Barker, N. Adult intestinal stem cells: critical drivers of epithelial homeostasis and regeneration. Nat. Rev. Mol. Cell Biol. 15, 19–33 (2014).
van der Flier, L. G. & Clevers, H. Stem cells, self-renewal, and differentiation in the intestinal epithelium. Annu. Rev. Physiol. 71, 241–260 (2009).
Tian, C. M. et al. Stem cell therapy in inflammatory bowel disease: a review of achievements and challenges. J. Inflamm. Res. 16, 2089–2119 (2023).
Kang, E. J. et al. The secreted protein Amuc_1409 from Akkermansia muciniphila improves gut health through intestinal stem cell regulation. Nat. Commun. 15, 2983 (2024).
Hou, Q. et al. Bacillus subtilis programs the differentiation of intestinal secretory lineages to inhibit Salmonella infection. Cell Rep. 40, 111416 (2022).
Sato, T. et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262–265 (2009).
Almeqdadi, M., Mana, M. D., Roper, J. & Yilmaz Ö. H. Gut organoids: mini-tissues in culture to study intestinal physiology and disease. Am. J. Physiol. Cell Physiol. 317, C405–C419 (2019).
Liao, Y. et al. Fungal symbiont transmitted by free-living mice promotes type 2 immunity. Nature 636, 697–704 (2024).
Destruelle, M., Holzer, H. & Klionsky, D. J. Identification and characterization of a novel yeast gene: the YGP1 gene product is a highly glycosylated secreted protein that is synthesized in response to nutrient limitation. Mol. Cell. Biol. 14, 2740–2754 (1994).
Hageman, J. H. et al. Intestinal regeneration: regulation by the microenvironment. Dev. Cell 54, 435–446 (2020).
Eichele, D. D. & Kharbanda, K. K. Dextran sodium sulfate colitis murine model: an indispensable tool for advancing our understanding of inflammatory bowel diseases pathogenesis. World J. Gastroenterol. 23, 6016–6029 (2017).
Chassaing, B., Aitken, J. D., Malleshappa, M. & Vijay-Kumar, M. Dextran sulfate sodium (DSS)-induced colitis in mice. Curr. Protoc. Immunol. 104, 15.25.11–15.25.14 (2014).
Sonis, S. T. The pathobiology of mucositis. Nat. Rev. Cancer 4, 277–284 (2004).
Longley, D. B., Harkin, D. P. & Johnston, P. G. 5-fluorouracil: mechanisms of action and clinical strategies. Nat. Rev. Cancer 3, 330–338 (2003).
Fink, M. et al. Chromatin remodelling in damaged intestinal crypts orchestrates redundant TGFβ and Hippo signalling to drive regeneration. Nat. Cell Biol. 26, 2084–2098 (2024).
Laschinger, M. et al. The CGRP receptor component RAMP1 links sensory innervation with YAP activity in the regenerating liver. FASEB J. 34, 8125–8138 (2020).
Moya, I. M. & Halder, G. Hippo-YAP/TAZ signalling in organ regeneration and regenerative medicine. Nat. Rev. Mol. Cell Biol. 20, 211–226 (2019).
Amitrano, A. et al. Extracellular fluid viscosity regulates human mesenchymal stem cell lineage and function. Sci. Adv. 11, eadr5023 (2025).
Kaneda, A. et al. The novel potent TEAD inhibitor, K-975, inhibits YAP1/TAZ-TEAD protein–protein interactions and exerts an anti-tumor effect on malignant pleural mesothelioma. Am. J. Cancer Res. 10, 4399–4415 (2020).
Sun, L. et al. ENO1 promotes liver carcinogenesis through YAP1-dependent arachidonic acid metabolism. Nat. Chem. Biol. 19, 1492–1503 (2023).
Sun, Y. et al. Integrative plasma and fecal metabolomics identify functional metabolites in adenoma-colorectal cancer progression and as early diagnostic biomarkers. Cancer Cell 42, 1386–1400.e8 (2024).
Leonard, P. G. et al. SF2312 is a natural phosphonate inhibitor of enolase. Nat. Chem. Biol. 12, 1053–1058 (2016).
Nash, A. K. et al. The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome 5, 153 (2017).
Zhang, F., Aschenbrenner, D., Yoo, J. Y. & Zuo, T. The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly. Lancet Microbe 3, e969–e983 (2022).
Huang, H. et al. The mycobiome as integral part of the gut microbiome: crucial role of symbiotic fungi in health and disease. Gut Microbes 16, 2440111 (2024).
Hiengrach, P., Chindamporn, A. & Leelahavanichkul, A. Kazachstania pintolopesii in blood and intestinal wall of macrophage-depleted mice with cecal ligation and puncture, the control of fungi by macrophages during sepsis. J. Fungi 9, 1164 (2023).
Sekeresova Kralova, J. et al. Competitive fungal commensalism mitigates candidiasis pathology. J. Exp. Med. 221, e20231686 (2024).
Avershina, E., Qureshi, A. I., Winther-Larsen, H. C. & Rounge, T. B. Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases. Microbiome 13, 66 (2025).
Porras, A. M. et al. Geographic differences in gut microbiota composition impact susceptibility to enteric infection. Cell Rep. 36, 109457 (2021).
Imbrizi, M., Magro, F. & Coy, C. S. R. Pharmacological therapy in inflammatory bowel diseases: a narrative review of the past 90 years. Pharmaceuticals 16, 1272 (2023).
Wynn, T. A. Type 2 cytokines: mechanisms and therapeutic strategies. Nat. Rev. Immunol. 15, 271–282 (2015).
Hams, E. et al. IL-25 and type 2 innate lymphoid cells induce pulmonary fibrosis. Proc. Natl Acad. Sci. USA 111, 367–372 (2014).
Lin, Z. et al. Cardiac-specific YAP activation improves cardiac function and survival in an experimental murine MI model. Circ. Res. 115, 354–363 (2014).
Xin, M. et al. Hippo pathway effector Yap promotes cardiac regeneration. Proc. Natl Acad. Sci. USA 110, 13839–13844 (2013).
Heallen, T. et al. Hippo signaling impedes adult heart regeneration. Development 140, 4683–4690 (2013).
Zhong, Z., Jiao, Z. & Yu, F. X. The Hippo signaling pathway in development and regeneration. Cell Rep. 43, 113926 (2024).
Wang, Y. et al. USP10 strikes down β-catenin by dual-wielding deubiquitinase activity and phase separation potential. Cell Chem. Biol. 30, 1436–1452.e10 (2023).
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, 2855 (2023).
Kondo, J. et al. LRIG1 regulates ontogeny of smooth muscle-derived subsets of interstitial cells of cajal in mice. Gastroenterology 149, 407–419.e8 (2015).
Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).
Pierce, B. G. et al. ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers. Bioinformatics 30, 1771–1773 (2014).
Kozakov, D. et al. The ClusPro web server for protein–protein docking. Nat. Protoc. 12, 255–278 (2017).
Honorato, R. V. et al. The HADDOCK2.4 web server for integrative modeling of biomolecular complexes. Nat. Protoc. 19, 3219–3241 (2024).
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