Judith Kraiczy, PhD

All Publications

• Smooth muscle contributes to the development and function of a layered intestinal stem cell niche DEVELOPMENTAL CELL McCarthy, N., Tie, G., Madha, S., He, R., Kraiczy, J., Maglieri, A., Shivdasani, R. A. 2023; 58 (7): 550-+

  Abstract

  Wnt and Rspondin (RSPO) signaling drives proliferation, and bone morphogenetic protein inhibitors (BMPi) impede differentiation, of intestinal stem cells (ISCs). Here, we identify the mouse ISC niche as a complex, multi-layered structure that encompasses distinct mesenchymal and smooth muscle populations. In young and adult mice, diverse sub-cryptal cells provide redundant ISC-supportive factors; few of these are restricted to single cell types. Niche functions refine during postnatal crypt morphogenesis, in part to oppose the dense aggregation of differentiation-promoting BMP+ sub-epithelial myofibroblasts at crypt-villus junctions. Muscularis mucosae, a specialized muscle layer, first appears during this period and supplements neighboring RSPO and BMPi sources. Components of this developing niche are conserved in human fetuses. The in vivo ablation of mouse postnatal smooth muscle increases BMP signaling activity, potently limiting a pre-weaning burst of crypt fission. Thus, distinct and progressively specialized mesenchymal cells together create the milieu that is required to propagate crypts during rapid organ growth and to sustain adult ISCs.

  View details for DOI 10.1016/j.devcel.2023.02.012

  View details for Web of Science ID 000982101700001

  View details for PubMedID 36924771

  View details for PubMedCentralID PMC10089980

• Graded BMP signaling within intestinal crypt architecture directs self-organization of the Wnt-secreting stem cell niche CELL STEM CELL Kraiczy, J., McCarthy, N., Malagola, E., Tie, G., Madha, S., Boffelli, D., Wagner, D. E., Wang, T. C., Shivdasani, R. A. 2023; 30 (4): 433-+

  Abstract

  Signals from the surrounding niche drive proliferation and suppress differentiation of intestinal stem cells (ISCs) at the bottom of intestinal crypts. Among sub-epithelial support cells, deep sub-cryptal CD81+ PDGFRAlo trophocytes capably sustain ISC functions ex vivo. Here, we show that mRNA and chromatin profiles of abundant CD81- PDGFRAlo mouse stromal cells resemble those of trophocytes and that both populations provide crucial canonical Wnt ligands. Mesenchymal expression of key ISC-supportive factors extends along a spatial and molecular continuum from trophocytes into peri-cryptal CD81- CD55hi cells, which mimic trophocyte activity in organoid co-cultures. Graded expression of essential niche factors is not cell-autonomous but dictated by the distance from bone morphogenetic protein (BMP)-secreting PDGFRAhi myofibroblast aggregates. BMP signaling inhibits ISC-trophic genes in PDGFRAlo cells near high crypt tiers; that suppression is relieved in stromal cells near and below the crypt base, including trophocytes. Cell distances thus underlie a self-organized and polar ISC niche.

  View details for DOI 10.1016/j.stem.2023.03.004

  View details for Web of Science ID 000976684400001

  View details for PubMedID 37028407

  View details for PubMedCentralID PMC10134073

• SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling CELL STEM CELL Gu, W., Wang, H., Huang, X., Kraiczy, J., Singh, P. P., Ng, C., Dagdeviren, S., Houghton, S., Pellon-Cardenas, O., Lan, Y., Nie, Y., Zhang, J., Banerjee, K. K., Onufer, E. J., Warner, B. W., Spence, J., Scherl, E., Rafii, S., Lee, R. T., Verzi, M. P., Redmond, D., Longman, R., Helin, K., Shivdasani, R. A., Zhou, Q. 2022; 29 (1): 101-+

  Abstract

  Adult stem cells maintain regenerative tissue structure and function by producing tissue-specific progeny, but the factors that preserve their tissue identities are not well understood. The small and large intestines differ markedly in cell composition and function, reflecting their distinct stem cell populations. Here we show that SATB2, a colon-restricted chromatin factor, singularly preserves LGR5+ adult colonic stem cell and epithelial identity in mice and humans. Satb2 loss in adult mice leads to stable conversion of colonic stem cells into small intestine ileal-like stem cells and replacement of the colonic mucosa with one that resembles the ileum. Conversely, SATB2 confers colonic properties on the mouse ileum. Human colonic organoids also adopt ileal characteristics upon SATB2 loss. SATB2 regulates colonic identity in part by modulating enhancer binding of the intestinal transcription factors CDX2 and HNF4A. Our study uncovers a conserved core regulator of colonic stem cells able to mediate cross-tissue plasticity in mature intestines.

