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Engineering transplantable jejunal mucosal grafts using patient-derived organoids from children with intestinal failure

Abstract

Intestinal failure, following extensive anatomical or functional loss of small intestine, has debilitating long-term consequences for children1. The priority of patient care is to increase the length of functional intestine, particularly the jejunum, to promote nutritional independence2. Here we construct autologous jejunal mucosal grafts using biomaterials from pediatric patients and show that patient-derived organoids can be expanded efficiently in vitro. In parallel, we generate decellularized human intestinal matrix with intact nanotopography, which forms biological scaffolds. Proteomic and Raman spectroscopy analyses reveal highly analogous biochemical profiles of human small intestine and colon scaffolds, indicating that they can be used interchangeably as platforms for intestinal engineering. Indeed, seeding of jejunal organoids onto either type of scaffold reliably reconstructs grafts that exhibit several aspects of physiological jejunal function and that survive to form luminal structures after transplantation into the kidney capsule or subcutaneous pockets of mice for up to 2 weeks. Our findings provide proof-of-concept data for engineering patient-specific jejunal grafts for children with intestinal failure, ultimately aiding in the restoration of nutritional autonomy.

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Fig. 1: Generation and characterization of primary intestinal organoids derived from the target pediatric patient group.
Fig. 2: Decellularization and biomolecular characterization of human SI and colon scaffolds.
Fig. 3: Bioengineering functional human jejunal mucosal grafts in vitro.
Fig. 4: Characterization of the engineered jejunal graft following in vivo transplantation.

Data availability

The data that support the findings of this study are available within the paper and its supplementary information files. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via PRIDE partner repository with the dataset identifier PXD019816, available for download at publication. Source data are provided with this paper.

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Acknowledgements

We thank STEMCELL Technologies for providing organoid culture reagent, A. Darbyshire for assistance with mechanical testing data, F. Scottoni for his surgical assistance in collecting pig intestine and B. Jones, P.S. Chia, SNAPS and the Gastroenterology Unit at GOSH for coordinating patient material and information. We also thank the Francis Crick Institute’s Science Technology Platforms, Experimental Histopathology (E. Nye), Electron Microscopy, Mass Spectrometry Proteomics, Mechanical Engineering, Biological Resources Facility and In Vivo Imaging, for their technical support and advice and J. Brock from the Research Illustration & Graphics team for the contributions to figure illustration. This work was funded by Horizon 2020 grant INTENS 668294 on the project ‘Intestinal Tissue Engineering Solution for Children with Short Bowel Syndrome’. The laboratory of V.S.W.L. is funded by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001105), the UK Medical Research Council (FC001105) and the Wellcome Trust (FC001105). P.D.C. is supported by an NIHR Professorship, NIHR UCL BRC-GOSH, the Great Ormond Street Hospital Children’s Charity and the Oak Foundation. L.M. and L.T. are funded by NIHR UCL BRC-GOSH Crick Clinical Research Training Fellowships. P.B. is supported by the European Research Council (no. 639429), the Rosetrees Trust (M553; M362-F1), the UCL Therapeutic Acceleration Support Fund (MRC CiC) and the National Institute for Health Research Biomedical Research Centre at Great Ormond Street Hospital for Children NHS Foundation Trust (GOSH BRC). S.C. was supported by GOSHCC Studentship V6116.

Author information

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Authors

Contributions

P.D.C. and V.S.W.L. conceived the project. L.M., P.D.C. and V.S.W.L. designed the study and wrote the manuscript. L.M. performed the experiments and analyzed data. A.K., L.T., I.M. and A.B. supported histology analyses. L.T. and I.M. performed mechanical testing experiments and supported in vitro cultures and in vivo graft analyses. L.M., A.E.W., E.H., J.K. and L.C. performed electron microscopy experiments and analyses. L.M., R.G. and G.M.H.T. performed Raman spectroscopy experiments and analyses. L.M., P.F. and A.P.S. performed mass spectrometry experiments and analyses. L.M., I.M., L.T., M.O. and S. Eaton performed functional analyses of the engineered intestinal grafts. L.N. and I.M. performed western blot analyses and supported in vivo teduglutide experiments. N.A. and I.M. performed qPCR analysis of the organoids. A.F.P., A.M.T. and S. Eli performed piglet scaffold decellularization experiments. S.C. and P.B. performed in vivo transplantation experiments. N.T. coordinated human tissue collection. L.M., I.M., S. Eaton, P.B., P.D.C. and V.S.W.L. critically discussed the data and manuscript.

Corresponding authors

Correspondence to Paolo De Coppi or Vivian S. W. Li.

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The authors declare no competing interests.

