Organoid technology provides an experimental in vitro platform for studying human physiology in health and disease. Compared with other in vitro systems, such as cancer-derived cell lines or explants, tissue stem cell (TSC)-derived organoids offer key advantages: they can be expanded indefinitely while maintaining genomic stability and are amenable to CRISPR modification. Since these organoids are generated from normal TSCs, they contain the cell types of their tissue of origin. This makes organoids particularly valuable for investigating interactions between bacteria and differentiated, non-tumoral human cells. Intestinal organoids are grown as two-dimensional polarized monolayers on cell culture inserts coated with Basement Membrane Extract (BME) or invasin, an animal-free, cost-effective alternative, and can be differentiated into major intestinal epithelial cell types for infection with pathogenic adherent-invasive E. coli. Key infection readouts include monitoring epithelial gene expression by Reverse Transcription quantitative PCR (RT-qPCR), visualizing bacteria-epithelium interactions by confocal microscopy, and quantifying epithelial barrier breaching. The protocol can be readily adapted to study other organs and bacterial species, providing a versatile platform for investigating host-microbe interactions in organoids.

Crohn’s disease (CD) is a chronic inflammatory bowel disease (IBD). Mycobacterium avium, which causes Johne’s disease in ruminants, has been suggested as a potential CD trigger due to shared pathology, but early epithelial responses remain unclear. This study established a mouse small intestinal organoid (mSIO) model of M. avium infection to assess CD-related inflammation. Infected mSIOs were examined by confocal microscopy, block-face scanning electron microscopy, and macrophage co-culture to track bacterial localization and immune cell behavior. The data give unprecedent dynamic and super high resolution insights in the responses of gut cells to mycobacterial infection. RNA-seq with GSEA revealed strong induction of inflammatory genes and enrichment of pro-inflammatory pathways. Comparative analysis with CD-humanized mouse data showed overlapping gene expression and enrichment of the IBD signaling pathway. Notably, Mmp7, which can be linked to epithelial remodeling and inflammation, was a common marker in both models. This study presents a robust mSIO model of M. avium infection that recapitulates features of CD-associated inflammation both with high-resolution imaging and transcriptomics and identifies Mmp7 as a potential molecular link between infection and CD-like pathology.

Polyploid cells, which contain more than two copies of the genome, are widely present across plants and animals, where they are often found in tissues with high biosynthetic and metabolic demands, such as the mammalian liver and placenta. While somatic polyploidy is frequently associated with increased cell growth and biosynthetic capacity, unscheduled polyploidization in cell types that are not normally programmed to become polyploid is often linked to reduced cellular fitness and genome instability. To understand whether these divergent outcomes stem from distinct immediate cellular responses to increased ploidy, we systematically compared the early consequences of polyploidization across naturally occurring and experimentally induced systems. Specifically, we examined physiological polyploid cells in the Caenorhabditis elegans intestine and human hepatocyte organoids, alongside unscheduled polyploid human retinal pigment epithelial (RPE1) cells generated through cytokinesis failure. Using quantitative imaging, flow cytometry, and FUCCI-based cell-cycle reporters we measured cell size and protein translation dynamics during G1 in diploid and polyploid cells. Across all systems, we observed a strikingly conserved relationship between ploidy, cell size, and biosynthetic capacity: both cell size and protein translation showed similar scaling patterns after polyploidization, regardless of whether polyploidization occurred as part of normal development or by inducing cytokinesis failure. These findings indicate that the immediate cellular response to increased ploidy is broadly similar across contexts. However, in contrast to unscheduled polyploid RPE1 cells, polyploid human hepatocytes extend their G1 phase, leading to a higher accumulation of proteins before cell-cycle progression. Together, our findings suggest that polyploidization elicits similar growth responses across contexts, and that cell-type specific cell-cycle adaptations may determine whether polyploidy becomes advantageous or deleterious.

