Parikh, K. et al. Colonic epithelial cell diversity in health and inflammatory bowel disease. Nature 567, 49–55 (2019).
Fawkner-Corbett, D. et al. Spatiotemporal analysis of human intestinal development at single-cell resolution. Cell 184, 810–826.e23 (2021).
Hickey, J. W. et al. Organization of the human intestine at single-cell resolution. Nature 619, 572–584 (2023).
Elmentaite, R. et al. Cells of the human intestinal tract mapped across space and time. Nature 597, 250–255 (2021).
Haber, A. L. et al. A single-cell survey of the small intestinal epithelium. Nature 551, 333–339 (2017).
Smillie, C. S. et al. Intra- and inter-cellular rewiring of the human colon during ulcerative colitis. Cell 178, 714–730.e22 (2019).
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).
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).
Graham, D. B. & Xavier, R. J. Pathway paradigms revealed from the genetics of inflammatory bowel disease. Nature 578, 527–539 (2020).
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).
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).
Wang, H. et al. TMPRSS2 and glycan receptors synergistically facilitate coronavirus entry. Cell 187, 4261–4271.e17 (2024).
Camp, J. G. et al. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Res. 24, 1504–1516 (2014).
McPherson, R. L. et al. Lectin-Seq: a method to profile lectin-microbe interactions in native communities. Sci. Adv. 9, eadd8766 (2023).
Brooks, J. F. II & Hooper, L. V. Interactions among microbes, the immune system, and the circadian clock. Semin. Immunopathol. 42, 697–708 (2020).
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).
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).
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).
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).
Jarick, K. J. et al. Non-redundant functions of group 2 innate lymphoid cells. Nature 611, 794–800 (2022).
Bergstrom, K. et al. Proximal colon–derived O-glycosylated mucus encapsulates and modulates the microbiota. Science 370, 467–472 (2020).
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).
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).
Nakata, T. et al. Genetic vulnerability to Crohn’s disease reveals a spatially resolved epithelial restitution program. Sci. Transl. Med. 15, eadg5252 (2023).
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).
Zindl, C. L. et al. Distal colonocytes targeted by C. rodentium recruit T-cell help for barrier defence. Nature 629, 669–678 (2024).
Jasso, G. J. et al. Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing. PLoS Biol. 20, e3001532 (2022).
Mkaouar, H. et al. Gut serpinome: emerging evidence in IBD. Int. J. Mol. Sci. 22, 6088 (2021).
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).
Barry, R. et al. Faecal neutrophil elastase-antiprotease balance reflects colitis severity. Mucosal Immunol. 13, 322–333 (2020).
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).
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).
Nyström, E. E. L. et al. An intercrypt subpopulation of goblet cells is essential for colonic mucus barrier function. Science 372, eabb1590 (2021).
Inaba, R., Vujakovic, S. & Bergstrom, K. The gut mucus network: a dynamic liaison between microbes and the immune system. Semin. Immunol. 69, 101807 (2023).
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).
Hooper, L. V., Littman, D. R. & Macpherson, A. J. Interactions between the microbiota and the immune system. Science 336, 1268–1273 (2012).
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).
Wallrapp, A. et al. Calcitonin gene-related peptide negatively regulates alarmin-driven type 2 innate lymphoid cell responses. Immunity 51, 709–723.e6 (2019).
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).
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).
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).
Molofsky, A. B. & Locksley, R. M. The ins and outs of innate and adaptive type 2 immunity. Immunity 56, 704–722 (2023).
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).
Ricardo-Gonzalez, R. R. et al. Tissue signals imprint ILC2 identity with anticipatory function. Nat. Immunol. 19, 1093–1099 (2018).
Vivier, E. et al. Innate lymphoid cells: 10 years on. Cell 174, 1054–1066 (2018).
Tsou, A. M. et al. Neuropeptide regulation of non-redundant ILC2 responses at barrier surfaces. Nature 611, 787–793 (2022).
Gurtner, A. et al. Active eosinophils regulate host defence and immune responses in colitis. Nature 615, 151–157 (2023).
Li, Y. et al. Neuromedin U programs eosinophils to promote mucosal immunity of the small intestine. Science 381, 1189–1196 (2023).
Ignacio, A. et al. Small intestinal resident eosinophils maintain gut homeostasis following microbial colonization. Immunity 55, 1250–1267.e12 (2022).
Naik, S. & Fuchs, E. Inflammatory memory and tissue adaptation in sickness and in health. Nature 607, 249–255 (2022).
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).
Mayassi, T. et al. Chronic inflammation permanently reshapes tissue-resident immunity in celiac disease. Cell 176, 967–981.e19 (2019).
Wilde, J., Slack, E. & Foster, K. R. Host control of the microbiome: mechanisms, evolution, and disease. Science 385, eadi3338 (2024).
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).
Nonnecke, E. B. et al. Characterization of an intelectin-1 (Itln1) knockout mouse model. Front. Immunol. 13, 894649 (2022).
Chiba, Y., Suto, W. & Sakai, H. Augmented Pla2g4c/Ptgs2/Hpgds axis in bronchial smooth muscle tissues of experimental asthma. PLoS ONE 13, e0202623 (2018).
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).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).
Xie, Z. et al. Gene set knowledge discovery with Enrichr. Curr. Protoc. 1, e90 (2021).
Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).
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).
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).
Kleshchevnikov, V. et al. Cell2location maps fine-grained cell types in spatial transcriptomics. Nat. Biotechnol. 40, 661–671 (2022).
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).
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).
Sollis, E. et al. The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Res. 51, D977–D985 (2023).
Huang, H. et al. Fine-mapping inflammatory bowel disease loci to single-variant resolution. Nature 547, 173–178 (2017).
Liu, Z. et al. Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries. Nat. Genet. 55, 796–806 (2023).
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).
Kurki, M. I. et al. FinnGen provides genetic insights from a well-phenotyped isolated population. Nature 613, 508–518 (2023).
Bolton, C. et al. An integrated taxonomy for monogenic inflammatory bowel disease. Gastroenterology 162, 859–876 (2022).
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).
Mayassi, T. et al. Spatially restricted immune and microbiota-driven adaptation of the gut. Zenodo https://doi.org/10.5281/zenodo.8383893 (2024).
A federal jury in Delaware determined on Friday that Qualcomm didn’t breach its agreement with…
Geese The Wendy Award The Apprentice What have you read/watched/listened to lately? Phoebe Ward, 22,…
15% ROI, 5% down loans!","body":"3.99% rate, 5% down! Access the BEST deals in the US…
Particles in ship exhaust inadvertently cause cloud brightening – some geoengineering projects would try to…
The weather outside is frightful, but the iOS games are so delightful, let it play,…
A few flagship bond funds from some big-name Southern California-based firms saw outflows of more…