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Peer review information Michael Basson and Brett Benedetti were the primary editors on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Extended data

Extended Data Fig. 1 Characterization of human jejunal organoids.

a, Quantitative RT-qPCR analysis of native tissue and human organoids for jejunal specific markers LCT and SI. Data represents mean ± s.e.m.: tissues, n=2 biologically distinct jejunal tissue samples [patients 22, 27]), and n=3 biologically distinct duodenal [patients 26, 27, 28] and ileal [patients 21, 25, 27]) samples; organoids, n=3 experimental replicates [patients 2, 10, 14]. Differences were analyzed by one-way ANOVA with Dunnett’s multiple comparisons test in organoid samples: LCT, Jejunum (J) versus Duodenum (D), p=0.0569, J versus Ileum (I), p=0.057; SI, J versus D, ***P=0.0002, J versus I, **P=0.0021. b, Immunostaining of patient 2 jejunal organoids in basal conditions, expansion culture (+CHIR) and differentiation culture (+DAPT) to mark presence of goblet cells (UEA-1). Scale bars represent 50µm. The experiment was performed once. c, Representative Western blot analysis of protein levels of SI, Sox9, Olfm4 and lysozyme in patient 2 jejunal organoids in basal, expansion (+CHIR) and differentiation (+DAPT) conditions, performed with 3 experimental replicates. d, Quantitation of Western blot in c. Data represent mean ± s.e.m. of n=3 experimental organoid culture replicates. One-way ANOVA with Dunnett’s multiple comparisons test: SI, basal (B) versus +CHIR (C), p=0.7279, B versus +DAPT (D), p=0.2719; SOX9, B versus C, p=0.6833, B versus D, p=0.7112; OLFM4, B versus C, **p=P 0.0051, B versus D, p=0.5715; LYZ, B versus C, p=0.9731, B versus D, p=0.684.

Source data

Extended Data Fig. 2 Piglet scaffold characterization and extended human scaffold characterization.

a, Representative H&E images and DAPI immunostainings of a native piglet intestine and following one and two cycles of DET. Scale bars represent 100µm. b, Quantification of DNA, glycosaminoglycans (GAGs) and collagen per milligram of wet tissue in native piglet intestine and following one and two cycles of DET. Data represent mean ± s.e.m of n = 3 biologically distinct piglet intestine samples (DNA and GAG quantification) and of n = 2 biologically distinct samples (collagen quantification). One-way ANOVA with Dunnett’s multiple comparisons test: DNA, ****p <0.0001 (Native versus cycles I and Native versus cycle II); GAG, p=0.4055 (Native and cycle I) and **p=0.0036 (Native and cycle II). The experiment was performed once. c, Representative histology images of Elastic Van Gieson (EVG) and Alcian blue (AB) stainings confirm preservation of elastin and GAGs respectively following one and two cycles of DET. Masson’s trichrome (MT) and Picro-sirius red (PS) histological stainings confirms maintenance of connective tissue and collagens following one and two cycles of DET. Scale bars represent 200µm. d, Representative immunohistochemical staining for Collagen I (Col-1), Collagen IV (Col-4), Fibronectin, Laminin indicating the preservation of these ECM proteins in a piglet scaffold following two cycles of DET. Scale bars represent 100µm. Images are representative of 3 biological replicates. e, Stress-strain curves of human colon [patients 19, 20, 21] and small intestinal [patients 21, 23, 24] scaffolds and calculated Young’s modulus. Data represent mean ± s.e.m. of n = 3 biologically distinct patient samples. No significant difference identified between human SI and colon samples; unpaired t test, p=0.5871. The experiment was performed once. f, PC1 loading plot associated with the PC1 vs PC2 scores plot shown in Fig. 2f. The spectral features show distinct biochemical differences that facilitate the differentiation of the mucosal region of the SI [patient 1] and colon [patient 18] from the remaining intestinal layers (submucosa and muscularis propria). The intensity of the corresponding peaks found within the loadings plot indicate their influence on the separation in the scores plotted along the associated axis. g,h, Representative immunohistochemical staining of the native pediatric SI [patient 1] and colon [patient 18] tissue using the indicated antibodies, n = 2 biologically distinct patient tissue samples. Scale bars represent 100μm.

