Biology subjects

Jonkers, I. H.

Publications and source records attributed to Jonkers, I. H..

7 recordsLinked to original sources

bioRxiv2026

Autologous biopsy-derived co-culture platform for interrogation of intestinal epithelial-T cell crosstalk

Interactions between intraepithelial lymphocytes (IELs) and the intestinal epithelium are central to mucosal homeostasis and disease. However, mechanistic in vitro studies describing their crosstalk in humans are limited by scarceness of primary material and insufficient knowledge about co-culture requirements. Here, we establish an autologous human duodenal IEL-organoid co-culture system encompassing expandable and bankable IEL and organoid protocols, with co-culture conditions that allow viability of both cell types. This system enables successive interrogation of lympho-epithelial interactions starting from minimal biopsy material. Under baseline conditions, CD45CD8CD103TCR{beta} IELs retain tissue-residency and effector features and induce an epithelial interferon response and chemokine production, without overt epithelial apoptosis. IL-15 and IL-21, essential cytokines involved in IEL-activation in intestinal enteropathies like celiac disease, increases granzyme B expression and interferon-{gamma} secretion but do not trigger epithelial cell death. However, enforcing IEL-epithelial contact using an anti-CD3-anti-Ep-CAM bispecific antibody induces epithelial apoptosis accompanied by increased tumor necrosis factor (TNF) and FAS-ligand (FASLG) secretion. These findings validate the platforms ability to resolve non-destructive and cytotoxic lympho-epithelial interaction and provide a tractable system for studying intestinal inflammation and immune-mediated epithelial cell death.

immunology↗

bioRxiv2025

Butyrate blocks specific histone acetylation by preventing recruitment of p300 to acetylated histones

Butyrate, a short-chain fatty acid (SCFA) produced by microbial fermentation of dietary fiber, exerts beneficial metabolic and immunomodulatory functions through hyperactivation of the histone acetylase (HAT) p300 and inhibition of histone deacetylases (HDAC). These effects are widely believed to result in the acetylation of distinct histones that regulate specific genes, including at transcription starting sites (TSS) and enhancers. However, we show that this is not the case, as butyrate dose-dependently increases the acetylation of histones throughout the entire genome. Molecular dynamics simulations suggest that the RING-loop prevents the recruitment of p300 to acetylated histones through its bromodomain, and thereby cannot maintain the acetylation of specific histones through positive feedback. This was confirmed by showing that only catalytically inactive p300 stably binds to acetylated histones. Thus, the epigenetic regulation of specific genes by butyrate is limited, but butyrate instead increases histone acetylation globally resulting in opening of the entire chromatin structure.

molecular biology↗

bioRxiv2024

Intestine-on-chip enhances nutrient and drug metabolism and maturation of iPSC-derived intestinal epithelial cells relative to organoids and Transwells

The human intestinal epithelial barrier is shaped by various biological and biomechanical influences such as growth factor gradients and the flow of intestinal contents. Exposure to these cues in vitro impacts the cell type composition and function of adult stem cell (ASC)-derived intestinal epithelial cells, but their effect on human induced pluripotent stem cell (hiPSC)-derived cells is largely unexplored. Here, we characterize and compare the cellular composition and gene expression profiles of hiPSC-derived intestinal epithelial cells exposed to various medium compositions and cultured as organoids, in Transwell and in microfluidic intestine-on-chip systems. We demonstrate that inhibition and activation of the WNT, BMP, NOTCH and MAPK pathways regulates the presence of dividing, absorptive and secretory epithelial lineages within these systems, as has been described for ASC-based systems. Upon differentiation, intestinal epithelial organoids and monolayers in Transwell systems expressed genes involved in important intestinal functions, including digestive enzymes, nutrient transporters and members of the Cytochrome P450 family implicated in drug metabolism. However, the dynamic microenvironment of the intestine-on-chip system induced the strongest upregulation of these genes, with an expression profile that suggests a more mature developmental state. Overall, these results underscore the value of hiPSC-derived intestinal epithelial cells for modeling important functions of the human intestinal epithelial barrier and facilitates the selection of relevant culture conditions for specific applications.

cell biology↗

bioRxiv2024

High-resolution analysis of the treated coeliac disease microbiome reveals increased inter-individual variability

