The protective and absorptive functions of the intestinal epithelium rely on differentiated enterocytes in the villi. The differentiation of enterocytes is orchestrated by sub-epithelial mesenchymal cells producing distinct ligands along the villus axis, in particular Bmps and Tgfβ. Here, we show that individual Bmp ligands and Tgfβ drive distinct enterocytic programs specific to villus zonation. Bmp4 is expressed from the centre to the upper part of the villus and activates preferentially genes connected to lipid uptake and metabolism. In contrast, Bmp2 is produced by villus tip mesenchymal cells and it influences the adhesive properties of villus tip epithelial cells and the expression of immunomodulators. Additionally, Tgfβ induces epithelial gene expression programs similar to those triggered by Bmp2. Bmp2-driven villus tip program is activated by a canonical Bmp receptor type I/Smad-dependent mechanism. Finally, we establish an organoid cultivation system that enriches villus tip enterocytes and thereby better mimics the cellular composition of the intestinal epithelium. Our data suggest that not only a Bmp gradient but also the activity of individual Bmp drives specific enterocytic programs.

Beijing Institute for Stem Cell and Regenerative Medicine Beijing China

Department of Molecular Life Sciences University of Zurich Zurich Switzerland

Friedrich Miescher Institute for Biomedical Research Basel Switzerland

Institute for Stem Cell and Regeneration Chinese Academy of Sciences Beijing China

Laboratory of Cell and Developmental Biology Institute of Molecular Genetics of the Czech Academy of Sciences Prague Czech Republic

Laboratory of Genomics and Bioinformatics Institute of Molecular Genetics of the Czech Academy of Sciences Prague Czech Republic

State Key Laboratory of Stem Cell and Reproductive Biology Institute of Zoology Chinese Academy of Sciences Beijing China

University of Chinese Academy of Sciences Beijing China

Zobrazit více v PubMed

Antebi YE, Linton JM, Klumpe H, Bintu B, Gong M, Su C, McCardell R, Elowitz MB (2017) Combinatorial signal perception in the BMP pathway. Cell 170: 1184–1196 PubMed PMC

Bahar Halpern K, Massalha H, Zwick RK, Moor AE, Castillo‐Azofeifa D, Rozenberg M, Farack L, Egozi A, Miller DR, Averbukh I PubMed PMC

Bauché D, Marie JC (2017) Transforming growth factor β: a master regulator of the gut microbiota and immune cell interactions. Clin Trans Immunol 6: e136 PubMed PMC

Beumer J, Puschhof J, Yengej FY, Zhao L, Martinez‐Silgado A, Blotenburg M, Begthel H, Boot C, van Oudenaarden A, Chen YG PubMed

Bragdon B, Moseychuk O, Saldanha S, King D, Julian J, Nohe A (2011) Bone morphogenetic proteins: a critical review. Cell Signal 23: 609–620 PubMed

Brügger MD, Valenta T, Fazilaty H, Hausmann G, Basler K (2020) Distinct populations of crypt‐associated fibroblasts act as signaling hubs to control colon homeostasis. PLoS Biol 18: e3001032 PubMed PMC

Buchauer L, Itzkovitz S (2021) Cellanneal: a user‐friendly deconvolution software for omics data. bioRxiv 10.48550/ARXIV.2110.08209 [PREPRINT] DOI

Cosovanu C, Resch P, Jordan S, Lehmann A, Ralser M, Farztdinov V, Spranger J, Mülleder M, Brachs S, Neumann C (2022) Intestinal epithelial c‐Maf expression determines enterocyte differentiation and nutrient uptake in mice. J Exp Med 219: e20220233 PubMed PMC

Degirmenci B, Valenta T, Dimitrieva S, Hausmann G, Basler K (2018) GLI1‐expressing mesenchymal cells form the essential Wnt‐secreting niche for colon stem cells. Nature 558: 449–453 PubMed

