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An organoid-based organ-repurposing approach to treat short bowel syndrome

Abstract

The small intestine is the main organ for nutrient absorption, and its extensive resection leads to malabsorption and wasting conditions referred to as short bowel syndrome (SBS). Organoid technology enables an efficient expansion of intestinal epithelium tissue in vitro1, but reconstruction of the whole small intestine, including the complex lymphovascular system, has remained challenging2. Here we generate a functional small intestinalized colon (SIC) by replacing the native colonic epithelium with ileum-derived organoids. We first find that xenotransplanted human ileum organoids maintain their regional identity and form nascent villus structures in the mouse colon. In vitro culture of an organoid monolayer further reveals an essential role for luminal mechanistic flow in the formation of villi. We then develop a rat SIC model by repositioning the SIC at the ileocaecal junction, where the epithelium is exposed to a constant luminal stream of intestinal juice. This anatomical relocation provides the SIC with organ structures of the small intestine, including intact vasculature and innervation, villous structures, and the lacteal (a fat-absorbing lymphatic structure specific to the small intestine). The SIC has absorptive functions and markedly ameliorates intestinal failure in a rat model of SBS, whereas transplantation of colon organoids instead of ileum organoids invariably leads to mortality. These data provide a proof of principle for the use of intestinal organoids for regenerative purposes, and offer a feasible strategy for SBS treatment.

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Fig. 1: Xenotransplanted human ileum organoids rebuild villus structures in the mouse colon.
Fig. 2: Two-dimensional culture of human small intestinal and colon organoids.
Fig. 3: Generation of SIC.
Fig. 4: Therapeutic effect of SIC in rat SBS models.

Data availability

Raw RNA-seq data have been deposited to the Japanese Genotype-phenotype Archive under accession number JGAS000256. The approved ethical protocol requires that the raw data be deposited at the National Bioscience Database Center (NBDC; https://biosciencedbc.jp/en/) and available under controlled access for protection of patients’ privacy. Data users need to fulfil the NBDC Guidelines for Human Data Sharing (https://humandbs.biosciencedbc.jp/en/guidelines/data-sharing-guidelines) and the NBDC Security Guidelines for Human Data (for Data Users) (https://humandbs.biosciencedbc.jp/en/guidelines/security-guidelines-for-users). In detail, data users need to conform to the following requirements. First, indicate that the head of the institution to which the data users belong has given permission to implement the research plan that includes the dataset the data users plan to use. Second, provide evidence that the data users have engaged in research related to the dataset the data users plan to use. Third, indicate that the data users have implemented security measures appropriate to the access level of the dataset the data user plans to use. Fourth, obtain approval from the NBDC Human Data Review Board (details on how to apply can be found at https://humandbs.biosciencedbc.jp/en/data-use). The read count data are freely available from Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE163706. Whole 16S rRNA sequencing data are freely available from the DNA Data Bank of Japan (DDBJ; https://www.ddbj.nig.ac.jp/index-e.html) under accession number DRA009677. Source data are provided with this paper.

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Acknowledgements

This work was in part supported by the Japan Agency for Medical Research and Development (AMED)–CREST (grant number JP20gm1210001), AMED (grant number JP20bm0304001), JSPS KAKENHI (grant numbers 20H03746 and JP17H06176), The Mochida Memorial Foundation for Medical and Pharmaceutical Research, and Keio University Academic Development Funds. K.T. was supported by the Japan Society for the Promotion of Science Research Fellowships for Young Scientists. We thank the Collaborative Research Resources and JSR–Keio University Medical and Chemical Innovation Center (JKiC), Keio University School of Medicine for technical support (T. Tajima from Olympus).

Author information

Affiliations

Authors

Contributions

S.S., E.K. and Y.H. performed and analysed animal experiments. E.K. developed the surgical techniques for SIC generation. S.S., Y.O., K.I. and S.T. performed imaging analyses. S.S., M.F., K.A., M.M. and K.N. established and cultured the organoids. S.S., Y.O. and K.T. analysed the data. K.M. carried out sequencing of faecal 16S rRNA and microbial analyses. T.K. provided materials and resources. S.S., E.K. and T.S. conceived the project and designed experiments. S.S., M.F. and T.S. wrote the manuscript with input from the other authors.

Corresponding authors

Correspondence to Eiji Kobayashi or Toshiro Sato.