Pulmonary neuroendocrine cells (PNECs) are rare chemosensory epithelial cells, facultative stem cells, and a cell-of-origin for neuroendocrine lung cancers, yet the mechanisms governing their differentiation and heterogeneity are poorly understood. Here we establish NEr-fAOs, a human fetal airway organoid platform that robustly enriches PNECs, and identify a synergistic requirement for dual GSK3 and NOTCH inhibition to drive directed PNEC differentiation. This strategy yields stable cultures with up to 60-fold expansion of PNECs whose transcriptomes closely match fetal and adult PNECs. In addition to PNEC-enrichment, NEr-fAOs retain diverse airway epithelial cell types, preserving epithelial complexity. Time-resolved single-cell transcriptomics maps PNEC trajectories in NEr-fAOs, resolving precursor and mature states. Comparative analyses further reveal a distal airway bias in NEr-fAOs and enrichment for lower-airway progenitors. NEr-fAOs thus provide a scalable, tractable platform to dissect human PNEC biology and distal airway progenitor hierarchies relevant to lung development, cancer, and disease. ### Competing Interest Statement The authors have declared no competing interest.

Zoonoses pose substantial global health risks, highlighting the need to better understand animal-to-human transmission. Reptiles are increasingly recognized as hosts of diverse pathogens, including numerous viruses, yet the diversity and prevalence of reptile pathogens, as well as their potential risk to humans, remain poorly understood. Here, we establish and characterize airway organoids derived from Python regius, providing an in vitro model to study reptile airway infection. Through de novo assembly of a Python regius reference genome, we characterize airway organoids at single-cell resolution, which suggests the presence of diverse cell populations including ionocytes, ciliated, secretory, goblet, endocrine, tuft, and basal cells. The organoids support productive infection with Ball Python Nidovirus (BPNV) and mount a robust epithelial antiviral response through the induction of interferon-stimulated genes, cytokines, and genes involved in chemical defense. As a proof-of-concept, treating organoids with antiviral drugs during infection reduces BPNV levels, highlighting the model’s utility for drug testing. By providing a reductionist system of the serpentes airway, these organoids constitute a physiologically relevant in vitro model to study reptile viruses and host–pathogen interactions in their native host. Ball python airway organoids, characterized at single-cell resolution, support productive infection with a reptile virus and respond to antiviral drugs, establishing a physiologically relevant model for studying reptile host–pathogen interactions.

Protein synthesis is dynamically regulated to control cell growth, differentiation, and stress responses. Recent single-cell sequencing methods can map ribosome positions on individual transcripts 1–4 , but cannot capture the global translational states that coordinate protein synthesis across the transcriptome. In contrast, methods that measure the global translational landscape, such as polysome profiling and cryogenic electron tomography 5 , lack either single-cell resolution or throughput. Here we introduce SCISSOR (Single-Cell Inference of Structural States of Ribosomes), a strategy that infers global translation activity in individual cells from the differential protection of ribosomal RNA (rRNA) against nuclease digestion. By integrating these protection signatures with the structure of the ribosome, SCISSOR resolves multiple ribosomal states and quantifies their abundance across thousands of individual cells. Applying SCISSOR reveals systematic variation in global translation across the cell cycle in human cells, as well as during the differentiation of murine intestinal stem cells into distinct epithelial lineages. These findings uncover principles of global translational regulation that are invisible to transcriptomic or ribosome-profiling assays, establishing a framework for studying global translation control at single-cell resolution.

Plasticity is a central mechanism underlying the robust regenerative capacity of the intestinal epithelium. Two major forms of plasticity have been described: spatial plasticity, in which differentiated cells revert to crypt base columnar cells (CBCs), and fetal reversion into revival stem cells (revSCs). However, the relationship among these two stem cell populations and differentiated cells remains to be clarified. Here, we demonstrated the bidirectional interconversion between CBCs and revSCs. Using lineage tracing, injury models and villus culture, we show that absorptive enterocytes can reprogram into revSCs and regenerate CBCs. These findings position fetal reversion as an entry point to spatial plasticity, establishing a regenerative hierarchy where CBCs, revSCs, and enterocytes collectively orchestrate intestinal repair. Furthermore, we identified revSCs as a highly stress-tolerant stem cell population, whose emergence would preserve the stem cell pool. Our results establish fetal reversion as a cellular escape mechanism safeguarding epithelial regeneration under inflammatory conditions. Capturing the cellular dynamics of intestinal repair, focusing on the interactions between differentiated cells and two distinct stem cell populations, crypt base columnar cells (CBCs) and revSCs, to illustrate how intestinal epithelial cells acquire stress resilience.