  View details for DOI 10.1016/j.stem.2021.09.004

  View details for Web of Science ID 000807999000011

  View details for PubMedID 34582804

  View details for PubMedCentralID PMC8741647

• Cellular and molecular architecture of the intestinal stem cell niche NATURE CELL BIOLOGY McCarthy, N., Kraiczy, J., Shivdasani, R. A. 2020; 22 (9): 1033-1041

  Abstract

  Intestinal stem and progenitor cells replicate and differentiate in distinct compartments, influenced by Wnt, BMP, and other subepithelial cues. The cellular sources of these signals were long obscure because intestinal mesenchyme was insufficiently characterised. In this Review, we discuss how recent mRNA profiles of mouse and human intestinal submucosa, coupled with fine-resolution microscopy and gene and cell disruptions, reveal a coherent picture of an organised tissue carrying cells with distinct molecular properties and functions.

  View details for DOI 10.1038/s41556-020-0567-z

  View details for Web of Science ID 000565806900005

  View details for PubMedID 32884148

  View details for PubMedCentralID 196179

• Genome-Wide Epigenetic and Transcriptomic Characterization of Human-Induced Pluripotent Stem Cell-Derived Intestinal Epithelial Organoids CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY Kraiczy, J., Ross, A. B., Forbester, J. L., Dougan, G., Vallier, L., Zilbauer, M. 2019; 7 (2): 285-288

  View details for DOI 10.1016/j.jcmgh.2018.10.008

  View details for Web of Science ID 000459860200003

  View details for PubMedID 30704978

  View details for PubMedCentralID PMC6354438

• DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development GUT Kraiczy, J., Nayak, K. M., Howell, K. J., Ross, A., Forbester, J., Salvestrini, C., Mustata, R., Perkins, S., Andersson-Rolf, A., Leenen, E., Liebert, A., Vallier, L., Rosenstiel, P. C., Stegle, O., Dougan, G., Heuschkel, R., Koo, B., Zilbauer, M. 2019; 68 (1): 49-61

  Abstract

  Human intestinal epithelial organoids (IEOs) are increasingly being recognised as a highly promising translational research tool. However, our understanding of their epigenetic molecular characteristics and behaviour in culture remains limited.We performed genome-wide DNA methylation and transcriptomic profiling of human IEOs derived from paediatric/adult and fetal small and large bowel as well as matching purified human gut epithelium. Furthermore, organoids were subjected to in vitro differentiation and genome editing using CRISPR/Cas9 technology.We discovered stable epigenetic signatures which define regional differences in gut epithelial function, including induction of segment-specific genes during cellular differentiation. Established DNA methylation profiles were independent of cellular environment since organoids retained their regional DNA methylation over prolonged culture periods. In contrast to paediatric and adult organoids, fetal gut-derived organoids showed distinct dynamic changes of DNA methylation and gene expression in culture, indicative of an in vitro maturation. By applying CRISPR/Cas9 genome editing to fetal organoids, we demonstrate that this process is partly regulated by TET1, an enzyme involved in the DNA demethylation process. Lastly, generating IEOs from a child diagnosed with gastric heterotopia revealed persistent and distinct disease-associated DNA methylation differences, highlighting the use of organoids as disease-specific research models.Our study demonstrates striking similarities of epigenetic signatures in mucosa-derived IEOs with matching primary epithelium. Moreover, these results suggest that intestinal stem cell-intrinsic DNA methylation patterns establish and maintain regional gut specification and are involved in early epithelial development and disease.

