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OBJECTIVES: High energy long bone fractures with critical bone loss are at risk for nonunion without strategic intervention. We hypothesize that a synthetic membrane implanted at a single stage improves bone healing in a preclinical nonunion model. METHODS: Using standard laboratory techniques, microspheres encapsulating bone morphogenic protein-2 (BMP2) or platelet derived growth factor (PDGF) were designed and coupled to a type 1 collagen sheet. Critical femoral defects were created in rats and stabilized by locked retrograde intramedullary nailing. The negative control group had an empty defect. The induced membrane group (positive control) had a polymethylmethacrylate spacer inserted into the defect for four weeks and replaced with a bare polycaprolactone/beta-tricalcium phosphate (PCL/β-TCP) scaffold at a second stage. For the experimental groups, a bioactive synthetic membrane embedded with BMP2, PDGF or both enveloped a PCL/β-TCP scaffold was implanted in a single stage. Serial radiographs were taken at 1, 4, 8, and 12 weeks postoperatively from the definitive procedure and evaluated by two blinded observers using a previously described scoring system to judge union as primary outcome. RESULTS: All experimental groups demonstrated better union than the negative control (p=0.01). The groups with BMP2 incorporated into the membrane demonstrated higher average union Mehta scores than the other groups (p=0.01). The induced membrane group performed similarly to the PDGF group. Complete union was only demonstrated in groups with BMP2-eluting membranes. CONCLUSIONS: A synthetic membrane comprised of type 1 collagen embedded with controlled release BMP2 improved union of critical bone defects in a preclinical nonunion model.

We retrace Prof. François Diederich's consultancy work for Roche and its impact over the years he worked with us. François Diederich uniquely shaped our approach to molecular design, and interactions with him and his research group at ETH Zurich have created deep insights into molecular recognition. Herein we share how his style and approach continue to inspire us.

The Torsion Library is a collection of torsion motifs associated with angle distributions, derived from crystallographic databases. It is used in strain assessment, conformer generation, and geometry optimization. A hierarchical structure of expert curated SMARTS defines the chemical environments of rotatable bonds and associates these with preferred angles. SMARTS can be very complex and full of implications, which make them difficult to maintain manually. Recent developments in automatically comparing SMARTS patterns can be applied to the Torsion Library to ensure its correctness. We specifically discuss the implementation and the limits of such a procedure in the context of torsion motifs and show several examples of how the Torsion Library benefits from this. All automated changes are validated manually and then shown to have an effect on the angle distributions by correcting matching behavior. The corrected Torsion Library itself is available including both PDB as well as CSD histograms in the Supporting Information and can be used to evaluate rotatable bonds at https://torsions.zbh.uni-hamburg.de.

Background & Aims. T-regulatory (Treg) cells suppress immune responses to maintain homeostasis. There are two main subsets of Treg cells, FOXP3-positive Treg cells that do not produce high levels of effector cytokines and Type 1 Treg (Tr1) cells that are FOXP3-negative and secrete interleukin 10 (IL10). IL10 is an important anti-inflammatory cytokine, therefore Tr1 cells might be uniquely suited for development as a treatment for inflammatory bowel diseases. We aimed to develop methods to isolate and expand human Tr1 cells and define their functions. Methods. We obtained blood samples and colon biopsies from patients with Crohn’s disease or ulcerative colitis or healthy individuals (controls). CD4+ T cells were isolated from blood samples, stimulated with anti-CD3/CD28 beads and Tr1 cells purified using an IL10 cytokine capture assay and cell sorting. FOXP3-positive Treg cells were sorted as CD4+CD25highCD127low cells from unstimulated cells. Tr1 and FOXP3-positive Treg cells were expanded, and phenotypes and gene expression profiles were compared. T cells in peripheral blood mononuclear cells from healthy donors were stimulated with anti-CD3/CD28 beads and the suppressive abilities of Tr1 and FOXP3-positive Treg cells were measured. Human colonic organoid cultures were established then cultured with Tr1 or FOXP3-positive Treg cell culture supernatants and analyzed by immunofluorescence and flow cytometry. T84 cells (human colonic adenocarcinoma epithelial cells) were incubated with Tr1 or FOXP3-positive Treg cell culture supernatants and trans-epithelial electrical resistance was measured to determine epithelial cell barrier function. Results. Phenotypes of Tr1 cells isolated from healthy subjects or patients with Crohn’s disease or ulcerative colitis did not differ significantly following expansion. Tr1 cells and FOXP3-positive Treg cells suppressed proliferation of effector T cells, but only Tr1 cells suppressed secretion of IL1beta (IL1B) and TNF from myeloid cells. Tr1 cells, but not FOXP3-positive Treg cells, isolated from healthy subjects and IBD patients secreted IL22, which regulated repair of the epithelium and promoted barrier function of human intestinal epithelial cells. Tr1 cell culture supernatants promoted differentiation of mucin-producing goblet cells in intestinal organoid cultures. Conclusion. Human Tr1 cells suppress proliferation of effector T cells (adaptive immune response) and production of IL1B and TNF by myeloid cells (innate immune response). They also secrete IL22 to regulate repair of the epithelium and promote barrier function. They might be developed as a cell-based therapy for intestinal inflammatory disorders.