Cell-to-cell heterogeneity in infection outcome is a general feature of most viruses, but the underlying mechanisms are poorly understood. Here, we developed a live-cell single-molecule imaging technology to visualize infection by unmodified influenza A viruses (IAVs) with unprecedented resolution. Using this approach, we generated a detailed kinetic map of IAV infection, which identified viral ribonucleoprotein (vRNP) replication, nuclear export, and virion budding as important sources of heterogeneity. Mechanistically, we show that infection heterogeneity is caused by differential viral gene expression signatures, resulting from widespread transcriptional defects and loss of viral genome segments. For example, loss of NS, but surprisingly not polymerase subunits, severely delays replication onset, and loss of M and NS, but not HA, underlies vRNP nuclear export defects. In summary, our work identifies the origin and consequences of infection heterogeneity and provides a broadly applicable technology that allows high-resolution phenotyping of unmodified IAVs and other negative-strand RNA viruses.

Chemotherapies and targeted therapies alike are limited by toxicity to normal tissue, because they act on pathways shared between tumor cells and the normal epithelium. Whether a compound spares normal tissue is rarely tested directly, because the cancer cell-line databases that guide oncology hold no normal counterpart. Here, we screened more than 5,600 clinical and preclinical compounds on patient-derived tumor and normal organoids from head and neck squamous cell carcinoma, to identify compounds active across tumors while sparing normal tissue. Such pan-tumor selectivity was rare: most tumor-active compounds also damaged normal organoids, so normal-tissue toxicity, not weak potency, was the challenge. Cell-line potency related only modestly, and equally, to tumor and normal responses, and was blind to selectivity. Selectivity was graded rather than all-or-none, occupying a narrow window between growth arrest and cell death. The compounds selective across tumors acted on conserved proliferative machinery, whereas activity against tumor-specific targets was donor-specific rather than broadly selective. A compact organoid panel measured this normal-tissue dimension reproducibly, arguing for differential organoid screening early in drug development.

Taste bud cells have a limited lifespan and must be continuously replaced along with the papilla epithelium in which they reside. Previous work has shown that expression of leucine-rich G protein-coupled receptor 5 (Lgr5), a Wnt pathway agonist, serves as a marker of adult stem/progenitor cells for taste buds located in posterior tongue (circumvallate and foliate), but not anterior tongue (fungiform), taste papillae. However, the specific location/niche of the Lgr5-expressing cells supporting renewal and their phenotypic properties have not been fully explored. To address this, the genesis and fate of Lgr5+ cells were examined in developing and adult mice using genetic reporter strains. Evidence from Lgr5-lacZ and Lgr5-GFP mice shows that, while Lgr5 is broadly expressed in the epithelium of nascent circumvallate papillae and their trenches during embryonic development, it becomes concentrated within the ducts of adjacent von Ebner's salivary glands during the first postnatal week, co-incident with the appearance of differentiated taste buds. In posterior tongue taste papillae of adult animals, sites of highest Lgr5-lacZ and Lgr5-GFP expression are found in excretory ducts, restricted to the outer (basal) layer of the bi-layered excretory zone. These Lgr5+ cells are immunoreactive for keratin 14, like cells in the basal layer of extragemmal taste epithelium, and are often seen to express Sox9, a marker of exocrine gland duct cells. Lineage tracing experiments with an Lgr5-EGFP-IRES-CreERT2; mTmG reporter show that Lgr5+ ductal cells become labeled one day following Cre induction, prior to the appearance of descendent cells in taste buds. Overall, the data support a role for Lgr5+ ductal cells as stem cells and suggest that a cooperative interaction exists between posterior taste epithelium and its associated salivary glands in taste cell turnover.