  View details for DOI 10.1136/gutjnl-2017-314817

  View details for Web of Science ID 000455727900011

  View details for PubMedID 29141958

  View details for PubMedCentralID PMC6839835

• DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome GASTROENTEROLOGY Howell, K., Kraiczy, J., Nayak, K. M., Gasparetto, M., Ross, A., Lee, C., Mak, T. N., Koo, B., Kumar, N., Lawley, T., Sinha, A., Rosenstiel, P., Heuschkel, R., Stegle, O., Zilbauer, M. 2018; 154 (3): 585-598

  Abstract

  We analyzed DNA methylation patterns and transcriptomes of primary intestinal epithelial cells (IEC) of children newly diagnosed with inflammatory bowel diseases (IBD) to learn more about pathogenesis.We obtained mucosal biopsies (N = 236) collected from terminal ileum and ascending and sigmoid colons of children (median age 13 years) newly diagnosed with IBD (43 with Crohn's disease [CD], 23 with ulcerative colitis [UC]), and 30 children without IBD (controls). Patients were recruited and managed at a hospital in the United Kingdom from 2013 through 2016. We also obtained biopsies collected at later stages from a subset of patients. IECs were purified and analyzed for genome-wide DNA methylation patterns and gene expression profiles. Adjacent microbiota were isolated from biopsies and analyzed by 16S gene sequencing. We generated intestinal organoid cultures from a subset of samples and genome-wide DNA methylation analysis was performed.We found gut segment-specific differences in DNA methylation and transcription profiles of IECs from children with IBD vs controls; some were independent of mucosal inflammation. Changes in gut microbiota between IBD and control groups were not as large and were difficult to assess because of large amounts of intra-individual variation. Only IECs from patients with CD had changes in DNA methylation and transcription patterns in terminal ileum epithelium, compared with controls. Colon epithelium from patients with CD and from patients with ulcerative colitis had distinct changes in DNA methylation and transcription patterns, compared with controls. In IECs from patients with IBD, changes in DNA methylation, compared with controls, were stable over time and were partially retained in ex-vivo organoid cultures. Statistical analyses of epithelial cell profiles allowed us to distinguish children with CD or UC from controls; profiles correlated with disease outcome parameters, such as the requirement for treatment with biologic agents.We identified specific changes in DNA methylation and transcriptome patterns in IECs from pediatric patients with IBD compared with controls. These data indicate that IECs undergo changes during IBD development and could be involved in pathogenesis. Further analyses of primary IECs from patients with IBD could improve our understanding of the large variations in disease progression and outcomes.

  View details for DOI 10.1053/j.gastro.2017.10.007

  View details for Web of Science ID 000424741500031

  View details for PubMedID 29031501

  View details for PubMedCentralID PMC6381389

• Assessing DNA methylation in the developing human intestinal epithelium: potential link to inflammatory bowel disease MUCOSAL IMMUNOLOGY Kraiczy, J., Nayak, K., Ross, A., Raine, T., Mak, T. N., Gasparetto, M., Cario, E., Rakyan, V., Heuschkel, R., Zilbauer, M. 2016; 9 (3): 647-658

  Abstract

  DNA methylation is one of the major epigenetic mechanisms implicated in regulating cellular development and cell-type-specific gene expression. Here we performed simultaneous genome-wide DNA methylation and gene expression analysis on purified intestinal epithelial cells derived from human fetal gut, healthy pediatric biopsies, and children newly diagnosed with inflammatory bowel disease (IBD). Results were validated using pyrosequencing, real-time PCR, and immunostaining. The functional impact of DNA methylation changes on gene expression was assessed by employing in-vitro assays in intestinal cell lines. DNA methylation analyses allowed identification of 214 genes for which expression is regulated via DNA methylation, i.e. regulatory differentially methylated regions (rDMRs). Pathway and functional analysis of rDMRs suggested a critical role for DNA methylation in regulating gene expression and functional development of the human intestinal epithelium. Moreover, analysis performed on intestinal epithelium of children newly diagnosed with IBD revealed alterations in DNA methylation within genomic loci, which were found to overlap significantly with those undergoing methylation changes during intestinal development. Our study provides novel insights into the physiological role of DNA methylation in regulating functional maturation of the human intestinal epithelium. Moreover, we provide data linking developmentally acquired alterations in the DNA methylation profile to changes seen in pediatric IBD.

