IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-59459-x.html
   My bibliography  Save this article

Biomimetic culture substrates for modelling homeostatic intestinal epithelium in vitro

Author

Listed:
  • Sorosh Abdollahi

    (University of Calgary
    University of Calgary)

  • Bahareh Zarin

    (University of Calgary)

  • Maryam Vatani

    (University of Calgary
    University of Calgary)

  • Fereshteh Vajhadin

    (University of Calgary)

  • Mohsen Hassani

    (University of Calgary)

  • Pezhman Jalali

    (University of Calgary)

  • Keekyoung Kim

    (University of Calgary
    University of Calgary)

  • Amir Sanati-Nezhad

    (University of Calgary
    University of Calgary
    University of Calgary
    University of Calgary)

Abstract

The increasing interest in utilizing three-dimensional (3D) in vitro models with innovative biomaterials to engineer functional tissues arises from the limitations of conventional cell culture methods in accurately reproducing the complex physiological conditions of living organisms. This study presents a strategy for replicating the intricate microenvironment of the intestine by cultivating intestinal cells within bioinspired 3D interfaces that recapitulate the villus-crypt architecture and 3D tissue arrangement of the intestine. Intestinal cells cultured on these biomimetic substrates exhibited phenotypes and differentiation characteristics resembling intestinal-specific cell types, effectively replicating intestinal tissue. Notably, tissue proliferation and differentiation were achieved within 72–120 h—significantly faster than the several weeks required by conventional bioengineered materials, which often pose risks of tissue necrosis or cross-contamination. Additionally, the differentiated cells on these villi-crypts mimicking bio-interfaces exhibit higher production of natural antimicrobial peptides, resulting in reduced pathogenic infection compared to control samples. Furthermore, our method stands out for simplicity in fabrication, eliminating the need for cleanroom procedures and complex microfabrication techniques.