Hyperactivation of WNT signaling is a hallmark of cancer, often driven by increased expression of WNT ligands. In pancreatic ductal adenocarcinoma (PDAC), elevated WNT7B and WNT10A correlate with aggressive, basal-like disease and poor patient survival, but the mechanisms underlying this association remain unclear. Using patient-derived organoids, we show that WNT7B promotes proliferation and maintains basal-like transcriptional states by preventing differentiation toward a more classical PDAC signature. Clonal WNT7B reporter organoids reveal that WNT-high cells are heterogeneously distributed and stably coexist with WNT-low/negative lineages. Hybrid co-cultures demonstrate that WNT7B-expressing cells support the survival and growth of neighboring WNT-negative cells via short-range, contact-dependent signaling. These findings highlight the functional importance of heterogeneous WNT7B/10A expression in driving PDAC aggressiveness and suggest that targeted WNT inhibition may shift tumors toward a more differentiated, less aggressive state, offering potential therapeutic benefit.

Hepatoblastoma (HB) is a paediatric liver malignancy arising from hepatic precursor cells, with >90% of cases harbouring a mutation in exon 3 of CTNNB1. We present a fully genetically characterised HB tumour organoid (tumoroid) biobank, which allows for in vitro studies of disease progression and clonal dynamics in vitro. We established a biobank of 14 tumoroid lines from 9 different patients. Tumours and tumoroids were characterised by whole genome sequencing (WGS) and histology, revealing strong concordance in cell morphology and β-catenin staining. In tumour—tumoroid pairs, identical pathogenic CTNNB1 variants were found, alongside shared copy number alterations (CNAs) and mutations. Variant allele frequency (VAF) was consistently higher in tumoroids, indicating increased tumour purity in vitro. In addition to CTNNB1, we frequently observed ARID1A alterations (single-nucleotide variants [SNVs] or CNAs in 56% of patients), and MYC gains as described previously. In paired pre- and post-treatment samples, we observed a clear increase in mutational load, attributed to a chemotherapy signature. Notably, from one patient, we analysed 4 tumour samples (3 post-treatment) with 4 matching tumoroid lines, all carrying a novel BCL6 mutation and loss of ARID1A. Mutational profiles varied across samples from different locations, suggesting intratumoral heterogeneity and clonal selection during tumoroid derivation. Taken together, this biobank allows detailed analysis of HB tumour biology, including treatment-induced progression and clonal dynamics across temporally and spatially distinct samples.

In vitro kidney models play a crucial role in the study of renal development, (patho)physiology, drug development, and potential applications in bioartificial kidneys. Human in vitro kidney models have recently advanced significantly with the development of (induced) pluripotent stem cell ((i)PSC)-derived organoids, tissue/urine-derived tubuloids, and iPSC organoid-derived tubuloids (iPSCod tubuloids). However, challenges remain in understanding degree and diversity of differentiation and each model's benefits. Here, we compared the transcriptomic profiles of kidney tubular epithelial cell types across several advanced three-dimensional (3D) models with physiological in vivo profiles (adult and fetal). Our selected models included differentiated kidney tissue-derived tubuloids, iPSCod tubuloids, and four iPSC-derived organoid models from different protocols. Our findings highlight distinct transcriptional profiles, the presence of diverse adaptive cell states, and differences in maturation marker expression among models. This study offers insights into the characteristics of state-of-the-art kidney models and guidance for researchers choosing suitable models for their investigations.

Compromised intestinal regenerative responses drive severe inflammatory conditions, such as inflammatory bowel disease and graft-versus-host disease, affecting millions of people worldwide each year. Despite extensive research, effective therapies remain limited, and no curative treatments are currently available. We recently discovered that human intestinal tuft cells promote tissue repair following injury through Wnt and IL-4/IL-13 signaling pathways. Building on this discovery, here, we report the engineering and functional validation of a synthetic Wnt-IL-13 fusion protein that simultaneously activates both the Wnt and IL-4/IL-13 signaling pathways to enhance human intestinal tuft cell activity. Employing human organoid technology, we demonstrate that this therapeutic approach promotes mucosal healing.

