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Stomach-derived human insulin-secreting organoids restore glucose homeostasis

Nature Cell Biology volume 25, pages 778–786 (2023)Cite this article

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Abstract

Gut stem cells are accessible by biopsy and propagate robustly in culture, offering an invaluable resource for autologous cell therapies. Insulin-producing cells can be induced in mouse gut, but it has not been possible to generate abundant and durable insulin-secreting cells from human gut tissues to evaluate their potential as a cell therapy for diabetes. Here we describe a protocol to differentiate cultured human gastric stem cells into pancreatic islet-like organoids containing gastric insulin-secreting (GINS) cells that resemble β-cells in molecular hallmarks and function. Sequential activation of the inducing factors NGN3 and PDX1-MAFA led human gastric stem cells onto a distinctive differentiation path, including a SOX4High endocrine and GalaninHigh GINS precursor, before adopting β-cell identity, at efficiencies close to 70%. GINS organoids acquired glucose-stimulated insulin secretion in 10 days and restored glucose homeostasis for over 100 days in diabetic mice after transplantation, providing proof of concept for a promising approach to treat diabetes.

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Fig. 1: Generation of GINS organoids from human stomach samples.
Fig. 2: GINS organoids secrete human insulin in response to glucose and GLP-1 analogue.
Fig. 3: Four endocrine cell types identified in GINS organoids by scRNA-seq.
Fig. 4: Transplanted GINS organoids secrete human insulin and reversed diabetes in mice.
Fig. 5: Developmental trajectory of GINS cells.
Fig. 6: Galanin+ precursors give rise to GINS cells.

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Data availability

Sequencing data that support the findings of this study have been deposited in the GEO under accession code GSE205766. Previously published human islet scRNA-seq data (donors 1, 2, 3, 4 and 9) (ref. 30) that we re-analysed in this study are available under accession code GSE114297 (ref. 30). Source data are provided with this paper. All other data supporting the findings of this study are available from the corresponding author on reasonable request.

Code availability

Code for the data analysis is available at https://github.com/stevehxf/GINS_NCB2023.

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Acknowledgements

We thank X. He from Children’s Hospital Boston for the RS2 cell line, S. Houghton and D. Redmond for initial processing of the scRNA-seq data and for bioinformatic advice, the Starr Foundation Tri-Institutional Stem Cell Derivation Laboratory (R. Lis and T. Lu) and WCM Flow Cytometry Core Facility (J. McCormick and T. Baumgartner) for flow cytometry. We thank C. Martin for reviewing the paper. We thank WCM CLC Microscopy & Image Analysis Core (L. Cohen-Gould and J. Pablo Jimenez) for transmission electron microscopy, and WCM Genomics Resources Core Facility (J. Xiang, X. Wang and D. Xu) for 10x Genomics and next-generation sequencing. We are grateful to A. Chi Nok Chong and S. Chen for helping with dynamic GSIS, The National Disease Research Interchange and the International Institute for the Advancement of Medicine for providing some of the human samples, and Prodo lab for supplying human islets. This work was supported by awards from NIDDK (R01 DK106253, R01 DK13332, R01 DK125817 and UC4DK116280 awarded to Q.Z. and P30 DK034854 to D.T.B.).

Author information

Author notes

  1. Jian Zhu

    Present address: Department of Endocrinology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China

Authors and Affiliations

  1. Division of Regenerative Medicine and Hartman Institute for Therapeutic Organ Regeneration, Department of Medicine, Weill Cornell Medicine, New York, NY, USA

    Xiaofeng Huang, Wei Gu, Jiaoyue Zhang, Ying Lan, Jonathan L. Colarusso, Sanlan Li, Christoph Pertl, Jiaqi Lu, Hyunkee Kim, Jian Zhu & Qiao Zhou

  2. Division of Endocrinology, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA, USA

    David T. Breault

  3. Harvard Stem Cell Institute, Cambridge, MA, USA

    David T. Breault

  4. Département de Microbiologie-Infectiologie et d’Immunologie, Faculté de Médecine, Université Laval, Quebec City, Quebec, Canada