Ethics declarations

Competing interests

T.S. is an inventor on several patents related to organoid culture, which are not directly based on the current work. K.A. is an employee of JSR Corporation. A patent application for the technology involved in rotating monolayer organoid cultures and cultured organoids was filed on 3 December 2020 (Japanese Patent Application 2020-201332); the applicants are Keio University and JSR Corporation; the inventors are T.S., S.S. and K.A. All other authors declare no competing interests.

Additional information

Peer review information Nature thanks Robert Cowles, Kim Jensen, Matthias Lutolf and Christopher Stewart for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 Histological and ultrastructural analysis of xenotransplanted human ileum tissue.

a, Toluidine blue staining of a xenotransplanted human ileum tissue. b, Representative TEM images of enterocytes and goblet cells, Paneth cells and enteroendocrine cells. c, Immunostaining of IBAT in xenotransplanted ileum and colon epithelium. d, Representative images of the areas used to measure LYVE-1-positive lacteal vessels in human ileum (n = 6) and colon (n = 10) xenografts. Regions surrounded by black lines are xenografts of human tissues. White arrowheads show lacteals. e, Area of enclosed LYVE-1-positive lacteal vessels per crypt in human ileum (n = 6) and colon (n = 10) xenografts. f, Representative images of podoplanin (D2-40)-positive lacteal vessels in human ileum (n = 3) and colon (n = 3) tissues. g, Area of enclosed podoplanin-positive lacteal vessels per crypt in human ileum (n = 3) and colon (n = 3). ad, f, Representative images from two (a, b), three (c, f) and six or ten (d) biologically independent samples analysed with similar results. Scale bars, 4 μm (b), 100 μm (c), 200 μm (a) and 500 μm (d, f). e, g, Bars represent means (e, g). *P = 0.041 (two-sided Welch’s t-test) (e).

Source data

Extended Data Fig. 2 Analysis of 2D human duodenum and ileum organoids.

a, Microscopic views of 2D ileum organoids cultured for four days after confluence in the presence (bottom) or absence (top) of continuous medium agitation. Shown is histopathology (haematoxylin-and-eosin staining, H&E) of the vertical cross-sectional view for each condition. b, Multiphoton imaging of 2D ileum organoids with flow (LGR5 reporter, red). c, Immunofluorescence staining of ACE2 in flow-stimulated 2D duodenum organoids and a human duodenum tissue. d, Immunofluorescence staining of Ki67 and markers of differentiated intestinal cells in 2D duodenum organoids with (top) or without (bottom) flow. e, Hierarchical clustering of 2D duodenum organoids after 0, 1, 2 or 4 days of medium rotation, using genes that were differentially expressed among the time points. f, Staining of sucrase-isomaltase and IBAT in 2D cultures of ileum organoids with or without continuous flow. g, Left, TEM images of 2D ileum organoids. Right, length of microvilli in 2D ileum organoids with or without flow. bd, Nuclear counterstaining is in white. a, Representative images from ten experiments with similar results using two different organoid lines (n = 2). bd, f, g, Representative images from one (g), two (b) and three (c, d, f) experiments with similar results. Scale bars, 1 μm (g, right), 4 μm (g, left), 50 μm (c, d), 100 μm (b) and 200 μm (a, f). g, Centre lines show means; ***P < 0.001 (one-way ANOVA with post-hoc Tukey’s multiple comparison test).

Source data

Extended Data Fig. 3 Surgical procedures for performing jejunoileal resection in rats.

a, b, Diagrams and images showing total (a) and subtotal (b) jejunoileal resection. In the subtotal resection group, 3 cm of the terminal ileum was preserved. White arrowheads indicate anastomosis sites.

Extended Data Fig. 4 Rat SBS models.

a, Diagrams showing the SBS models. In the total resection group, jejunoileum from the beginning of the jejunum to the terminal ileum was resected. In the subtotal resection group, 3 cm of the terminal ileum was preserved. b, c, Changes in body weight (b) and overall survival (c) of the rats in the control (n = 4; black), subtotal resection (n = 4; orange) and total resection (n = 4; blue) groups. Data are normalized to the body weight at day 0. Each cross mark shows that the rat was killed according to the euthanasia criteria. Boxed crosses represent scheduled euthanasia for sample analysis. P = 0.002; two-sided log-rank test (c). d, Serum levels of vitamin B12, albumin and total cholesterol in each group (n = 4 each). Bars represent mean values, with data collected from two independent experiments. d, *P = 0.032; **P = 0.002; ***P < 0.001 (one-way ANOVA with post-hoc Tukey’s multiple comparison test).