  View details for DOI 10.1038/mi.2015.88

  View details for Web of Science ID 000375275300008

  View details for PubMedID 26376367

  View details for PubMedCentralID PMC4854977

• Patient-derived organoid biobank identifies epigenetic dysregulation of intestinal epithelial MHC-I as a novel mechanism in severe Crohn's Disease GUT Dennison, T. W., Edgar, R. D., Payne, F., Nayak, K. M., Ross, A. B., Cenier, A., Glemas, C., Giachero, F., Foster, A. R., Harris, R., Kraiczy, J., Salvestrini, C., Stavrou, G., Torrente, F., Brook, K., Trayers, C., Elmentaite, R., Youssef, G., Tel, B., Winton, D., Skoufou-Papoutsaki, N., Adler, S., Bufler, P., Azabdaftari, A., Jenke, A., Natasha, G., Thomas, N., Miele, E., Al-Mohammad, A., Guarda, G., Kugathasan, S., Venkateswaran, S., Clatworthy, M. R., Castro-Dopico, T., Suchanek, O., Strisciuglio, C., Gasparetto, M., Lee, S., Xu, X., Bello, E., Han, N., Zerbino, D. R., Teichmann, S. A., Nys, J., Heuschkel, R., Perrone, F., Zilbauer, M. 2024

  Abstract

  Epigenetic mechanisms, including DNA methylation (DNAm), have been proposed to play a key role in Crohn's disease (CD) pathogenesis. However, the specific cell types and pathways affected as well as their potential impact on disease phenotype and outcome remain unknown. We set out to investigate the role of intestinal epithelial DNAm in CD pathogenesis.We generated 312 intestinal epithelial organoids (IEOs) from mucosal biopsies of 168 patients with CD (n=72), UC (n=23) and healthy controls (n=73). We performed genome-wide molecular profiling including DNAm, bulk as well as single-cell RNA sequencing. Organoids were subjected to gene editing and the functional consequences of DNAm changes evaluated using an organoid-lymphocyte coculture and a nucleotide-binding oligomerisation domain, leucine-rich repeat and CARD domain containing 5 (NLRC5) dextran sulphate sodium (DSS) colitis knock-out mouse model.We identified highly stable, CD-associated loss of DNAm at major histocompatibility complex (MHC) class 1 loci including NLRC5 and cognate gene upregulation. Single-cell RNA sequencing of primary mucosal tissue and IEOs confirmed the role of NLRC5 as transcriptional transactivator in the intestinal epithelium. Increased mucosal MHC-I and NLRC5 expression in adult and paediatric patients with CD was validated in additional cohorts and the functional role of MHC-I highlighted by demonstrating a relative protection from DSS-mediated mucosal inflammation in NLRC5-deficient mice. MHC-I DNAm in IEOs showed a significant correlation with CD disease phenotype and outcomes. Application of machine learning approaches enabled the development of a disease prognostic epigenetic molecular signature.Our study has identified epigenetically regulated intestinal epithelial MHC-I as a novel mechanism in CD pathogenesis.

  View details for DOI 10.1136/gutjnl-2024-332043

  View details for Web of Science ID 001248324000001

  View details for PubMedID 38857990

• Single-cell atlas of human liver development reveals pathways directing hepatic cell fates NATURE CELL BIOLOGY Wesley, B. T., Ross, A. B., Muraro, D., Miao, Z., Saxton, S., Tomaz, R. A., Morell, C. M., Ridley, K., Zacharis, E. D., Petrus-Reurer, S., Kraiczy, J., Mahbubani, K. T., Brown, S., Garcia-Bernardo, J., Alsinet, C., Gaffney, D., Horsfall, D., Tysoe, O. C., Botting, R. A., Stephenson, E., Popescu, D., MacParland, S., Bader, G., McGilvray, I. D., Ortmann, D., Sampaziotis, F., Saeb-Parsy, K., Haniffa, M., Stevens, K. R., Zilbauer, M., Teichmann, S. A., Vallier, L. 2022; 24 (10): 1487-+

  Abstract

  The liver has been studied extensively due to the broad number of diseases affecting its vital functions. However, therapeutic advances have been hampered by the lack of knowledge concerning human hepatic development. Here, we addressed this limitation by describing the developmental trajectories of different cell types that make up the human liver at single-cell resolution. These transcriptomic analyses revealed that sequential cell-to-cell interactions direct functional maturation of hepatocytes, with non-parenchymal cells playing essential roles during organogenesis. We utilized this information to derive bipotential hepatoblast organoids and then exploited this model system to validate the importance of signalling pathways in hepatocyte and cholangiocyte specification. Further insights into hepatic maturation also enabled the identification of stage-specific transcription factors to improve the functionality of hepatocyte-like cells generated from human pluripotent stem cells. Thus, our study establishes a platform to investigate the basic mechanisms directing human liver development and to produce cell types for clinical applications.