    Jean Sévigny

  5. Centre de recherche du CHU de Québec-Université Laval, Quebec City, Quebec, Canada

    Jean Sévigny

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Contributions

X.H. and Q.Z. designed all the experiments, interpreted data, and wrote the paper. X.H. performed all the experiments and the scRNA-seq data analysis. W.G. participated in all the animal surgery. J. Zhang and Y.L. were involved in stomach sample processing, gastric stem cell isolation and cell line establishment. J.L.C. collected data from the animal experiments. S.L. performed independent validation of the functionality of the GINS organoids. W.G., J. Zhang, C.P., J.L., H.K. and J. Zhu contributed to conducting preliminary experiments. D.T.B. provided some of the human gastric samples. J.S. produced antibodies against ENTPD3 (NTPDase3).

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Correspondence to Qiao Zhou.

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Nature Cell Biology thanks Eiji Yoshihara and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 Optimizing conditions to induce insulin-expressing cells from cultured human gastric stem cells.

a, Top: stomach samples from 3 different donors; middle, primary hGSC colonies derived from the stomach samples; bottom, immunofluorescence of passage-10 hGSC colony staining for SOX9 and KI67. b, Growth kinetics of hGSCs from three different donors. c, Co-expression of Ngn3, Pdx1, and Mafa using a polycistronic inducible construct in hGSCs yielded low levels of insulin expression (n=3 biological independent samples). Ubc: ubiquitin promoter. d, To optimize the relative timing of Ngn3 and Pdx1- MafA expression, we expressed a Ngn3ER fusion protein in which Ngn3 activity was induced by 4-OH Tamoxifen (4-OH-TAM). Polycistronic PDX1 and MAFA co-expression was controlled by rtTA-TetO and activated by the addition of Doxycycline in the culture medium. Higher INS expression was achieved by sequential activation of the transcription factors NGN3 and PDX1-MAFA. n=3 independent experiments. e, Comparison of PDX1-MAFA with the other transcription factor combinations in insulin induction. 2-day Ngn3ER induction (by 4-OH-TAM) preceded the other TFs, or alternatively, co-expression cassettes were used. ND: not detected. n=3 independent experiments. c, d, e, Data presented as mean ± s.d.; two-tailed unpaired t-test (c), or one-way ANOVA with Dunnett multiple comparisons test (d, e).

Source data

Extended Data Fig. 2 Formulating chemically defined serum-free medium for GINS organoid differentiation.

a, Experimental design for the supplement screen. Ngn3ER: fusion gene in which NGN3 activity was induced by 4-OH-TAM. Polycistronic PDX1 and MAFA co-expression was controlled by rtTA-TetO and activated by the addition of Doxycycline in the culture medium. mCherry was co-expressed with Ngn3ER in the cell line. Ngn3 was activated from day 0 to day 2. Culture medium was switched to a basal serum-free medium (advanced DMEM/F12, 10 mM HEPES, 1X GlutaMAX, 1X B-27, 1X N-2, and 500 μM N-Acetyl-L-Cysteine) on day 2 with addition of a single supplement and Doxycycline. b, The list of supplements that were screened and the pathways they targeted. Up and down arrows indicate agonists or antagonists, respectively. c, Relative expression of INS mRNA on day-7 post differentiation in comparison with no supplement control. N = 3 (treatments) or 5 (control) independent samples. Nicotinamide and Y-27632 treatment significantly up-regulated INS. d, Spontaneous clustering of cells was evaluated by mCherry live imaging on day-7 post differentiation. Select conditions were shown. A8301 treatment had the most observable clustering effect on the nascent GINS cells. Repeated independently 3 times with similar results. e, Relative expression of β-cell markers measured on day-7 post differentiation in comparison with no supplement control. N = 6 independent samples. c, e, Data presented as mean ± s.d.; one-way ANOVA (c), or two-way ANOVA (e) with Holm–Sidak’s multiple comparisons test.

