James M. Wells

Multiple signaling pathways and transcription factors (TFs) establish organ domains in the developing gastrointestinal tract. How these are integrated into spatial-temporal networks to regulate organogenesis and how disruptions to those networks lead to congenital syndromes remain poorly understood. Using human pluripotent stem cell cultures and Xenopus embryos, we demonstrate that retinoic acid (RA) from the lateral plate mesoderm directly activates expression of the TF rfx6 in posterior foregut endoderm. Rfx6 subsequently promotes posterior foregut identity while suppressing Wnt-dependent hindgut and Bmp-dependent pharyngeal fates through direct and indirect mechanisms. Rfx6 can directly activate the expression of several key foregut TFs (onecut1 and pdx1) and Wnt antagonists (sfrp2/5) while indirectly restricting expression of Wnt and Bmp ligands. Rfx6 also directly suppresses transcription of the Wnt-dependent hindgut TF cdx2 and the Bmp-dependent pharyngeal TFs nkx2-5 and nkx2-6. Thus, Rfx6 acts at multiple levels to integrate RA, Wnt and Bmp activity into a network with lineage-promoting TFs to control gut tube patterning. These results provide insight into the molecular basis of Mitchell–Riley Syndrome congenital anomalies, which are caused by RFX6 mutations.

Esophageal atresia and tracheoesophageal fistula (EA/TEF) are congenital malformations of the foregut. We identified two distinct variants in the BMP/TGFβ repressor SMAD6 in two individuals exhibiting EA/TEF. We investigated the function of SMAD6 in tracheoesophageal development using two orthogonal approaches in Xenopus embryos, both resulting in foregut malformations similar to those observed in EA/TEF. We then used human pluripotent stem cell-derived foregut epithelium and mesenchyme to explore the separate roles of SMAD6 in these germ layers. CRISPR-mediated disruption of human SMAD6 caused an increase in BMP signaling in foregut epithelium and mesenchyme consistent with its role as a BMP repressor. Loss of SMAD6 caused patterning defects in both tissue types; SMAD6−/− endoderm showed increased expression of distal gut tube markers and SMAD6−/− mesenchyme showed increased expression of ventral and posterior markers, including markers of cardiac and liver mesenchyme lineages. Furthermore, SMAD6−/− mesenchyme had decreased ability to form CD31-positive endothelial cells. Our results demonstrate that SMAD6 is required for foregut development and that rare variants in this gene are likely causative for foregut malformations in EA/TEF.

Key limitations of current human gastrointestinal organoids include incomplete physiological maturation and the need for complex, time-consuming assembloid approaches to integrate a functional nervous system for transplantation. Here we present a confined culture system (CCS) method that generates large-scale, elongated and functional human small intestinal, colonic and gastric tissues with a de novo enteric nervous system (ENS). We use a 3D-printed scaffolding tray to restrict spheroid fusion and growth, promoting the spontaneous co-development of a functional ENS. Transcriptomic and electrophysiological data demonstrate selective neuromuscular function and the presence of excitatory and inhibitory neurons within the tissues. When compared to traditional methods, the CCS expedites tissue maturation for transplantation, yielding organoids that are up to ten times larger, reaching widths of 8 cm after 10 weeks, and exhibit enhanced engraftment rate. CCS organoids integrate and adapt to murine luminal environment while maintaining barrier integrity and functional capacity. The CCS methodology simplifies current protocols while accelerating the production of complex, functional and clinically relevant gut tissues.

