open black histograms) and CD103−Sirpα+ DCs (black dashed lines). b) Expression of CX3CR1 (same as in a)).
Supplementary Figure 4 Pairwise comparison of gene expression profiles of gut DC subsets with blood and skin CD1c+ and CD141+ DCs, skin CD14+ DCs and blood CD14+ monocytes.
Pearson correlation of expression profiles using the same genes as in Fig. 3a. In the comparison of CD103+Sirpα+ (hDP) DCs with blood and skin CD1c+, the individual samples with solid and open symbols correlate significantly (p≤0.001, ANOVA) with blood CD1c+ or with skin CD1c+ DCs, respectively
Supplementary Figure 5 Classification of DCs vs macrophages.
a) CD4 T cell proliferation in allogeneic cultures of responder T cells stimulated by the indicated subsets. b) Gene Expression values of MafB and Spi1 and their ratio in gut and blood DC subsets and tissue macrophages. Dataset for tissue macrophages was obtained from GSE40484.
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Supplementary Figures 1–6 and Supplementary Table 3 (PDF 492 kb)
Supplementary Table 1
Gene list to accompany Figure 3. (XLSX 235 kb)
Supplementary Table 2
Gene list to accompany Figure 5. (XLSX 127 kb)
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Watchmaker, P., Lahl, K., Lee, M. et al. Comparative transcriptional and functional profiling defines conserved programs of intestinal DC differentiation in humans and mice. Nat Immunol 15, 98–108 (2014). https://doi.org/10.1038/ni.2768
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DOI: https://doi.org/10.1038/ni.2768
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