Spatially restricted immune and microbiota-driven adaptation of the gut – Nature

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  • Parikh, K. et al. Colonic epithelial cell diversity in health and inflammatory bowel disease. Nature 567, 49–55 (2019).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Fawkner-Corbett, D. et al. Spatiotemporal analysis of human intestinal development at single-cell resolution. Cell 184, 810–826.e23 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hickey, J. W. et al. Organization of the human intestine at single-cell resolution. Nature 619, 572–584 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Elmentaite, R. et al. Cells of the human intestinal tract mapped across space and time. Nature 597, 250–255 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Haber, A. L. et al. A single-cell survey of the small intestinal epithelium. Nature 551, 333–339 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Smillie, C. S. et al. Intra- and inter-cellular rewiring of the human colon during ulcerative colitis. Cell 178, 714–730.e22 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kong, L. et al. The landscape of immune dysregulation in Crohn’s disease revealed through single-cell transcriptomic profiling in the ileum and colon. Immunity 56, 444–458.e5 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zwick, R. K. et al. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains. Nat. Cell Biol. 26, 250–262 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Graham, D. B. & Xavier, R. J. Pathway paradigms revealed from the genetics of inflammatory bowel disease. Nature 578, 527–539 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Meier, K. H. U. et al. Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities. Nat. Metab. https://doi.org/10.1038/s42255-023-00802-1 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chen, C. & Sibley, E. Expression profiling identifies novel gene targets and functions for Pdx1 in the duodenum of mature mice. Am. J. Physiol. Gastrointest. Liver Physiol. 302, G407–G419 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Wang, H. et al. TMPRSS2 and glycan receptors synergistically facilitate coronavirus entry. Cell 187, 4261–4271.e17 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Camp, J. G. et al. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Res. 24, 1504–1516 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • McPherson, R. L. et al. Lectin-Seq: a method to profile lectin-microbe interactions in native communities. Sci. Adv. 9, eadd8766 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Brooks, J. F. II & Hooper, L. V. Interactions among microbes, the immune system, and the circadian clock. Semin. Immunopathol. 42, 697–708 (2020).

    Article 
    PubMed 

    Google Scholar 

  • Artis, D. et al. RELMβ/FIZZ2 is a goblet cell-specific immune-effector molecule in the gastrointestinal tract. Proc. Natl Acad. Sci. USA 101, 13596–13600 (2004).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bergstrom, K. S. B. et al. Goblet cell derived RELM-β recruits CD4+ T cells during infectious colitis to promote protective intestinal epithelial cell proliferation. PLoS Pathog. 11, e1005108 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hooper, L. V., Stappenbeck, T. S., Hong, C. V. & Gordon, J. I. Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nat. Immunol. 4, 269–273 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Forman, R. A. et al. The goblet cell is the cellular source of the anti-microbial angiogenin 4 in the large intestine post Trichuris muris infection. PLoS ONE 7, e42248 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jarick, K. J. et al. Non-redundant functions of group 2 innate lymphoid cells. Nature 611, 794–800 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bergstrom, K. et al. Proximal colon–derived O-glycosylated mucus encapsulates and modulates the microbiota. Science 370, 467–472 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Matute, J. D. et al. Intelectin-1 binds and alters the localization of the mucus barrier-modifying bacterium Akkermansia muciniphila. J. Exp. Med. 220, e20211938 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Xi, R. et al. Up-regulation of gasdermin C in mouse small intestine is associated with lytic cell death in enterocytes in worm-induced type 2 immunity. Proc. Natl Acad. Sci. USA 118, e2026307118 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nakata, T. et al. Genetic vulnerability to Crohn’s disease reveals a spatially resolved epithelial restitution program. Sci. Transl. Med. 15, eadg5252 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ferdinande, L. et al. Inflamed intestinal mucosa features a specific epithelial expression pattern of indoleamine 2,3-dioxygenase. Int. J. Immunopathol. Pharmacol. 21, 289–295 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zindl, C. L. et al. Distal colonocytes targeted by C. rodentium recruit T-cell help for barrier defence. Nature 629, 669–678 (2024).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jasso, G. J. et al. Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing. PLoS Biol. 20, e3001532 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mkaouar, H. et al. Gut serpinome: emerging evidence in IBD. Int. J. Mol. Sci. 22, 6088 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mkaouar, H. et al. Siropins, novel serine protease inhibitors from gut microbiota acting on human proteases involved in inflammatory bowel diseases. Microb. Cell Fact. 15, 201 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Barry, R. et al. Faecal neutrophil elastase-antiprotease balance reflects colitis severity. Mucosal Immunol. 13, 322–333 (2020).