BackgroundCoeliac disease (CeD) is an immune-mediated disorder primarily affecting the small intestine, characterised by an inflammatory immune reaction to dietary gluten. CeD onset results from a multifaceted interplay of genetic and environmental factors. While recent data show that alterations in gut microbiome composition could play an important role, many current studies are constrained by small sample sizes and limited resolution. MethodsTo address these limitations, we analysed faecal gut microbiota from two Dutch cohorts, CeDNN (128 treated CeD patients (tCeD), 106 controls) and the Lifelines Dutch Microbiome Project (24 self-reported tCeD, 654 controls), using shotgun metagenomic sequencing. Self-reported IBS (570 cases, 1710 controls) and IBD (93 cases, 465 controls) were used as comparative conditions of the gastrointestinal tract. Interindividual variation within the case and control groups was calculated at whole microbiome and strain level. Finally, species-specific gene repertoires were analysed in tCeD patients and controls. ResultsWithin-individual microbiome diversity was decreased in patients with self-reported IBS and IBD but not in tCeD patients. Each condition displayed a unique microbial pattern and, in addition to confirming previously reported microbiome associations, we identify an increase in the levels of Clostridium sp. CAG:253, Roseburia hominis, and Eggerthella lenta, amongst others. We further show that the observed changes can partially be explained by gluten-free diet adherence. We also observe increased interindividual variation of gut microbiome composition among tCeD patients and a higher bacterial mutation frequency in tCeD that contributes to higher interindividual variation at strain level. In addition, the immotile European subspecies of Eubacterium rectale, which has a distinct carbohydrate metabolism potential, was nearly absent in tCeD patients. ConclusionOur study sheds light on the complex interplay between the gut microbiome and CeD, revealing increased interindividual variation and strain-level variation in tCeD patients. These findings expand our understanding of the microbiomes role in intestinal health and disease. HighlightsO_LIThis is the largest microbiome collection of coeliac disease (CeD) patients assembled to date, providing insights into gut microbiome composition down to strain level. C_LIO_LICompared to controls, treated CeD (tCeD) patients adhering to a gluten-free diet show novel gut microbiome associations. C_LIO_LItCeD patients also have a less uniform gut microbiome than controls. C_LIO_LIBacteria display higher mutation frequency in tCeD compared to controls. C_LIO_LIHallmarks of the European subspecies of Eubacterium rectale are nearly absent in tCeD patients, implying selection at strain level. C_LI

microbiology↗

bioRxiv2024

Gene expression and eQTL analysis reflect the heterogeneity in the inflammatory status of the duodenal epithelial lining in coeliac disease

In coeliac disease (CeD), the epithelial lining (EL) of the small intestine is severely damaged through a complex auto-inflammatory response that results in intraepithelial lymphocytes (IELs) attacking epithelial cells (ECs). To better understand the changes occurring in the EL in CeD, including after initiation of a gluten-free diet, and the regulatory mechanisms that affect mucosal homeostasis, we investigated ECs and IELs in the CeD duodenal EL using RNA-seq and eQTL analysis on predicted cell types. The study included 82 duodenal biopsies from volunteers, grouped into controls (CTRL), gluten-free diet treated CeD (TCD) and untreated CeD (UCD). We identified 2,868 differential expressed genes, which clustered into four sets with specific functions related to CeD. Two sets, one upregulated for cell cycle function and one downregulated for digestion, transmembrane transport, and laminin pathways, defined three groups of samples based on inflammation status: non-inflamed, mild inflammation or severe inflammation. These inflammation states correlated with but were not specific to disease state. The remaining two sets of genes were enriched for immune, extracellular matrix, and barrier functions. These latter two sets allowed the classification of samples into their disease conditions: CTRL, TCD, and UCD. Finally, deconvoluting eQTL effects from ECs and immune cells in the EL identified 7 and 9 cell-type-mediated eQTL genes, respectively. In sum, we identified genes expressed in the duodenal EL whose expression might be used as biomarkers to assess CeD condition and its mucosal and immune status. HighlightsO_LIGene expression in epithelial lining in CeD patients reflects inflammation status C_LIO_LIThe transcriptome can classify epithelium as no, mild, or severe inflammation C_LIO_LICell cycle, absorption, and basal lamina genes are indicators of mucosal damage C_LIO_LIImmune and extracellular matrix genes distinguish untreated from treated cases C_LIO_LIPredicted-cell-type eQTLs pinpoint effects in immune and epithelial cells C_LI

immunology↗

bioRxiv2024

An iPSC-derived small intestine-on-chip with self-organizing epithelial, mesenchymal and neural cells

Human induced pluripotent stem cell (hiPSC)-derived intestinal organoids are valuable tools for researching developmental biology and personalized therapies, but their closed topology and relative immature state limits their applications. Here we use organ-on-chip technology to develop a hiPSC-derived intestinal barrier with apical and basolateral access in a more physiological in vitro microenvironment. To replicate growth factor gradients along the crypt- villus axis, we locally exposed the cells to expansion and differentiation media. In these conditions, intestinal epithelial cells self-organize into villus-like folds with physiological barrier integrity and myofibroblast and neural subtypes emerge and form a layer in the bottom channel underneath the epithelial tissue. The growth factor gradients efficiently balance dividing and mature cell types and induce an intestinal epithelial composition, including absorptive and secretory lineages, resembling the composition of the human adult small intestine. The result is a well-characterized hiPSC-derived intestine-on-chip system that can facilitate personalized studies on physiological processes and therapy development in the human small intestine.

cell biology↗

bioRxiv2021

Genetic, environmental and intrinsic determinants of the human antibody epitope repertoire

Phage-displayed immunoprecipitation sequencing (PhIP-Seq) has successfully enabled high-throughput profiling of human antibody profiles. However, a comprehensive overview of environmental and genetic determinants shaping human adaptive immunity is currently lacking. In this study, we aimed to investigate the effects of genetic, environmental and intrinsic factors on the variation in human antibody repertoires. We characterized serological antibody repertoires against 344,000 peptides using PhIP-Seq libraries from a wide range of microbial and environmental antigens in 1,443 participants from a population cohort. We demonstrate individual-specificity, temporal consistency and co-housing similarities in antibody repertoire. Genetic analyses showed involvement of the HLA, IGHV and FUT2 regions. Furthermore, we uncovered associations between 48 phenotypic factors and 544 antibody-bound peptides, including age, cell counts, sex, smoking behavior and allergies, among others. Overall, our results indicate that human antibody epitope repertoires are shaped by both host genetics and environmental exposures and highlight unique signatures of distinct phenotypes and genotypes.

immunology↗