  View details for DOI 10.1038/s41556-022-00989-7

  View details for Web of Science ID 000854723100002

  View details for PubMedID 36109670

• Culture-Associated DNA Methylation Changes Impact on Cellular Function of Human Intestinal Organoids CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY Edgar, R. D., Perrone, F., Foster, A. R., Payne, F., Lewis, S., Nayak, K. M., Kraiczy, J., Cenier, A., Torrente, F., Salvestrini, C., Heuschkel, R., Hensel, K. O., Harris, R., Jones, D., Zerbino, D. R., Zilbauer, M. 2022; 14 (6): 1295-1310

  Abstract

  Human intestinal epithelial organoids (IEOs) are a powerful tool to model major aspects of intestinal development, health, and diseases because patient-derived cultures retain many features found in vivo. A necessary aspect of the organoid model is the requirement to expand cultures in vitro through several rounds of passaging. This is of concern because the passaging of cells has been shown to affect cell morphology, ploidy, and function.Here, we analyzed 173 human IEO lines derived from the small and large bowel and examined the effect of culture duration on DNA methylation (DNAm). Furthermore, we tested the potential impact of DNAm changes on gene expression and cellular function.Our analyses show a reproducible effect of culture duration on DNAm in a large discovery cohort as well as 2 publicly available validation cohorts generated in different laboratories. Although methylation changes were seen in only approximately 8% of tested cytosine-phosphate-guanine dinucleotides (CpGs) and global cellular function remained stable, a subset of methylation changes correlated with altered gene expression at baseline as well as in response to inflammatory cytokine exposure and withdrawal of Wnt agonists. Importantly, epigenetic changes were found to be enriched in genomic regions associated with colonic cancer and distant to the site of replication, indicating similarities to malignant transformation.Our study shows distinct culture-associated epigenetic changes in mucosa-derived human IEOs, some of which appear to impact gene transcriptomic and cellular function. These findings highlight the need for future studies in this area and the importance of considering passage number as a potentially confounding factor.

  View details for DOI 10.1016/j.jcmgh.2022.08.008

  View details for Web of Science ID 000892242700001

  View details for PubMedID 36038072

  View details for PubMedCentralID PMC9703134

• Regional Differences in Human Biliary Tissues and Corresponding In Vitro-Derived Organoids HEPATOLOGY Rimland, C. A., Tilson, S. G., Morell, C. M., Tomaz, R. A., Lu, W., Adams, S. E., Georgakopoulos, N., Otaizo-Carrasquero, F., Myers, T. G., Ferdinand, J. R., Gieseck, R. L., Sampaziotis, F., Tysoe, O. C., Ross, A., Kraiczy, J. M., Wesley, B., Muraro, D., Zilbauer, M., Oniscu, G. C., Hannan, N. F., Forbes, S. J., Saeb-Parsy, K., Wynn, T. A., Vallier, L. 2021; 73 (1): 247-267

  Abstract

  Organoids provide a powerful system to study epithelia in vitro. Recently, this approach was applied successfully to the biliary tree, a series of ductular tissues responsible for the drainage of bile and pancreatic secretions. More precisely, organoids have been derived from ductal tissue located outside (extrahepatic bile ducts; EHBDs) or inside the liver (intrahepatic bile ducts; IHBDs). These organoids share many characteristics, including expression of cholangiocyte markers such as keratin (KRT) 19. However, the relationship between these organoids and their tissues of origin, and to each other, is largely unknown.Organoids were derived from human gallbladder, common bile duct, pancreatic duct, and IHBDs using culture conditions promoting WNT signaling. The resulting IHBD and EHBD organoids expressed stem/progenitor markers leucine-rich repeat-containing G-protein-coupled receptor 5/prominin 1 and ductal markers KRT19/KRT7. However, RNA sequencing revealed that organoids conserve only a limited number of regional-specific markers corresponding to their location of origin. Of particular interest, down-regulation of biliary markers and up-regulation of cell-cycle genes were observed in organoids. IHBD and EHBD organoids diverged in their response to WNT signaling, and only IHBDs were able to express a low level of hepatocyte markers under differentiation conditions.Taken together, our results demonstrate that differences exist not only between extrahepatic biliary organoids and their tissue of origin, but also between IHBD and EHBD organoids. This information may help to understand the tissue specificity of cholangiopathies and also to identify targets for therapeutic development.

