Preterm infants are prone to gastrointestinal complications such as infectious diseases and necrotizing enterocolitis, which are associated with intestinal inflammation and increased intestinal permeability. Intestinal epithelial barrier (IEB) function is known to be immature in preterm neonates; however, our understanding of how the IEB develops - particularly the formation of junctional complexes - remains limited. Here, we analyzed intestinal tissue specimens from healthy resection margins of six very immature preterm infants who underwent bowel resection due to focal intestinal perforation (at the chronological age of 25 to 28 weeks' gestation), and compared the composition of tight junctions, adherens junctions and desmosomes to that of adults. Using immunostaining, our observations show, that tight junction proteins Claudin-2, Claudin-3 and Occludin, adherens junction proteins E-cadherin and β-Catenin as well as desmosomal proteins Plakoglobin and Plakophilin-2 appeared as mature as in adults as early as 25 weeks' gestation. However, Claudin-1, -4 and -5, as well as ZO-1 staining patterns increased and became more defined with increasing gestational age, suggesting junctional maturation during gestational week 26 and 27. Desmosomal protein Desmocollin-2 was increased until 26 weeks' gestation whereas Desmoglein-2 and Desmoplakin expression was immature at 28 weeks' gestation compared to the expression in adults. Our study provides the first sequential characterization of junctional protein maturation across all major IEB components early in life in human samples. These findings may help identify key mechanisms underlying intestinal barrier-associated pathologies in preterm infants.

Endemic and emerging infectious diseases pose major public health, economic and societal challenges. To advance our understanding of infectious disease pathophysiology and develop effective interventions, experimental models are required that closely mimic human biology. In particular, organoid platforms have begun to address key limitations of 2D cell line cultures and animal models in infectious disease research. In this Review, we explore the diverse applications of human organoids in investigating organ-specific infections and disease manifestations across major physiological systems, including the respiratory, digestive, nervous, cardiovascular, integumentary, urinary, reproductive and lymphatic systems, with a primary emphasis on viral pathogens. We further discuss the importance of immune-competent and vascularized organoids for modelling complex host–pathogen interactions, and we examine organoid-on-a-chip platforms as tools to investigate dynamic processes and inter-organ mechanisms. In addition, we outline how organoid technologies can support vaccine and therapeutic development, enable the study of zoonotic transmission and contribute to pandemic preparedness. Finally, we underscore key priorities for the field, including enhancing tissue-like complexity and maturity, improving standardization, and increasing the scalability and throughput of organoid models. Human organoids offer experimental models that closely replicate human biology, enabling the investigation of infectious disease mechanisms across diverse organ systems, especially for viral pathogens. This Review highlights their applications in studying host–virus interactions, supporting therapeutic and vaccine development, and improving pandemic preparedness, while emphasizing the need for greater complexity, standardization and scalability.

Contrary to short-lived plasma cells, which survive only 3-5 days, long-lived plasma cells (LLPCs) contribute to the humoral memory of the body and thus also to many antibody-related diseases. The ability of plasma cells to persist over months, years, and even a lifetime has been demonstrated in vivo. Yet, the in vitro culture of human primary bone marrow-derived plasma cells has been limited to a few days. Here, we establish culture conditions for human primary bone marrow-derived plasma cells for 21 days. Plasma cells and stromal cells are isolated from human bone marrow and cultured in 2D or a 3D ceramic scaffold. The plasma cells' survival and antibody secretion depend on direct contact with stromal cells. The culture promotes CD19-negative PCs. Inhibition of the PI3K or NF-kappaB pathways using chemical inhibitors reduced the survival of the plasma cells. These results underline the supportive role of the stromal cells for the survival of the LLPC and confirm mechanisms that were identified in mouse LLPCs also for human LLPCs. The culture described here will promote further studies to deepen our understanding of the human LLPC.