    Article 
    MathSciNet 
    CAS 
    PubMed 

    Google Scholar 

  • Sasaki, N. et al. Reg4+ deep crypt secretory cells function as epithelial niche for Lgr5+ stem cells in colon. Proc. Natl Acad. Sci. USA 113, E5399–E5407 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Birchenough, G. M. H., Nyström, E. E. L., Johansson, M. E. V. & Hansson, G. C. A sentinel goblet cell guards the colonic crypt by triggering Nlrp6-dependent Muc2 secretion. Science 352, 1535–1542 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nyström, E. E. L. et al. An intercrypt subpopulation of goblet cells is essential for colonic mucus barrier function. Science 372, eabb1590 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Inaba, R., Vujakovic, S. & Bergstrom, K. The gut mucus network: a dynamic liaison between microbes and the immune system. Semin. Immunol. 69, 101807 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Akiyama, S. et al. CCN3 expression marks a sulfomucin-nonproducing unique subset of colonic goblet cells in mice. Acta Histochem. Cytochem. 50, 159–168 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hooper, L. V., Littman, D. R. & Macpherson, A. J. Interactions between the microbiota and the immune system. Science 336, 1268–1273 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Monticelli, L. A. et al. Arginase 1 is an innate lymphoid-cell-intrinsic metabolic checkpoint controlling type 2 inflammation. Nat. Immunol. 17, 656–665 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wallrapp, A. et al. Calcitonin gene-related peptide negatively regulates alarmin-driven type 2 innate lymphoid cell responses. Immunity 51, 709–723.e6 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mohapatra, A. et al. Group 2 innate lymphoid cells utilize the IRF4-IL-9 module to coordinate epithelial cell maintenance of lung homeostasis. Mucosal Immunol. 9, 275–286 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Pokrovskii, M. et al. Characterization of transcriptional regulatory networks that promote and restrict identities and functions of intestinal innate lymphoid cells. Immunity 51, 185–197.e6 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Xu, H. et al. Transcriptional atlas of intestinal immune cells reveals that neuropeptide α-CGRP modulates group 2 innate lymphoid cell responses. Immunity 51, 696–708.e9 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Molofsky, A. B. & Locksley, R. M. The ins and outs of innate and adaptive type 2 immunity. Immunity 56, 704–722 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Flamar, A.-L. et al. Interleukin-33 induces the enzyme tryptophan hydroxylase 1 to promote inflammatory group 2 innate lymphoid cell-mediated immunity. Immunity 52, 606–619.e6 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ricardo-Gonzalez, R. R. et al. Tissue signals imprint ILC2 identity with anticipatory function. Nat. Immunol. 19, 1093–1099 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Vivier, E. et al. Innate lymphoid cells: 10 years on. Cell 174, 1054–1066 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Tsou, A. M. et al. Neuropeptide regulation of non-redundant ILC2 responses at barrier surfaces. Nature 611, 787–793 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gurtner, A. et al. Active eosinophils regulate host defence and immune responses in colitis. Nature 615, 151–157 (2023).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Li, Y. et al. Neuromedin U programs eosinophils to promote mucosal immunity of the small intestine. Science 381, 1189–1196 (2023).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Ignacio, A. et al. Small intestinal resident eosinophils maintain gut homeostasis following microbial colonization. Immunity 55, 1250–1267.e12 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Naik, S. & Fuchs, E. Inflammatory memory and tissue adaptation in sickness and in health. Nature 607, 249–255 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gustafsson, J. K. & Johansson, M. E. V. The role of goblet cells and mucus in intestinal homeostasis. Nat. Rev. Gastroenterol. Hepatol. 19, 785–803 (2022).

    Article 
    PubMed 

    Google Scholar 

  • Mayassi, T. et al. Chronic inflammation permanently reshapes tissue-resident immunity in celiac disease. Cell 176, 967–981.e19 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wilde, J., Slack, E. & Foster, K. R. Host control of the microbiome: mechanisms, evolution, and disease. Science 385, eadi3338 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • McCallum, G. & Tropini, C. The gut microbiota and its biogeography. Nat. Rev. Microbiol. 22, 105–118 (2023).

  • Casanova, J.-L. & Abel, L. The microbe, the infection enigma, and the host. Annu. Rev. Microbiol. https://doi.org/10.1146/annurev-micro-092123-022855 (2024).

  • Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nonnecke, E. B. et al. Characterization of an intelectin-1 (Itln1) knockout mouse model. Front. Immunol. 13, 894649 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chiba, Y., Suto, W. & Sakai, H. Augmented Pla2g4c/Ptgs2/Hpgds axis in bronchial smooth muscle tissues of experimental asthma. PLoS ONE 13, e0202623 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Tao, H.-P. et al. Pancreatic lipase-related protein 2 is selectively expressed by peritubular myoid cells in the murine testis and sustains long-term spermatogenesis. Cell. Mol. Life Sci. 80, 217 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Xie, Z. et al. Gene set knowledge discovery with Enrichr. Curr. Protoc. 1, e90 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fleming, S. J. et al. Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender. Nat. Methods 20, 1323–1335 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Bergen, V., Lange, M., Peidli, S., Wolf, F. A. & Theis, F. J. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat. Biotechnol. 38, 1408–1414 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kleshchevnikov, V. et al. Cell2location maps fine-grained cell types in spatial transcriptomics. Nat. Biotechnol. 40, 661–671 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Li, B. et al. Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution. Nat. Methods 19, 662–670 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Hu, H. et al. AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. Nucleic Acids Res. 47, D33–D38 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Sollis, E. et al. The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Res. 51, D977–D985 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Huang, H. et al. Fine-mapping inflammatory bowel disease loci to single-variant resolution. Nature 547, 173–178 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Liu, Z. et al. Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries. Nat. Genet. 55, 796–806 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sazonovs, A. et al. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility. Nat. Genet. 54, 1275–1283 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kurki, M. I. et al. FinnGen provides genetic insights from a well-phenotyped isolated population. Nature 613, 508–518 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bolton, C. et al. An integrated taxonomy for monogenic inflammatory bowel disease. Gastroenterology 162, 859–876 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Wu, Y. et al. 150 risk variants for diverticular disease of intestine prioritize cell types and enable polygenic prediction of disease susceptibility. Cell Genom. 3, 100326 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mayassi, T. et al. Spatially restricted immune and microbiota-driven adaptation of the gut. Zenodo https://doi.org/10.5281/zenodo.8383893 (2024).

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