  View details for DOI 10.1002/hep.31252

  View details for Web of Science ID 000615369800019

  View details for PubMedID 32222998

  View details for PubMedCentralID PMC8641381

• Transcription and DNA Methylation Patterns of Blood-Derived CD8<SUP>+</SUP> T Cells Are Associated With Age and Inflammatory Bowel Disease But Do Not Predict Prognosis GASTROENTEROLOGY Gasparetto, M., Payne, F., Nayak, K., Kraiczy, J., Glemas, C., Philip-McKenzie, Y., Ross, A., Edgar, R. D., Zerbino, D. R., Salvestrini, C., Torrente, F., Ventham, N. T., Kalla, R., Satsangi, J., Sarkies, P., Heuschkel, R., Zilbauer, M. 2021; 160 (1): 232-+

  Abstract

  Gene expression patterns of CD8+ T cells have been reported to correlate with clinical outcomes of adults with inflammatory bowel diseases (IBD). We aimed to validate these findings in independent patient cohorts.We obtained peripheral blood samples from 112 children with a new diagnosis of IBD (71 with Crohn's disease and 41 with ulcerative colitis) and 19 children without IBD (controls) and recorded medical information on disease activity and outcomes. CD8+ T cells were isolated from blood samples by magnetic bead sorting at the point of diagnosis and during the course of disease. Genome-wide transcription (n = 192) and DNA methylation (n = 66) profiles were generated using Affymetrix and Illumina arrays, respectively. Publicly available transcriptomes and DNA methylomes of CD8+ T cells from 3 adult patient cohorts with and without IBD were included in data analyses.Previously reported CD8+ T-cell prognostic expression and exhaustion signatures were only found in the original adult IBD patient cohort. These signatures could not be detected in either a pediatric or a second adult IBD cohort. In contrast, an association between CD8+ T-cell gene expression with age and sex was detected across all 3 cohorts. CD8+ gene transcription was clearly associated with IBD in the 2 cohorts that included non-IBD controls. Lastly, DNA methylation profiles of CD8+ T cells from children with Crohn's disease correlated with age but not with disease outcome.We were unable to validate previously reported findings of an association between CD8+ T-cell gene transcription and disease outcome in IBD. Our findings reveal the challenges of developing prognostic biomarkers for patients with IBD and the importance of their validation in large, independent cohorts before clinical application.

  View details for DOI 10.1053/j.gastro.2020.08.017

  View details for Web of Science ID 000600644700036

  View details for PubMedID 32814113

  View details for PubMedCentralID PMC7428744

• Intestinal Epithelial Organoids as Tools to Study Epigenetics in Gut Health and Disease STEM CELLS INTERNATIONAL Kraiczy, J., Zilbauer, M. 2019; 2019: 7242415

  Abstract

  The intestinal epithelium forms the inner layer of the human intestine and serves a wide range of diverse functions. Its constant exposure to a vast amount of complex microbiota highlights the critical interface that this single-cell layer forms between the host and our environment. Importantly, the well-documented contribution of environmental factors towards the functional development of the human intestinal epithelium directly implies epigenetic mechanisms in orchestrating this complex interplay. The development of intestinal epithelial organoid culture systems that can be generated from human tissue provides researchers with unpresented opportunities to study functional aspects of human intestinal epithelial pathophysiology. In this brief review, we summarise existing evidence for the role of epigenetics in regulating intestinal epithelial cell function and highlight the great potential for human gut organoids as translational research tools to investigate these mechanisms in vitro.