Necrotizing enterocolitis (NEC) is a major cause of mortality in preterm infants. Its pathophysiology remains poorly understood but intestinal epithelial barrier dysfunction contributes to the disease. We characterized junctional proteins in intestinal specimens from preterm infants. Samples from 27 patients with NEC and 20 patients with focal intestinal perforation (FIP) from the center of the specimens (affected) or the macroscopically healthy resection margins whenever available (non-affected) were collected. NEC patients displayed higher mortality and more commonly occurrence of impaired glucose homeostasis, patent ductus arteriosus, anemia and antibiotic treatment compared to FIP patients.Discrimination between NEC and FIP was not possible in affected areas based on H.E. staining using a newly developed scoring system. Immunofluorescence revealed reduced Claudin-3 in affected NEC samples and decreased Claudin-4 in affected FIP and all NEC samples. E-cadherin and Desmoglein-2 were reduced in a subgroup of the affected NEC samples. Plakophilin-2 was decreased in intestine affected by FIP and unaffected intestine in patients with NEC. In affected areas of NEC, Plakophilin-2 was completely lost. Plakoglobin reduction in affected NEC samples correlated with poor survival. This study provides novel insights into changes of junctional proteins in NEC, suggesting Claudin-3 and Plakophilin-2 as diagnostic markers to differentiate FIP from NEC and reduced Plakoglobin as a prognostic marker.

Enteropathogenic E. coli (EPEC) attaches to host intestinal epithelial cells, resulting in severe illness and diarrhoea. Different cell models have been used to study EPEC infection, but a direct comparison of infection of cell lines and primary cells is lacking. In this study, we compare EPEC infection in primary epithelial cells with HeLa cells. Jejunal organoid-derived cells contain differentiated intestinal epithelial cells and form a tight monolayer. Upon infection, they retain integrity over longer time periods than HeLa cells. Attachment of EPEC to host cells and innate immune response is strongly delayed in organoid-derived monolayers. These results indicate that host cell factors determine the outcome of infection. Future identification of these host factors will aid the development of new therapeutics.

Aberrant cellular glycosylation is a key event that accompanies and actively sustains gastric neoplastic transformation. Patient-derived organoids (PDOs) have recently emerged as promising ex vivo models to study human gastric diseases; however, their glycosylation landscape remains unknown. To evaluate gastric PDOs as avatars of in vivo tissue glycosylation, a biobank of gastric PDOs (n = 56) was generated from gastric mucosa samples of non-tumoral obese patients (n = 11), adjacent tumor mucosa (n = 26), and gastric tumor tissue (n = 19). PDOs reproduce distinct stages of gastric carcinogenesis and recapitulate the gastric tissue-associated glycosylation profiles. PDOs capture glycan inter- and intra-tumoral heterogeneity, which is maintained over time and upon biobanking and xenografting. Furthermore, expression of type I/II Lewis antigens is dynamically controlled by the PDO's differentiation status, influencing Helicobacter pylori binding, mirroring the gastric epithelium-tissue interactions. This study establishes PDOs as robust ex vivo tools to study gastric glycan dynamics in both gastric physiological and pathological settings.

BACKGROUND AND AIMS: Aberrant cellular glycosylation remains a key event that accompanies and actively sustains gastric neoplastic transformation. Patient-derived organoids (PDOs) have recently emerged as a promising ex vivo model to study human gastric disorders. Since the PDOs glycosylation landscape remains unknown, this study aims to evaluate PDOs as potential avatars of in vivo tissue glycosylation profiles in the gastric context. METHODS: Fresh gastric mucosa samples derived from non-tumoral obese patients (n=11), adjacent tumor mucosa samples (n=29), and tumor tissue samples derived from gastric cancer (GC) patients (n=30) were used to establish a biobank of gastric PDOs (n=56). The N- and O- glycophenotypes of normal, adjacent, and tumor PDOs and respective in vivo tissues were thoroughly characterized by immunostaining. Additionally, a comparative glycan analysis was performed over time, upon PDO biobanking and xenografting in mice. The binding of two Helicobacter pylori ( H. pylori ) isogenic strains with distinct glycan-binding affinities was assessed in parental gastric mucosa tissues and compared with the respective PDOs before and after modulation of their glycan landscape. RESULTS: Our results show that PDOs mimic different phenotypes of the carcinogenic cascade and recapitulate parental gastric tissues' glycosylation profile. Tumor PDOs recapitulate the inter- and intra-heterogeneity features observed in GC, which is maintained over time, upon biobanking and xenografting. We demonstrated that the expression of type I and type II Lewis antigens is dynamically controlled by PDOs differentiation status, which results in differential binding to H. pylori strains displaying distinct glycan-binding adhesins, mirroring the gastric epithelium tissue interactions. CONCLUSIONS: This study established PDOs as invaluable ex vivo tools to study the complex glycan dynamics in both gastric physiological and pathological settings. KEYWORDS: Glycosylation, Patient-derived organoids, Helicobacter pylori , Gastric carcinogenesis, Gastric cancer. ### Competing Interest Statement The authors have declared no competing interest.