Source data

Extended Data Fig. 3 Characterization of human intestinal fibroblasts and the jejunal grafts reconstructed on human scaffold.

a, Representative immunofluorescent images of primary human jejunal fibroblasts [patient 2] showing fibronectin (F-NEC, yellow), vimentin (VIM, green), fibroblast surface protein marker-1 (FSP-1, magenta), laminin alpha 5 (LAMA5, cyan) and alpha-smooth muscle actin (αSMA, red). b, Representative images showing a blank scaffold (left), after stromal cell injection (middle) and during organoid seeding (right) on a mounting stage. c, Photos showing the media reservoir (left), peristaltic pump (middle) and the perfusion plate (right) of the bioreactor. d, Representative immunofluorescent staining of an engineered graft [patient 7 fibroblasts; patient 2 colon scaffold] using the indicated antibodies. e, Electron micrograph showing a monolayer of epithelial cells on a graft [SI scaffold - patient 5]. All scale bars represent 50μm. All organoids used in this figure were from patient 2. Images are representative of cells from 3 independent experimental cultures (a) or 4 grafts (d,e).

Extended Data Fig. 4 Characterization of the human jejunal graft reconstructed on piglet scaffold.

a, 3D volume rendering of micro CT virtual slices showing jejunal epithelial layer (bright white and indicated by orange arrowheads) on a piglet scaffold (outlined by dashed white line) at different angles. Scale bars indicate 1mm. b, Representative H&E staining of a jejunal graft showing epithelial lining with invaginated crypts (black arrowheads). c, H&E staining of a jejunal graft showing regions of columnar epithelial monolayers (bottom right) as well as regions of new matrix deposition (black asterisks, top and bottom left). d, New matrix deposition indicated by black asterisk in H&E image (top) stains positive for collagen-1 (magenta, white asterisk, bottom). e-i, Representative immunohistochemistry images of engineered jejunal grafts using the indicated antibodies. Paneth-like cells are indicated with red arrowheads in (e) and goblet-like cells are indicated with yellow arrowheads in (f). All scale bars represent 50μm unless specified otherwise. Images are representative of 3 independently cultured grafts. All organoids in this figure originate from patient 2.

Extended Data Fig. 5 Histological characterization of the transplanted grafts.

a, Serial H&E staining of a jejunal graft 1 week after transplantation in vivo under the kidney capsule. Lumen are indicated by L. b, Luminal ring (L) of jejunal graft is negative for goblet cell (Alcian Blue - Periodic Acid Schiff, AB-PAS) and enterocyte brush border markers (Alkaline Phosphatase). c, Western blot analysis confirming the expression of the GLP2R in human jejunal fibroblasts and jejunal organoids [both from patient 2] when co-cultured in vitro. The experiment was performed once. d, H&E staining (left) of luminal ring (L) of intestinal epithelium present on grafts [patient 2 colon scaffold] harvested following 2 weeks of subcutaneous transplantation from mice exposed to Teduglutide and immunofluorescence staining of CD31 (right, green) indicating endothelial cell presence in the same graft. All data from subcutaneous Teduglutide transplantation experiments were performed with n=4 jejunal grafts per condition. e, Macroscopically visible neovascularization (red arrowhead) on a transplanted graft (white outline) formed of human SI scaffold [patient 24]. f, Quantification of jejunal graft vessel (left) and lumen formation (right) per scaffold following subcutaneous implantation with or without HUVEC co-seeding, measured as the percentage of sections with vessels (left) or lumen (right) per graft. Subcutaneous transplantation HUVEC experiments were performed with n=6 grafts [human SI scaffold - patient 1 & 24; human colon scaffold - patient 2]. Grafts that contained vessels upon harvest in the HUVEC group are indicated by red dots. Data represent mean ± s.e.m. Unpaired student’s t-test: vessels, p=0.7411; lumen, p=0.2066. g, Representative image indicating the proximity of blood vessels (red arrowheads) to the epithelial lumen (L) in a jejunal graft co-seeded with HUVECs. h, Representative immunostaining of an engineered jejunal graft co-seeded with HUVECs using the indicated antibodies and stainings. Lumen are indicated by L. Images are representative of 3 grafts (a,b) 4 grafts (d) and 2 grafts (e,g,h). All intestinal epithelial cells in this figure originate from patient 2 jejunal organoids. Jejunal fibroblasts in this figure originate from patient 7. All scale bars represent 50μm unless specified otherwise.

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Supplementary Tables 4–7

Reporting Summary

Supplementary Tables

Supplementary Tables 1–3

Supplementary Video 1

3D reconstruction video of jejunal graft transplanted under the kidney capsule.

Source data

Source Data Fig. 1

Statistical source data.

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Source Data Extended Data Fig. 1

Unprocessed western blots.

Source Data Extended Data Fig. 1

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Source Data Extended Data Fig. 5

Unprocessed western blots.

Source Data Extended Data Fig. 5

Statistical source data.

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Meran, L., Massie, I., Campinoti, S. et al. Engineering transplantable jejunal mucosal grafts using patient-derived organoids from children with intestinal failure. Nat Med 26, 1593–1601 (2020). https://doi.org/10.1038/s41591-020-1024-z

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