Source data

Extended Data Fig. 3 Molecular and functional characterization of GINS organoids derived from multiple donors.

a, Schematic diagram and representative images of cells at key stages in GINS organoid formation. Ngn3ER-hGSCs: human gastric stem cells that incorporated a Ngn3 and estrogen receptor (ER) fusion gene (Ngn3ER); 4-OH-TAM: 4-OH Tamoxifen; Lenti-CMV-PM, lentiviral integration of a polycistronic Pdx1-Mafa co-expression cassette. b, Representative immunofluorescent staining of corpus GINS organoids derived from three different donors, and co-localization of INS and CPPT in GINS cells. a, b, Repeated independently 3 times with similar results. c, To assess CPPT+ mono-hormonal cells, a cocktail of GCG, SST and GHRL antibodies were stained together with CPPT in day-21 GINS organoids. Right panel shows immunofluorescent staining of CPPT (red) and a combination of GCG, GHRL and SST (green). left panel shows quantification of mono-hormonal CPPT+ cells (n = 10 organoids from donor #6). d, Relative expression of endocrine hormone genes including INS, GCG, SST, and GHRL in day-18 GINS organoids derived from four different donors in comparison with human islets. n = 4 (donor#6) or 3 (donor#7, #9, #10, or islet donors) separate batches of samples for each donor. e, Relative expression of key β-cell markers in GINS organoids derived from different donors in comparison with human islets. n = 4 (donor#6) or 3 (donor#7, #9, #10, or islet donors) separate batches of samples for each donor. f, Glucose-stimulated insulin secretion of GINS organoids at different time points (n = 3 independent samples from donor #6 for each batch of differentiation) or donor #9 (n = 3 independent samples, day-18). g, Insulin secretion of day-18 GINS organoids from donor #6 incubated with the indicated concentrations of glucose with or without 10 nM glibenclamide (Glib) or 0.5 mM diazoxide (Dzx) as indicated (n = 4 independent samples). c-g, Data presented as mean ± s.d.; one-way ANOVA (d, e, g) or repeated-measures two-way ANOVA with Holm–Sidak’s multiple comparisons test for different time points (f) or one-tailed paired t-test for donor#9 (f).

Source data

Extended Data Fig. 4 Characterizing GINS organoid cells with scRNA-seq.

a, Top UMAP, cells sampled from hGSC cultures (blue, n = 1, donor #6) or GINS organoids (red, n = 1, donor #6); middle UMAP, hGSC cultures included both stem cells (stem) and mucus-secreting cells (mucus) spontaneously differentiated from hGSCs. GINS organoids contained four endocrine cell types. Cells are colored according to cell types; bottom UMAP, relative expression of cell type-specific markers. b, Relative expression of endocrine cell type-specific markers. The shading displays scaled average gene expression, and diameter denotes fractional expression. c, Comparison of GINS β-like cells (n = 2 independent batch of organoids, one representative batch shown, donor #6) and islet β-cells (n = 4 independent donors, an integration of all samples) in expression profiles of key genes for β-cell function, identity, metabolism, and exocytosis. MODY: Maturity Onset Diabetes of the Young. d, Relative expression of disallowed genes in the indicated cell types (n = 1, donor #6). e, Violin plots showing the expression levels of proliferative markers in the indicated cell types (n = 1, donor #6).

Extended Data Fig. 5 scRNA-seq comparison of GINS organoids derived from human antrum vs corpus stomach.

a, Diagram of human stomach. b, Immunofluorescence of antral GINS organoid (donor#6) stained for CPPT and MAFA. Repeated independently 5 times with similar results. c, Comparison of corpus and antral GINS organoids (both from donor#6) in the expression of β-cell marker genes. n=3 independent experiments. Data presented as mean ± s.d.; one-way ANOVA with Dunnett multiple comparisons test comparing GINS with islets. d, t-distributed stochastic neighbor embedding (t-SNE) plots of integrated corpus and antral GINS organoids. Cells are colored according to cell types. G-like: G-like cells that expressed gastrin (GAST). Pie charts indicate cell-type proportions. e, Comparison of antral and corpus GINS β-like cells expression profiles of key genes for β-cell function and identity. Red, antral GINS β-like cells; Blue, corpus GINS β-like cells. f, Glucose-stimulated insulin secretion of antral GINS organoids at different time points (days post differentiation) or from different batches. n=4 independent groups of GINS organoids for the time course GSIS. n=5 independent groups of GINS organoids for batch 1, n=4 independent groups of GINS organoids for batch 2 and 3. Two-way repeated-measures ANOVA with Holm–Sidak’s multiple comparisons test.