Summary The epithelium of the gastrointestinal (GI) tract has been extensively characterized using advanced histological and RNA sequencing techniques, which has revealed great cellular diversity. Pathogens, such as viruses and bacteria, are highly adapted to their host and often exhibit not only species-specificity but also a preference or tropism for specific GI segments or even cell types—some of these preferences are so specific, that these pathogens still cannot be cultured in vitro. Organoid technology now provides a tool to generate human cell types, which enables the study of host cell tropism. Focussing on the GI tract, we provide an overview about cellular differentiation in vivo and in organoids and how differentiation in organoids and their derived models is used to advance our understanding of viral, bacterial, and parasitic infection. We emphasize that it is central to understand the composition of the model, as the alteration of culture conditions yields different cell types which affects infection. We examine future directions for wider application of cellular heterogeneity and potential advanced model systems for GI tract infection studies.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection primarily affects the lung but can also cause gastrointestinal (GI) symptoms. In vitro experiments confirmed that SARS-CoV-2 robustly infects intestinal epithelium. However, data on infection of adult gastric epithelium are sparse and a side-by-side comparison of the infection in the major segments of the GI tract is lacking. We provide this direct comparison in organoid-derived monolayers and demonstrate that SARS-CoV-2 robustly infects intestinal epithelium, while gastric epithelium is resistant to infection. RNA sequencing and proteome analysis pointed to angiotensin-converting enzyme 2 (ACE2) as a critical factor, and, indeed, ectopic expression of ACE2 increased susceptibility of gastric organoid-derived monolayers to SARS-CoV-2. ACE2 expression pattern in GI biopsies of patients mirrors SARS-CoV-2 infection levels in monolayers. Thus, local ACE2 expression limits SARS-CoV-2 expression in the GI tract to the intestine, suggesting that the intestine, but not the stomach, is likely to be important in viral replication and possibly transmission.

Several reports suggest that intestinal tissue may be a natural niche for Chlamydia trachomatis infection and a reservoir for persistent infections in the human body. Due to the human specificity of the pathogen and the lack of suitable host models, there is limited knowledge on this topic. In our study, we modelled the course of the chlamydial infection in human primary gastrointestinal (GI) epithelial cells originating from patient-derived organoids. We show that GI cells are resistant to apical infection and C. trachomatis needs access to the basolateral membrane to establish an infection. Transmission electron microscopy analysis reveals the presence of both normal as well as aberrant chlamydial developmental forms in the infected cells, suggesting a possible cell-type specific nature of the infection. Furthermore, we show that the plasmid-encoded Pgp3 is an important virulence factor for the infection of human GI cells. This is the first report of C. trachomatis infection in human primary intestinal epithelial cells supporting a possible niche for chlamydial infection in the human intestinal tissue.

The rapidly evolving stem cell field puts much stress on developing educational resources. The ISSCR Education Committee has created a flexible stem cell syllabus rooted in core concepts to facilitate stem cell literacy. The free syllabus will be updated regularly to maintain accuracy and relevance.

The human gastric epithelium forms highly organized gland structures with different subtypes of cells. The carcinogenic bacterium Helicobacter pylori can attach to gastric cells and subsequently translocate its virulence factor CagA, but the possible host cell tropism of H. pylori is currently unknown. Here, we report that H. pylori preferentially attaches to differentiated cells in the pit region of gastric units. Single-cell RNA-seq shows that organoid-derived monolayers recapitulate the pit region, while organoids capture the gland region of the gastric units. Using these models, we show that H. pylori preferentially attaches to highly differentiated pit cells, marked by high levels of GKN1, GKN2 and PSCA. Directed differentiation of host cells enable enrichment of the target cell population and confirm H. pylori preferential attachment and CagA translocation into these cells. Attachment is independent of MUC5AC or PSCA expression, and instead relies on bacterial TlpB-dependent chemotaxis towards host cell-released urea, which scales with host cell size.

In November 2021, the Institute for Regenerative Medicine (IRM) and the Institute for Immunology (IFI) at the University of Pennsylvania, USA, joined forces and organized a symposium featuring external speakers as well as locally based scientists to discuss how the immune system influences tissue stem cell biology. As we review here, the presentations highlighted emerging concepts in the field, revealing how tissue-specific immune cell activation can guide stem cells in regeneration and repair.

EDITORIAL article Front. Cell. Infect. Microbiol., 22 July 2022Sec. Bacteria and Host https://doi.org/10.3389/fcimb.2022.969132