The goal of engineering increasingly complex human organoid models is to more accurately model human organogenesis and disease. Recently, human antral gastric organoids (hAGOs) were engineered to contain splanchnic mesenchyme (SM) and enteric neural crest cells (NCCs), resulting in functional three germ layer gastric organoids. To determine the robustness of hAGOs and how additional germ layers impact development, we benchmarked these hAGOs with the developing human stomach. Human AGOs in vitro were most similar to 7 week fetal stomach with the epithelium comprising primarily mucous precursors. The SM and NCCs added to hAGOs formed fetal gastric-like mesenchymal or neuroglial precursors, respectively. Incorporation of SM and NCCs did not drastically alter the cellular diversity of the epithelium in vitro. Following transplantation, hAGOs with SM matured into tissue more like the 2nd trimester stomach. Bioinformatic inference confirmed known signaling crosstalk between germ layers and identified new signaling candidates that may regulate tissue assembly. Together, three germ layer hAGOs faithfully model the multilayer complexity of the fetal stomach at the single-cell transcriptomic level and provide insight into human stomach development.

Human pancreas development remains incompletely characterized due to restricted sample access. We investigate whether pigs resemble humans in pancreas development, offering a complementary large-animal model. As pig pancreas organogenesis is unexplored, we first annotate developmental hallmarks throughout its 114-day gestation. Building on this, we construct a pig single-cell multiome pancreas atlas across all trimesters. Cross-species comparisons reveal pigs resemble humans more closely than mice in developmental tempo, epigenetic and transcriptional regulation, and gene regulatory networks. This further extends to progenitor dynamics and endocrine fate acquisition. Transcription factors regulated by NEUROG3, the endocrine master regulator, are over 50% conserved between pig and human, many being validated in human stem cell models. Notably, we uncover that during embryonic development, emerging beta-cell heterogeneity coincides with a species-conserved primed endocrine cell (PEC) population alongside NEUROG3-expressing cells. Overall, our work lays the foundation for comparative investigations and offers unprecedented insights into evolutionarily conserved pancreas organogenesis mechanisms across animal models.

A confined culture system (CCS) establishes methods to generate complex functional human gastrointestinal tissues. This approach yields large-scale innervated small intestinal, colonic and gastric organoids with an elongated tubular shape for both in vitro and in vivo studies. Transcriptomic and electrophysiological data demonstrate the co-development of a functional de novo enteric nervous system, which is absent from conventional organoids. When compared to traditional methods, CCS derived small intestinal, colonic and gastric organoids reached maturation supporting transplantation in half of the time, resulting in enhanced engraftment rates and sizes. Murine luminal content exposure within CCS organoids in vivo further augmented function, supporting the potential translational benefits required to model complex intestinal diseases. In summary, the CCS methodology simplifies current protocols while adding complexity and expediting the generation of clinically relevant functional gut tissues.

Background and Aims: WNT2B mutations result in Diarrhea-9 (DIAR9), a congenital diarrhea syndrome with an extreme phenotype and unique histological defects. Attempts to model DIAR9 in rodents and study patient epithelial tissue have not been able to fully reproduce the human phenotype, making understanding this condition challenging. Here, we aimed to interrogate the mechanisms and the specific cellular compartment contributing to DIAR9 using a human intestinal organoid model. Methods: Human intestinal organoids (HIOs) generated from both a patient-derived WNT2B ^R69* iPSC line and a control line were transplanted into immunocompromised mice for 10 weeks. Grafts were harvested and histologically compared. Bulk RNA sequencing was performed on both organoid groups and on patient-biopsy derived enteroids. In vitro recombination experiments were performed to describe the causative cellular compartment. Results: Live and histological imaging revealed partial epithelial delamination in WNT2B ^R69* HIOs, which was absent in controls. A significant number of crypts in WNT2B ^R69* HIOs lacked OLFM4, a surrogate marker of stem cell activity. Key transcriptomic pathways altered between groups included trafficking of apical digestion proteins, which was confirmed via immunofluorescence. Patient derived enteroid proteomic analysis revealed similar results. Recombination experiments in HIOs revealed that while both epithelial and mesenchymal WNT2B are important for stem cell function, lack of mesenchymal WNT2B was sufficient to elicit the phenotype. Conclusion: We demonstrated that mesenchymal WNT2B is critical for supporting human intestinal epithelial development and function.