Suggested Citation

  • Sorosh Abdollahi & Bahareh Zarin & Maryam Vatani & Fereshteh Vajhadin & Mohsen Hassani & Pezhman Jalali & Keekyoung Kim & Amir Sanati-Nezhad, 2025. "Biomimetic culture substrates for modelling homeostatic intestinal epithelium in vitro," Nature Communications, Nature, vol. 16(1), pages 1-21, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59459-x
    DOI: 10.1038/s41467-025-59459-x
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-59459-x
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-025-59459-x?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Mikhail Nikolaev & Olga Mitrofanova & Nicolas Broguiere & Sara Geraldo & Devanjali Dutta & Yoji Tabata & Bilge Elci & Nathalie Brandenberg & Irina Kolotuev & Nikolce Gjorevski & Hans Clevers & Matthia, 2020. "Homeostatic mini-intestines through scaffold-guided organoid morphogenesis," Nature, Nature, vol. 585(7826), pages 574-578, September.
    2. Ohman Kwon & Hana Lee & Jaeeun Jung & Ye Seul Son & Sojeong Jeon & Won Dong Yoo & Naeun Son & Kwang Bo Jung & Eunho Choi & In-Chul Lee & Hyung-Jun Kwon & Chuna Kim & Mi-Ok Lee & Hyun-Soo Cho & Dae Soo, 2024. "Chemically-defined and scalable culture system for intestinal stem cells derived from human intestinal organoids," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    3. Frank A. Duca & T. M. Zaved Waise & Willem T. Peppler & Tony K. T. Lam, 2021. "The metabolic impact of small intestinal nutrient sensing," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    4. Maria Antfolk & Kim B. Jensen, 2020. "A bioengineering perspective on modelling the intestinal epithelial physiology in vitro," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    5. Cayetano Pleguezuelos-Manzano & Jens Puschhof & Axel Rosendahl Huber & Arne van Hoeck & Henry M. Wood & Jason Nomburg & Carino Gurjao & Freek Manders & Guillaume Dalmasso & Paul B. Stege & Fernanda L., 2020. "Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli," Nature, Nature, vol. 580(7802), pages 269-273, April.
    6. Yi Liu & Yuanyuan Zhang & Tong Li & Jinbo Han & Yiguo Wang, 2020. "The tight junction protein TJP1 regulates the feeding-modulated hepatic circadian clock," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Bin Xue & Zhengyu Xu & Lan Li & Kaiqiang Guo & Jing Mi & Haipeng Wu & Yiran Li & Chunmei Xie & Jing Jin & Juan Xu & Chunping Jiang & Xiaosong Gu & Meng Qin & Qing Jiang & Yi Cao & Wei Wang, 2025. "Hydrogels with programmed spatiotemporal mechanical cues for stem cell-assisted bone regeneration," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    2. Huiyuan Zhu & Man Li & Dexi Bi & Huiqiong Yang & Yaohui Gao & Feifei Song & Jiayi Zheng & Ruting Xie & Youhua Zhang & Hu Liu & Xuebing Yan & Cheng Kong & Yefei Zhu & Qian Xu & Qing Wei & Huanlong Qin, 2024. "Fusobacterium nucleatum promotes tumor progression in KRAS p.G12D-mutant colorectal cancer by binding to DHX15," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Candice R. Gurbatri & Georgette A. Radford & Laura Vrbanac & Jongwon Im & Elaine M. Thomas & Courtney Coker & Samuel R. Taylor & YoungUk Jang & Ayelet Sivan & Kyu Rhee & Anas A. Saleh & Tiffany Chien , 2024. "Engineering tumor-colonizing E. coli Nissle 1917 for detection and treatment of colorectal neoplasia," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    4. Junjun Gao & Song Zhang & Pan Deng & Zhigang Wu & Bruno Lemaitre & Zongzhao Zhai & Zheng Guo, 2024. "Dietary L-Glu sensing by enteroendocrine cells adjusts food intake via modulating gut PYY/NPF secretion," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    5. Luan Nguyen & Arne Hoeck & Edwin Cuppen, 2022. "Machine learning-based tissue of origin classification for cancer of unknown primary diagnostics using genome-wide mutation features," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    6. Anna Urciuolo & Giovanni Giuseppe Giobbe & Yixiao Dong & Federica Michielin & Luca Brandolino & Michael Magnussen & Onelia Gagliano & Giulia Selmin & Valentina Scattolini & Paolo Raffa & Paola Caccin , 2023. "Hydrogel-in-hydrogel live bioprinting for guidance and control of organoids and organotypic cultures," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    7. María A. Duque-Correa & David Goulding & Faye H. Rodgers & J. Andrew Gillis & Claire Cormie & Kate A. Rawlinson & Allison J. Bancroft & Hayley M. Bennett & Magda E. Lotkowska & Adam J. Reid & Annelies, 2022. "Defining the early stages of intestinal colonisation by whipworms," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    8. Seonghyeon Park & Ohman Kwon & Hana Lee & Younghak Cho & Jemin Yeun & Sung Hyun Yoon & Sang Yu Sun & Yubin Huh & Won Dong Yu & Sohee Park & Naeun Son & Sojeong Jeon & Sugi Lee & Dae-Soo Kim & Sun Youn, 2024. "Xenogeneic-free culture of human intestinal stem cells on functional polymer-coated substrates for scalable, clinical-grade stem cell therapy," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    9. Yuan Liang & Chao Luo & Lijun Sun & Tiange Feng & Wenzhen Yin & Yunhua Zhang & Michael W. Mulholland & Weizhen Zhang & Yue Yin, 2024. "Reduction of specific enterocytes from loss of intestinal LGR4 improves lipid metabolism in mice," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    10. Lulu Sun & Yi Zhang & Jie Cai & Bipin Rimal & Edson R. Rocha & James P. Coleman & Chenran Zhang & Robert G. Nichols & Yuhong Luo & Bora Kim & Yaozong Chen & Kristopher W. Krausz & Curtis C. Harris & A, 2023. "Bile salt hydrolase in non-enterotoxigenic Bacteroides potentiates colorectal cancer," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    11. Wanting Dong & Xinyue Fan & Yaqiong Guo & Siyi Wang & Shulei Jia & Na Lv & Tao Yuan & Yuanlong Pan & Yong Xue & Xi Chen & Qian Xiong & Ruifu Yang & Weigang Zhao & Baoli Zhu, 2024. "An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    12. Ewart Kuijk & Onno Kranenburg & Edwin Cuppen & Arne Van Hoeck, 2022. "Common anti-cancer therapies induce somatic mutations in stem cells of healthy tissue," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    13. Francesca Menghi & Edison T. Liu, 2022. "Functional genomics of complex cancer genomes," Nature Communications, Nature, vol. 13(1), pages 1-4, December.
    14. Sujath Abbas & Oriol Pich & Ginny Devonshire & Shahriar A. Zamani & Annalise Katz-Summercorn & Sarah Killcoyne & Calvin Cheah & Barbara Nutzinger & Nicola Grehan & Nuria Lopez-Bigas & Rebecca C. Fitzg, 2023. "Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    15. Stefan Harmansa & Alexander Erlich & Christophe Eloy & Giuseppe Zurlo & Thomas Lecuit, 2023. "Growth anisotropy of the extracellular matrix shapes a developing organ," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    16. Song-Yang Zhang & Tony K. T. Lam, 2022. "Metabolic regulation by the intestinal metformin-AMPK axis," Nature Communications, Nature, vol. 13(1), pages 1-3, December.
    17. Bernard C. H. Lee & Philip S. Robinson & Tim H. H. Coorens & Helen H. N. Yan & Sigurgeir Olafsson & Henry Lee-Six & Mathijs A. Sanders & Hoi Cheong Siu & James Hewinson & Sarah S. K. Yue & Wai Yin Tsu, 2022. "Mutational landscape of normal epithelial cells in Lynch Syndrome patients," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    18. Carmen Aguilar & Mindaugas Pauzuolis & Malvika Pompaiah & Ehsan Vafadarnejad & Panagiota Arampatzi & Mara Fischer & Dominik Narres & Mastura Neyazi & Özge Kayisoglu & Thomas Sell & Nils Blüthgen & Mar, 2022. "Helicobacter pylori shows tropism to gastric differentiated pit cells dependent on urea chemotaxis," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    19. Bingjie Chen & Daniele Ramazzotti & Timon Heide & Inmaculada Spiteri & Javier Fernandez-Mateos & Chela James & Luca Magnani & Trevor A. Graham & Andrea Sottoriva, 2023. "Contribution of pks+ E. coli mutations to colorectal carcinogenesis," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    20. Philip S. Robinson & Laura E. Thomas & Federico Abascal & Hyunchul Jung & Luke M. R. Harvey & Hannah D. West & Sigurgeir Olafsson & Bernard C. H. Lee & Tim H. H. Coorens & Henry Lee-Six & Laura Butlin, 2022. "Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells," Nature Communications, Nature, vol. 13(1), pages 1-12, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59459-x. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.