Organoid technology offers unique opportunities for studying human biology and disease in vitro. Organoids are self-organizing 3D structures, derived from pluripotent or tissue-resident stem cells that recapitulate key aspects of primary tissues. Compared with classical cell lines, organoids provide distinct advantages. They can be derived from both healthy tissues and diseased tissues, enabling the investigation of disease mechanisms and the development of personalized therapies, and they better recapitulate the cellular heterogeneity of the native tissue, allowing for better modelling of human (patho)physiology. Although current organoids have provided valuable insights, these insights are inherently reductionist and do not fully capture the complexity of human tissues. The research field is, therefore, moving towards next-generation models that more accurately represent the intricate cellular interactions, tissue architecture and microenvironmental cues that underlie human biology and disease. In this Review, we outline the limitations and challenges of current organoid systems, highlight recent advances aimed at increasing their complexity, and discuss innovations that support their translation into clinical applications. The focus is on human tissue stem cell-derived organoids, with comparisons to pluripotent stem cell-derived organoids where relevant. We conclude by identifying key factors and remaining challenges for developing the next generation of organoids.

Abstract Disease of the lung alveoli is frequently associated with acute or chronic inflammation. At present, there are no effective therapies to support regeneration of the alveolar epithelium, and ongoing inflammation adds an additional layer of complexity to many lung diseases. Here, we describe a primary adult human organoid model for investigating how inflammation shapes alveolar regeneration. Unlike previous models, this system supports long-term expansion of newly identified human-specific alveolar progenitor cells and serum-free differentiation into alveolar type 1 (AT1)-like cells. Using this platform, we find that interferon-gamma (IFN-γ) exerts cytotoxic effects on mature AT1-like cells while promoting survival of alveolar progenitor cells mediated by BIRC3. This unexpected selective positive effect of IFN-γ on alveolar progenitors underscores the need for nuanced and context-dependent evaluation of the influence of pro-inflammatory cytokines on alveolar regeneration. Our organoid model provides a reductionist platform for mechanistic studies and discovery of strategies to enhance alveolar regeneration.

BACKGROUND:Pediatric Inflammatory Bowel Disease (IBD) is a chronic condition characterized by persistent intestinal inflammation in children. It often presents with distinct clinical phenotypes and is more frequently linked to rare monogenic variants affecting epithelial barrier function or mucosal immunity. Although over 100 genes are associated with monogenic IBD, their roles in the intestinal epithelium remain poorly defined. This study aimed to improve our understanding of epithelial dysfunction in early-onset IBD through molecular and cellular analyses to uncover patient-specific phenotypes and potential therapeutic targets. METHODS:We generated intestinal epithelial organoids (IEOs) from 94 pediatric IBD patients, including those with monogenic variants (BTK, TTC7A, IL10RA, LRBA, STXBP2, TRNT1, SKIV2L), along with 46 non-IBD controls. RNA sequencing was performed on 38 patient and 20 control lines, under both baseline conditions and after immunological stimulation, yielding a valuable dataset for studying epithelial responses in IBD. RESULTS:IEOs effectively initiated inflammation upon bacterial lysate stimulation, regardless of disease status, origin, or genotype. Inflammatory stimulation triggered upregulation of IBD-linked genes SERPINA1 and LIFR in IBD organoids, suggesting their role in epithelial innate immunity. However, network analysis showed no consistent transcriptional signatures across all IBD cases. Instead, specific genotypes (TTC7A, STXBP2, LRBA) revealed responses, with STXBP2 and LRBA showing shared upregulation of IL-1 and SLC30-mediated zinc trafficking pathways. CONCLUSIONS:These findings underscore the potential of IEOs as a valuable model for studying IBD and offer key insights that could guide the development of targeted therapies for both monogenic and non-monogenic forms of IBD.