  View details for DOI 10.1155/2019/7242415

  View details for Web of Science ID 000458441100001

  View details for PubMedID 30809264

  View details for PubMedCentralID PMC6369455

• Interleukin-22 promotes phagolysosomal fusion to induce protection against <i>Salmonella enterica</i> Typhimurium in human epithelial cells PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Forbester, J. L., Lees, E. A., Goulding, D., Forrest, S., Yeung, A., Speak, A., Clare, S., Coomber, E. L., Mukhopadhyay, S., Kraiczy, J., Schreiber, F., Lawley, T. D., Hancock, R. W., Uhlig, H. H., Zilbauer, M., Powrie, F., Dougan, G. 2018; 115 (40): 10118-10123

  Abstract

  Intestinal epithelial cells (IECs) play a key role in regulating immune responses and controlling infection. However, the direct role of IECs in restricting pathogens remains incompletely understood. Here, we provide evidence that IL-22 primed intestinal organoids derived from healthy human induced pluripotent stem cells (hIPSCs) to restrict Salmonella enterica serovar Typhimurium SL1344 infection. A combination of transcriptomics, bacterial invasion assays, and imaging suggests that IL-22-induced antimicrobial activity is driven by increased phagolysosomal fusion in IL-22-pretreated cells. The antimicrobial phenotype was absent in hIPSCs derived from a patient harboring a homozygous mutation in the IL10RB gene that inactivates the IL-22 receptor but was restored by genetically complementing the IL10RB deficiency. This study highlights a mechanism through which the IL-22 pathway facilitates the human intestinal epithelium to control microbial infection.

  View details for DOI 10.1073/pnas.1811866115

  View details for Web of Science ID 000446078700082

  View details for PubMedID 30217896

  View details for PubMedCentralID PMC6176607

• Combining Histologic and Molecular Techniques to Distinguish Inflamed From Uninflamed Tissue Reply GASTROENTEROLOGY Howell, K., Kraiczy, J., Stegle, O., Zilbauer, M. 2018; 155 (1): 230-231

  View details for DOI 10.1053/j.gastro.2018.06.033

  View details for Web of Science ID 000439705600064

  View details for PubMedID 29894680

• Epigenetics in Gastrointestinal Health and Disease: Spotlight on DNA Methylation in the Intestinal Epithelium Zilbauer, M., Kraiczy, J., Isolauri, E., Sherman, P. M., Walker, W. A. KARGER. 2017: 35-44

  Abstract

  Epigenetics can be defined as stable, potentially heritable changes in cellular phenotype caused by mechanisms other than alterations in the underlying DNA sequence. DNA methylation is amongst the most intensely studied epigenetic mechanisms and has been shown to play a major role in regulating fundamental aspects of cell biology including cellular differentiation, organ development, and cell type-specific gene expression. Importantly, it is becoming increasingly clear that epigenetic mechanisms operate at the interface between the genetic code and our environment and are able to mediate environmental changes into stable phenotypic alterations. Given existing evidence supporting the important effects of environmental factors (e.g., diet, nutrition, and infections) on human health, epigenetic mechanisms provide a plausible mechanistic framework for the development of many multifactorial diseases including inflammatory bowel disease (IBD). Impaired function of the intestinal epithelium has been implicated in IBD pathogenesis, yet underlying mechanisms remain ill defined. The work of our group focuses on investigating the role of DNA methylation in regulating cellular function of the human intestinal epithelium during gastrointestinal health and IBD. In addition to performing an analysis of primary human intestinal epithelium, we utilize human intestinal organoid culture systems allowing us to perform functional analysis in a patient-derived ex vivo model.

  View details for DOI 10.1159/000455211

  View details for Web of Science ID 000413698400004

  View details for PubMedID 28346922

• Epigenetics in Paediatric Gastroenterology, Hepatology, and Nutrition: Present Trends and Future Perspectives JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION Zilbauer, M., Zellos, A., Heuschkel, R., Gasparetto, M., Kraiczy, J., Postberg, J., Greco, L., Auricchio, R., Galatola, M., Embleton, N., Wirth, S., Jenke, A. 2016; 62 (4): 521-529

  Abstract

  Epigenetics can be defined as stable, potentially heritable changes in the cellular phenotype caused by mechanisms other than alterations to the underlying DNA sequence. As such, any observed phenotypic changes including organ development, aging, and the occurrence of disease could be driven by epigenetic mechanisms in the presence of stable cellular DNA sequences. Indeed, with the exception of rare mutations, the human genome-sequence has remained remarkably stable over the past centuries. In contrast, substantial changes to our environment as part of our modern life style have not only led to a significant reduction of certain infectious diseases but also seen the exponential increase in complex traits including obesity and multifactorial diseases such as autoimmune disorders. It is becoming increasingly clear that epigenetic mechanisms operate at the interface between the genetic code and our environment, and a large body of existing evidence supports the importance of environmental factors such as diet and nutrition, infections, and exposure to toxins on human health. This seems to be particularly the case during vulnerable periods of human development such as pregnancy and early life. Importantly, as the first point of contact for many of such environmental factors including nutrition, the digestive system is being increasingly linked to a number of "modern" pathologies. In this review article, we aim to give a brief introduction to the basic molecular principals of epigenetics and provide a concise summary of the existing evidence for the role of epigenetic mechanisms in gastrointestinal health and disease, hepatology, and nutrition.