ObjectiveHyperglycemia and type 2 diabetes (T2D) are caused by failure of pancreatic beta cells. The role of the gut microbiota in T2D has been studied but causal links remain enigmatic.DesignObese individuals with or without T2D were included from two independent Dutch cohorts. Human data was translated in vitro and in vivo by using pancreatic islets from C57BL6/J mice and by injecting flagellin into obese mice.ResultsFlagellin is part of the bacterial locomotor appendage flagellum, present on gut bacteria including Enterobacteriaceae, which we show to be more abundant in the gut of individuals with T2D. Subsequently, flagellin induces a pro-inflammatory response in pancreatic islets mediated by the Toll-like receptor (TLR)-5 expressed on resident islet macrophages. This inflammatory response associated with beta-cell dysfunction, characterized by reduced insulin gene expression, impaired proinsulin processing and stress-induced insulin hypersecretion in vitro and in vivo in mice.ConclusionWe postulate that increased systemically disseminated flagellin in T2D is a contributing factor to beta cell failure in time and represents a novel therapeutic target.Graphical abstract

Reducing food intake is a common host response to infection, yet it remains unclear whether fasting is detrimental or beneficial to an infected host. Despite the gastrointestinal tract being the primary site of nutrient uptake and a common route for infection, studies have yet to examine how fasting alters the host’s response to an enteric infection. To test this, mice were fasted before and during oral infection with the invasive bacterium Salmonella enterica serovar Typhimurium. Fasting dramatically interrupted infection and subsequent gastroenteritis by suppressing Salmonella’s SPI-1 virulence program, preventing invasion of the gut epithelium. Virulence suppression depended on the gut microbiota, as Salmonella’s invasion of the epithelium proceeded in fasting gnotobiotic mice. Despite Salmonella’s restored virulence within the intestines of gnotobiotic mice, fasting downregulated pro-inflammatory signaling, greatly reducing intestinal pathology. Our study highlights how food intake controls the complex relationship between host, pathogen and gut microbiota during an enteric infection., Author summary Most animals, including humans, lose their appetites when sick. Whether this sickness behavior has evolved as a protective mechanism is unclear. In addition, fasting therapies have become popular in recent years and show promise for treating chronic inflammatory diseases, but it is uncertain whether fasting-induced immunosuppression could leave an already fasted host more vulnerable to infection than a fed host. To test this, we fasted mice and orally infected them with the invasive bacterium Salmonella Typhimurium. This pathogen causes gastroenteritis (food poisoning) in humans and in antibiotic-pretreated mice. Notably, the fasted mice were protected from infection. While Salmonella rapidly expanded in the intestines of fed mice, their expansion was reduced in fasted mice. Moreover, Salmonella in the fasted mice did not cause any intestinal tissue damage as the bacteria were unable to invade the intestinal wall. This protection was found to be partially due to the gut microbiome, since fasting was unable to prevent Salmonella infection in mice lacking a microbiome, although the mice suffered less gastroenteritis. We therefore conclude that fasting can protect hosts from intestinal bacterial infections, in part through the actions of the gut microbiome.