Doncheva NT, Morris JH, Gorodkin J, Jensen LJ (2019) Cytoscape String App: network analysis and visualization of proteomics data. J Proteome Res 18: 623–632 PubMed PMC

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S (2020) The nf‐core framework for community‐curated bioinformatics pipelines. Nat Biotechnol 38: 276–278 PubMed

Fazilaty H, Brügger MD, Valenta T, Szczerba BM, Berkova L, Doumpas N, Hausmann G, Scharl M, Basler K (2021) Tracing colonic embryonic transcriptional profiles and their reactivation upon intestinal damage. Cell Rep 36: 109484 PubMed

Fujii M, Matano M, Toshimitsu K, Takano A, Mikami Y, Nishikori S, Sugimoto S, Sato T (2018) Human intestinal organoids maintain self‐renewal capacity and cellular diversity in niche‐inspired culture condition. Cell Stem Cell 23: 787–793 PubMed

Galili T, O'Callaghan A, Sidi J, Sievert C (2017) Heatmaply: an R package for creating interactive cluster heatmaps for online publishing. Bioinformatics 34: 1600–1602 PubMed PMC

Gao CH, Yu G, Cai P (2021) ggVennDiagram: An intuitive, easy‐to‐use, and highly customizable R package to generate Venn diagram. Front Genet 12: 1598 PubMed PMC

Gehart H, Clevers H (2019) Tales from the crypt: new insights into intestinal stem cells. Nat Rev Gastroenterol Hepatol 16: 19–34 PubMed

González‐Loyola A, Bernier‐Latmani J, Roci I, Wyss T, Langer J, Durot S, Munoz O, Prat‐Luri B, Delorenzi M, Lutolf MP PubMed PMC

Gracz AD, Puthoff BJ, Magness ST (2012) Identification, isolation, and culture of intestinal epithelial stem cells from murine intestine. In Somatic stem cells, Singh SR (ed), pp 89–107. Totowa, NJ: Humana Press; PubMed PMC

Greicius G, Kabiri Z, Sigmundsson K, Liang C, Bunte R, Singh MK, Virshup DM (2018) PDGFRα PubMed PMC

Grün D, Lyubimova A, Kester L, Wiebrands K, Basak O, Sasaki N, Clevers H, van Oudenaarden A (2015) Single‐cell messenger RNA sequencing reveals rare intestinal cell types. Nature 525: 251–255 PubMed

Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, Burgin G, Delorey TM, Howitt MR, Katz Y PubMed PMC

Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, Burgin G, Delorey TM, Howitt MR, Katz Y

Hamilton TG, Klinghoffer RA, Corrin PD, Soriano P (2003) Evolutionary divergence of platelet‐derived growth factor alpha receptor signaling mechanisms. Mol Cell Biol 23: 4013–4025 PubMed PMC

Han T, Goswami S, Hu Y, Tang F, Zafra MP, Murphy C, Cao Z, Poirier JT, Khurana E, Elemento O PubMed PMC

Hao Y, Hao S, Andersen‐Nissen E, Mauck WM, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M PubMed PMC

Haramis APG, Begthel H, van den Born M, van Es J, Jonkheer S, Offerhaus GJA, Clevers H (2004) PubMed

Harnik Y, Buchauer L, Ben‐Moshe S, Averbukh I, Levin Y, Savidor A, Eilam R, Moor AE, Itzkovitz S (2021) Spatial discordances between mRNAs and proteins in the intestinal epithelium. Nat Metab 3: 1680–1693 PubMed

Howe KL, Reardon C, Wang A, Nazli A, McKay DM (2005) Transforming growth factor‐β regulation of epithelial tight junction proteins enhances barrier function and blocks enterohemorrhagic PubMed PMC

Howe KL, Achuthan P, Allen J, Allen J, Alvarez‐Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J PubMed PMC

Klumpe HE, Langley MA, Linton JM, Su CJ, Antebi YE, Elowitz MB (2022) The context‐dependent, combinatorial logic of BMP signaling. Cell Syst 13: 388–407 PubMed PMC

Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA‐seq data with DESeq2. Genome Biol 15: 550 PubMed PMC

McCarthy N, Manieri E, Storm EE, Saadatpour A, Luoma AM, Kapoor VN, Madha S, Gaynor LT, Cox C, Keerthivasan S PubMed PMC

McCarthy N, Manieri E, Storm EE, Saadatpour A, Luoma AM, Kapoor VN, Madha S, Gaynor LT, Cox C, Keerthivasan S PubMed PMC

Miyoshi H, Ajima R, Luo CT, Yamaguchi TP, Stappenbeck TS (2012) Wnt5a potentiates TGF‐β signaling to promote colonic crypt regeneration after tissue injury. Science 338: 108–113 PubMed PMC

Moor AE, Harnik Y, Ben‐Moshe S, Massasa EE, Rozenberg M, Eilam R, Bahar Halpern K, Itzkovitz S (2018a) Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus Axis. Cell 175: 1156–1167 PubMed

Moor AE, Harnik Y, Ben‐Moshe S, Massasa EE, Rozenberg M, Eilam R, Bahar Halpern K, Itzkovitz S (2018b) Zenodo 3403670. (https://zenodo.org/record/3403670) [DATASET] PubMed

Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C (2017) Salmon provides fast and bias‐aware quantification of transcript expression. Nat Methods 14: 417–419 PubMed PMC

Qi Z, Li Y, Zhao B, Xu C, Liu Y, Li H, Zhang B, Wang X, Yang X, Xie W PubMed PMC

Salazar VS, Gamer LW, Rosen V (2016) BMP signalling in skeletal development, disease and repair. Nat Rev Endocrinol 12: 203–221 PubMed

Sato T, Vries RG, Snippert HJ, van de Wetering M, Barker N, Stange DE, van Es JH, Abo A, Kujala P, Peters PJ PubMed

Sato T, van Es JH, Snippert HJ, Stange DE, Vries RG, van den Born M, Barker N, Shroyer NF, van de Wetering M, Clevers H (2011) Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts. Nature 469: 415–418 PubMed PMC

Schindelin J, Arganda‐Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B PubMed PMC

Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M (2011) Global quantification of mammalian gene expression control. Nature 473: 337–342 PubMed

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498–2504 PubMed PMC

Spit M, Koo BK, Maurice MM (2018) Tales from the crypt: intestinal niche signals in tissue renewal, plasticity and cancer. Open Biol 8: 180120 PubMed PMC

Stolfi C, Troncone E, Marafini I, Monteleone G (2020) Role of TGF‐Beta and Smad7 in gut inflammation, fibrosis and cancer. Biomolecules 11: 17 PubMed PMC

Wang RN, Green J, Wang Z, Deng Y, Qiao M, Peabody M, Zhang Q, Ye J, Yan Z, Denduluri S PubMed PMC

Wickham H (2016) ggplot2: elegant graphics for data analysis. New York, NY: Springer‐Verlag New York;

Wickham H, François R, Henry L, Müller K, Vaughan D (2023) Dplyr: a grammar of data manipulation. (https://dplyr.tidyverse.org, https://github.com/tidyverse/dplyr)

Yan KS, Gevaert O, Zheng GXY, Anchang B, Probert CS, Larkin KA, Davies PS, Cheng ZF, Kaddis JS, Han A PubMed PMC

Yan KS, Gevaert O, Zheng GXY, Anchang B, Probert CS, Larkin KA, Davies PS, Cheng ZF, Kaddis JS, Han A

Yang Q, Xue SL, Chan CJ, Rempfler M, Vischi D, Maurer‐Gutierrez F, Hiiragi T, Hannezo E, Liberali P (2021) Cell fate coordinates mechano‐osmotic forces in intestinal crypt formation. Nat Cell Biol 23: 733–744 PubMed PMC