Source data

Extended Data Fig. 5 Rat SBS models with various patterns of jejunoileum preservation.

a, Diagrams showing the SBS models. In the total resection group, jejunoileum from the beginning of the jejunum to the terminal ileum was resected. In the subtotal resection group, 1 cm of the terminal ileum was preserved. b, c, Changes in body weight (b) and overall survival (c) of rats in the subtotal resection (n = 5; green) and total resection (n = 5; blue) groups. P = 0.008; two-sided log-rank test (b). d, Diagrams showing SBS models with jejunum preservation. In the total resection group, 4 cm of the jejunum were preserved; the ileum was not. In the subtotal resection group, 4 cm of the jejunum and 1 cm or 3 cm of the terminal ileum were preserved. e, f, Changes in body weight (e) and overall survival (f) of rats in the control (n = 3; black), subtotal resection (1 cm, n = 5, green; 3 cm, n = 3, orange) and total resection (n = 3; blue) groups. P = 0.025; two-sided log-rank test for trend (f). Data are normalized to the body weight at day 0 (b, e). Each cross shows that the rat was killed according to euthanasia criteria. Boxed crosses represent scheduled euthanasia for sample analysis.

Source data

Extended Data Fig. 6 Gene-expression profiles in rat jejunum and ileum organoids.

a, b, Expression of Gip, Pdx1 (a), Slc10a2 (IBAT) and Reg3g (b) in rat jejunum, ileum and colon organoids in the presence or absence of afamin/WNT3A and noggin. Expression values are shown relative to Actb expression. Data are means ± s.e.m. N.D., not detected. Data are representative of two independent experiments performed in technical triplicate with similar results.

Source data

Extended Data Fig. 7 Transplantation of rat ileum organoids and the refined anastomosis method.

a, Procedures for organoid transplantation, showing clamping of vessels in the dissected colon (left), transplantation of colon or ileum organoids (middle) and retention of organoids in the lumen (right). b, H&E staining of control colon and epithelium-removed colon; and H&E and sucrose-isomaltase staining of epithelium-removed colonic segment one week after organoid transplantation. c, Diagrams and images showing the conventional and refined methods for anastomosing the start of the jejunum and the oral side of SIC. Each end of the intestine was diagonally cut to broaden the calibre of the anastomosis and to prevent stenosis. d, Crypt-villus lengths in the rat control ileum, transplanted ileum in stoma, and transplanted ileum in interposition (n = 3 rats each, n = 20 crypts each). The crypt-villus length was measured by an independent researcher in a blinded manner. e, Diagram and image of the SIC returned to its initial position one week after the initial surgery. f, H&E and sucrase-isomaltase staining of the transplanted ileum returned to the initial position one month after organoid transplantation. g, Alcian blue/PAS staining of the transplanted ileum, control colon and ileum. c, e, White arrowheads indicate anastomosis sites. b, f, g, Representative images from three (b) and four (f, g) biologically independent samples analysed with similar results; scale bars, 50 μm (b) and 200 μm (f, g). d, Centre lines show means; ***P < 0.001 (one-way ANOVA with post-hoc Tukey’s multiple comparison test).

Source data

Extended Data Fig. 8 Histopathology of transplanted ileum and colon epithelium in the rat colostomy.

a, Sucrase-isomaltase staining of the transplanted ileum returned to the interposition (days 1, 2, 4, 7, 10 and 30). b, Percentage of sucrose-isomaltase-positive crypt-villus lengths in the rat control ileum, transplanted ileum in stoma at the time of interposition, and transplanted ileum in interposition in each time point (n = 20 or 40 crypts each). c, Co-staining of luciferase ISH (red; transplanted cells) and Muc2 (green; goblet cells) in SIC. df, Rat Lgr5 ISH (red; stem cells) and lysozyme staining (green; Paneth cells) in SIC. White arrowheads indicate Paneth cells (d). The areas framed with white lines in d are shown in higher magnification in e, f. g, Luciferase ISH (red) and NPC1L1 staining (green) in the transplanted ileum (left) and colon (right) epithelium. h, The border between the recipient colon and transplanted ileum epithelium in the interposed SIC, identified by H&E (top) and Alcian blue/PAS (bottom) staining. i, Representative bioluminescent images of ileum organoid-transplanted rats, showing stable engraftment of luciferase-positive grafts. j, Estimated area of engrafted luciferase-positive transplanted ileum (n = 5; red) and colon (n = 3; blue) organoids in criteria-based or scheduled euthanized rats. k, l, Immunostaining of TUBB3 (k) and S100 (l) in the transplanted ileum and control ileum. m, Whole-mount staining of LYVE-1 in colon organoid-transplanted tissue. n, Immunostaining of CD31 in the transplanted ileum tissue. Insets show higher magnification. c, d, h, White dotted line indicates the margin between the colon and transplanted ileum epithelium. a, ch, kn, Representative images from one (a), two (cg, km), three (n) and ten (h) biologically independent samples analysed with similar results; scale bars, 50 μm (e, f), 100 μm (c, d, g) and 200 μm (a, h, kn). cg, kn, Nuclear counterstaining is in white. b, Centre lines show medians; ***P < 0.001 (one-way ANOVA).

