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Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis

Nature Microbiology volume 4, pages 492–503 (2019)Cite this article

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Abstract

Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease and its frequent complication with ulcerative colitis highlights the pathogenic role of epithelial barrier dysfunction. Intestinal barrier dysfunction has been implicated in the pathogenesis of PSC, yet its underlying mechanism remains unknown. Here, we identify Klebsiella pneumonia in the microbiota of patients with PSC and demonstrate that K. pneumoniae disrupts the epithelial barrier to initiate bacterial translocation and liver inflammatory responses. Gnotobiotic mice inoculated with PSC-derived microbiota exhibited T helper 17 (TH17) cell responses in the liver and increased susceptibility to hepatobiliary injuries. Bacterial culture of mesenteric lymph nodes in these mice isolated K. pneumoniae, Proteus mirabilis and Enterococcus gallinarum, which were prevalently detected in patients with PSC. A bacterial-organoid co-culture system visualized the epithelial-damaging effect of PSC-derived K. pneumoniae that was associated with bacterial translocation and susceptibility to TH17-mediated hepatobiliary injuries. We also show that antibiotic treatment ameliorated the TH17 immune response induced by PSC-derived microbiota. These results highlight the role of pathobionts in intestinal barrier dysfunction and liver inflammation, providing insights into therapeutic strategies for PSC.

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Fig. 1: Magnitude of TH17 priming in the liver and colon of gnotobiotic mice transplanted with human faecal samples.
Fig. 2: Increased susceptibility to DDC-induced hepatobiliary injury in PSCUC mice.
Fig. 3: Gnotobiotic mice with PSC/UC microbiota identified specific bacterial species associated with PSC/UC from the MLN.
Fig. 4: Inhibition of ROR-γt protects mice from DDC-induced hepatobiliary injury.
Fig. 5: K. pneumoniae derived from the MLNs of PSCUC mice induces epithelial pore formation of colonic epithelial cells.
Fig. 6: Bacterial translocation and TH17 priming in the liver are dependent on K. pneumoniae strains.

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Data availability

The data supporting the findings of this study are available from the corresponding authors upon request. 16S rRNA sequencing and whole-genome sequencing data have been deposited in the DNA Data Bank of Japan (DDBJ) database with the accession numbers DRA007475 and DRA007476 for 16S rRNA sequencing and PRJDB7545 for whole-genome sequencing. RNA sequencing data have been deposited in the European Genome-phenome Archive (EGA) database with the accession number EGAS00001003332.

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Acknowledgements

We thank S. Chiba, S. Shiba, R. Morikawa, T. Katayama, A. Ikura, Y. Mikami and T. Sujino (Division of Gastroenterology and Hepatology, Keio University) for technical assistance and critical reading of this manuscript. This study was supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI Grant-in-Aid (C) 16K09374 and (A) 15H02534, the Advanced Research and Development Programs for Medical Innovation (AMED-CREST; 16gm1010003h0001), the TAKEDA Science Fund, Ezaki Glico Co. Ltd and Keio University Medical Fund. K.H. was funded through AMED LEAP under grant number JP17gm0010003. A. Yoshimura was supported by the JSPS KAKENHI Grant-in-Aid (S) JP17H06175, Challenging Research (P) JP18H05376 and AMED-CREST JP18gm0510019 and JP18gm1110009.

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Authors and Affiliations

  1. Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Shinanomachi, Tokyo, Japan

    Nobuhiro Nakamoto, Nobuo Sasaki, Ryo Aoki, Kentaro Miyamoto, Toshiaki Teratani, Takahiro Suzuki, Yuzo Koda, Po-Sung Chu, Nobuhito Taniki, Akihiro Yamaguchi, Toshiro Sato & Takanori Kanai

  2. AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan

    Nobuo Sasaki & Takanori Kanai

  3. Institute of Health Science, Ezaki Glico Co., Ltd, Osaka, Japan

    Ryo Aoki

  4. Miyarisan Pharmaceutical Co., Ltd, Tokyo, Japan

    Kentaro Miyamoto & Takahiro Suzuki

  5. Department of Microbiology and Immunology, Keio University School of Medicine, Shinanomachi, Tokyo, Japan

    Wataru Suda, Mitsuhiro Kanamori, Koji Atarashi, Seiko Narushima, Akihiko Yoshimura & Kenya Honda

  6. Laboratory of Metagenomics, Department of Computational Biology and Medical Sciences, The University of Tokyo, Chiba, Japan

    Wataru Suda & Masahira Hattori

  7. Research Unit/Immunology & Inflammation, Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Kanagawa, Japan

    Yuzo Koda

  8. Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA

    Nobuhiko Kamada

  9. Cooperative Major in Advanced Health Science, Graduate School of Advanced Science and Engineering, Faculty of Science and Engineering, Waseda University, Tokyo, Japan

    Masahira Hattori

  10. Department of Bacterial Infection and Host Response, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan

    Hiroshi Ashida

  11. Department of Pathology, Keio University School of Medicine, Shinanomachi, Tokyo, Japan

    Michiie Sakamoto

  12. RIKEN Center for Integrative Medical Sciences, Laboratory for Gut Homeostasis, Kanagawa, Japan

    Koji Atarashi, Seiko Narushima & Kenya Honda

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  1. Nobuhiro Nakamoto
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Contributions

N.N. and T.K. designed the project. N.N., N.S., R.A., K.M., T.T., Takahiro S., Y.K., P.-S.C., N.T., Akihiro Y., M.K. and H.A. performed the experiments. W.S. and M.H. performed the bacterial sequence, microbiome analyses and contributed to data discussions. K.A., S.N. and K.H. provided essential materials and contributed to data discussions. N.N., N.K., M.S., Akihiko Y., Toshiro S. and T.K. interpreted the experimental data. N.N., N.K. and Toshiro S. wrote the manuscript. T.K. critically revised the manuscript and supervised the study.

Corresponding authors

Correspondence to Toshiro Sato or Takanori Kanai.

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Supplementary information

Supplementary Information

Supplementary Figures 1–8.

Reporting Summary

Supplementary Table 1

Demographic characteristics of study subjects.

Supplementary Table 2

Fpkm values in RNA-seq analysis.

Supplementary Table 3

Phylogenetic relationship among K. pneumoniae strains used in this study.

Supplementary Table 4

Genes positively correlated with the epithelial pore-forming capacity.

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Nakamoto, N., Sasaki, N., Aoki, R. et al. Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis. Nat Microbiol 4, 492–503 (2019). https://doi.org/10.1038/s41564-018-0333-1

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