Source data

Extended Data Fig. 6 GINS organoids are not fully mature.

a, Volcano plot comparing gene expression of GINS β-like cells (n = 2 independent batch of organoids, one representative batch is shown, donor #6) versus islet β cells (n = 4 independent donors, an integration of all samples) identified in Fig. 3a. The number of differentially expressed genes (DEGs) enriched in either cell group is shown in the plot. Threshold of DEGs: adjusted-P < 0.01 and log2 fold-change > 1. P-value calculated by Wilcoxon Rank Sum test and adjusted based on Bonferroni correction. b, Gene Ontology (GO) analysis of DEGs enriched in GINS β-like cells (blue) or islet β-cells (red). P-value calculated by hypergeometric distribution followed by Benjamini-Hochberg adjustment.

Source data

Extended Data Fig. 7 Phenotypic characterization of GINS grafts.

a, Quantification from immunofluorescent staining of marker proteins, n = 3 independent experiments. Representative image showing co-expression of INS and CPPT in the GINS graft. b, Electron microscopy imaging of GINS graft. The electron-dense core granules were partially condensed. Repeated independently 3 times with similar results. c, SLC30A8 relative expression levels in GINS organoids, GINS grafts, and human islets. n=3 independent groups of GINS organoids, independent GINS grafts from different mice, or independent human islets from different donors. Data presented as mean ± s.d.; one-way ANOVA with Dunnett multiple comparisons test comparing GINS with islets. d, Images of the kidney from mice transplanted with GINS cells on day 0 and day 110 post transplantation. e, mCherry-labeled hGSCs (0.5 x 106) transplanted under the renal capsule and visualized under fluorescent microscope on day 0 and day 80 post transplantation. No Cherry+ cells were found at day 80. Repeated independently 5 times with similar results. f, tSNE projection of integrated GINS organoids and grafts. Cells are colored according to cell types. Horizontal bars indicate cell type ratios. g, Violin plots showing the expression levels of select ribonucleoproteins. h, Relative expression of select genes in the pathways elevated in cultured GINS β-like cells compared with human islet-β cells.

Source data

Extended Data Fig. 8 Dynamic gene and signaling pathway activations in hGSC differentiation to GINS organoid.

a, Relative expression levels of cell type-specific markers in UMAP. b, Expression of select genes shown along pseudotime in GINS organoid formation. Each dot represents a cell. a, b, n = 1, donor #6. c, Heat map showing transcription factor expression clusters along the pseudotime trajectory from hGSCs to GINS organoid cells (n = 1, donor #6) and islet β cells (n = 1, donor #1). Density plot on the top showing cell populations along pseudotime. Stem: hGSCs; Endo 1: endocrine progenitors 1; Endo 2: endocrine progenitors 2; GINS pre: GINS precursors.

Extended Data Fig. 9 Characterization of the developmental path of GINS organoids.

a, Heatmap showing waves of transcription factor regulon activations. Key regulons are labeled on the right with the number of their predicted target genes. Stem: hGSCs; Endo 1: endocrine progenitors 1; Endo 2: endocrine progenitors 2; GINS pre: GINS precursors. b, Select regulon activity overlaid on UMAP. c, RNA velocity and pseudotime trajectory analysis in UMAP showing the developmental path from GINS precursors to endocrine cells in GINS organoids. a, b, n = 1, donor #6.

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Supplementary Tables

Supplementary Table 1: Information of stomach tissue donors. Supplementary Table 2: Differentiation protocol of GINS organoids. Supplementary Table 3: Taqman assay list for qPCR. Supplementary Table 4: Cell type signature gene sets.

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Huang, X., Gu, W., Zhang, J. et al. Stomach-derived human insulin-secreting organoids restore glucose homeostasis. Nat Cell Biol 25, 778–786 (2023). https://doi.org/10.1038/s41556-023-01130-y

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