Source data

Extended Data Fig. 9 Absorptive analysis of AMCA peptide and NBD–glucose in SIC.

a, b, Representative images of the superficial epithelium (colon, ileum, ileum-transplanted tissue, or colon-transplanted tissue) after exposure to AMCA peptide (a) or NBD–glucose (b) with or without the indicated inhibitors. c, d, Comparison of the sums of AMCA (c) or NBD (d) intensities divided by the total nucleus area per single microscopic field in each tissue. Each dot represents one microscopic field (n = 10 field, each) and each colour shows an individual experiment. ad, Results are shown from three (control colon and control ileum), four (ileum-transplanted tissue) and two (colon-transplanted tissue) biologically independent samples with similar results. a, b, Scale bars, 100 μm; white, nuclear counterstaining. c, d, Centre lines show medians; box limits show upper and lower quartiles; whiskers show 1.5 × interquartile range.

Source data

Extended Data Fig. 10 Faecal microbial profile of SBS rats.

a, Left, PCoA based on the Bray–Curtis dissimilarity of bacterial community structures for rat faecal microbiota from the control (n = 6), total resection (0 cm; n = 8), subtotal resection (1 cm, n = 5; 3 cm, n = 4) and transplanted (colon, n = 4; ileum, n = 4) groups. Right, distribution of Bray–Curtis distances between the microbiota of each group. A distance of 0 represents an identical microbiota composition; 1 represents a complete dissimilarity. b, Number of OTUs in the faecal microbiota of the control (n = 6), total resection (0 cm; n = 8), subtotal resection (1 cm, n = 5; 3 cm, n = 4) and transplanted (colon, n = 4; ileum, n = 4) groups. ce, Bar charts showing LDA effect size scores of taxa that are differentially abundant among groups. Red bars represent the relative abundance of microbiota identified in healthy control rats (c) that are also identified in the ileum organoid-transplanted group (d, e). Blue bars represent the relative abundance of microbiota identified in the total resection group (d) or the colon organoid-transplanted group (e) that are also identified in the total resection group in c. a, Right, centre lines show medians; box limits show upper and lower quartiles; whiskers show 1.5 × interquartile range. f_, species of the family; g_, species of the genus; g__, undefined species of the genus. b, Data are shown as means ± s.d. a, b, *P = 0.033; **P = 0.001; ***P < 0.001 (one-way ANOVA with post-hoc Tukey’s multiple comparison test).

Source data

Supplementary information

Supplementary Table

Supplementary Table 1. List of sequences of qPCR primers.

Reporting Summary

Video 1

: Whole-mount staining of Lyve-1 in a human ileum xenograft. Whole-mount Lyve-1 staining (red) of a human ileum xenograft tissue (blue; RFP, right) overlaid with NBD cholesterol fluorescence (green; NBD, left).

Video 2

: Generation of luminal flow on a rotary shaker. Human intestinal organoid monolayers were cultured on ThinCert 24-well plates, and medium flow was generated by shaking them on a rotary shaker at 150 rpm.

Video 3

: Whole-mount image of monolayer human duodenum organoids cultured with continuous flow. Multi-photon Z stack images of monolayer cultured human duodenum organoids. Membrane counterstaining; red. Nuclear counterstaining; white. Scale bar, 100 μm.

Video 4

: Periodic peristalsis of organoid-transplanted colon segment. Periodic peristalsis of ileum organoid-transplanted colon segment interposed between the jejunum and ileum ends with metoclopramide administration (4× speed). Bioluminescent images of SIC (left) demonstrates stable engraftment of Luciferase+ organoids.

Video 5

: 3D-reconstruction of a Lyve-1+ lacteal in SIC. Whole-mount staining of Lyve-1 (red) in an ileum organoid-transplanted rat tissue. Nuclear counterstaining; white.

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Sugimoto, S., Kobayashi, E., Fujii, M. et al. An organoid-based organ-repurposing approach to treat short bowel syndrome. Nature 592, 99–104 (2021). https://doi.org/10.1038/s41586-021-03247-2

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