  View details for DOI 10.1097/MPG.0000000000001053

  View details for Web of Science ID 000373209900004

  View details for PubMedID 26628441

• Matrix-Assisted Transplantation of Functional Beige Adipose Tissue DIABETES Tharp, K. M., Jha, A. K., Kraiczy, J., Yesian, A., Karateev, G., Sinisi, R., Dubikovskaya, E. A., Healy, K. E., Stahl, A. 2015; 64 (11): 3713-3724

  Abstract

  Novel, clinically relevant, approaches to shift energy balance are urgently needed to combat metabolic disorders such as obesity and diabetes. One promising approach has been the expansion of brown adipose tissues that express uncoupling protein (UCP) 1 and thus can uncouple mitochondrial respiration from ATP synthesis. While expansion of UCP1-expressing adipose depots may be achieved in rodents via genetic and pharmacological manipulations or the transplantation of brown fat depots, these methods are difficult to use for human clinical intervention. We present a novel cell scaffold technology optimized to establish functional brown fat-like depots in vivo. We adapted the biophysical properties of hyaluronic acid-based hydrogels to support the differentiation of white adipose tissue-derived multipotent stem cells (ADMSCs) into lipid-accumulating, UCP1-expressing beige adipose tissue. Subcutaneous implantation of ADMSCs within optimized hydrogels resulted in the establishment of distinct UCP1-expressing implants that successfully attracted host vasculature and persisted for several weeks. Importantly, implant recipients demonstrated elevated core body temperature during cold challenges, enhanced respiration rates, improved glucose homeostasis, and reduced weight gain, demonstrating the therapeutic merit of this highly translatable approach. This novel approach is the first truly clinically translatable system to unlock the therapeutic potential of brown fat-like tissue expansion.

  View details for DOI 10.2337/db15-0728

  View details for Web of Science ID 000363832500012

  View details for PubMedID 26293504

  View details for PubMedCentralID PMC4613967

• Mice lacking the intestinal peptide transporter display reduced energy intake and a subtle maldigestion/malabsorption that protects them from diet-induced obesity AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY Kolodziejczak, D., Spanier, B., Pais, R., Kraiczy, J., Stelzl, T., Gedrich, K., Scherling, C., Zietek, T., Daniel, H. 2013; 304 (10): G897-G907

  Abstract

  The intestinal transporter PEPT1 mediates the absorption of di- and tripeptides originating from breakdown of dietary proteins. Whereas mice lacking PEPT1 did not display any obvious changes in phenotype on a high-carbohydrate control diet (HCD), Pept1(-/-) mice fed a high-fat diet (HFD) showed a markedly reduced weight gain and reduced body fat stores. They were additionally protected from hyperglycemia and hyperinsulinemia. Energy balance studies revealed that Pept1(-/-) mice on HFD have a reduced caloric intake, no changes in energy expenditure, but increased energy content in feces. Cecal biomass in Pept1(-/-) mice was as well increased twofold on both diets, suggesting a limited capacity in digesting and/or absorbing the dietary constituents in the small intestine. GC-MS-based metabolite profiling of cecal contents revealed high levels and a broad spectrum of sugars in PEPT1-deficient mice on HCD, whereas animals fed HFD were characterized by high levels of free fatty acids and absence of sugars. In search of the origin of the impaired digestion/absorption, we observed that Pept1(-/-) mice lack the adaptation of the upper small intestinal mucosa to the trophic effects of the diet. Whereas wild-type mice on HFD adapt to diet with increased villus length and surface area, Pept1(-/-) mice failed to show this response. In search for the origin of this, we recorded markedly reduced systemic IL-6 levels in all Pept1(-/-) mice, suggesting that IL-6 could contribute to the lack of adaptation of the mucosal architecture to the diets.

  View details for DOI 10.1152/ajpgi.00160.2012

  View details for Web of Science ID 000318968100006

  View details for PubMedID 23494121