The lining of the gut epithelium is made up of a simple layer of specialized epithelial cells that expose their apical side to the lumen and respond to external cues. Recent optimization of in vitro culture conditions allows for the re-creation of the intestinal stem cell niche and the development of advanced 3-dimensional (3D) culture systems that recapitulate the cell composition and the organization of the epithelium. Intestinal organoids embedded in an extracellular matrix (ECM) can be maintained for long-term and self-organize to generate a well-defined, polarized epithelium that encompasses an internal lumen and an external exposed basal side. This restrictive nature of the intestinal organoids presents challenges in accessing the apical surface of the epithelium in vitro and limits the investigation of biological mechanisms such as nutrient uptake and host-microbiota/host-pathogen interactions. Here, we describe two methods that facilitate access to the apical side of the organoid epithelium and support the differentiation of specific intestinal cell types. First, we show how ECM removal induces an inversion of the epithelial cell polarity and allows for the generation of apical-out 3D organoids. Second, we describe how to generate 2-dimensional (2D) monolayers from single cell suspensions derived from intestinal organoids, comprised of mature and differentiated cell types. These techniques provide novel tools to study apical-specific interactions of the epithelium with external cues in vitro and promote the use of organoids as a platform to facilitate precision medicine.

Intestinal epithelial cells (IEC) reside in close proximity to the gut microbiota and are hypo-responsive to bacterial products, likely to prevent maladaptive inflammatory responses. This is in part due to their strong expression of Single Ig IL-1 related receptor (SIGIRR), a negative regulator of interleukin (IL)-1 and toll-like receptor signaling. IL-37, an anti-inflammatory cytokine that inhibits innate signaling in diverse cells by signaling through SIGIRR. Despite the strong expression of SIGIRR by IEC, few studies have examined whether IL-37 can suppress their innate immune signaling. We characterized innate immune responses of human and murine colonoids to bacteria (FliC, LPS) and host (IL-1β) products and the role of IL-37/SIGIRR in regulating these responses. We demonstrated that human colonoids responded only to FliC, but not to LPS or IL-1β. While colonoids derived from different donors displayed significant inter-individual variability in the magnitude of their innate responses to FliC stimulation, all colonoids released a variety of chemokines. Interestingly, IL-37 attenuated these responses through inhibition of p38 and NFκB signaling pathways. We determined that this suppression by IL-37 was SIGIRR dependent, in murine organoids. Along with species-specific differences in IEC innate responses, we show that IL-37 can promote IEC hypo-responsiveness by supressing inflammatory signaling.

Intestinal epithelial cells (IEC) reside in close proximity to the gut microbiota and are hypo-responsive to bacterial products, likely to prevent maladaptive inflammatory responses. This is in part due to their strong expression of Single Ig IL-1 related receptor (SIGIRR), a negative regulator of interleukin (IL)-1 and toll-like receptor signaling. IL-37 is an anti-inflammatory cytokine that inhibits innate signaling in diverse cells by signaling through SIGIRR. Despite the strong expression of SIGIRR by IEC, few studies have examined whether IL-37 can suppress their innate immune signaling. We characterized innate immune responses of human and murine colonoids to bacteria (FliC, LPS) and host (IL-1β) products and the role of IL-37/SIGIRR in regulating these responses. We demonstrated that human colonoids responded only to FliC, but not to LPS or IL-1β. While colonoids derived from different donors displayed significant inter-individual variability in the magnitude of their innate responses to FliC stimulation, all colonoids released a variety of chemokines. Interestingly, IL-37 attenuated these responses through inhibition of p38 and NFκB signaling pathways. We determined that this suppression by IL-37 was SIGIRR dependent, in murine organoids. Along with species-specific differences in IEC innate responses, we show that IL-37 can promote IEC hypo-responsiveness by suppressing inflammatory signaling.

We investigated the role of the inflammasome effector caspases-1 and -11 during Salmonella enterica serovar Typhimurium infection of murine intestinal epithelial cells (IECs). Salmonella burdens were significantly greater in the intestines of caspase-1/11 deficient (Casp1/11−/−), Casp1−/− and Casp11−/− mice, as compared to wildtype mice. To determine if this reflected IEC-intrinsic inflammasomes, enteroid monolayers were derived and infected with Salmonella. Casp11−/− and wildtype monolayers responded similarly, whereas Casp1−/− and Casp1/11−/− monolayers carried significantly increased intracellular burdens, concomitant with marked decreases in IEC shedding and death. Pretreatment with IFN-γ to mimic inflammation increased caspase-11 levels and IEC death, and reduced Salmonella burdens in Casp1−/− monolayers, while high intracellular burdens and limited cell shedding persisted in Casp1/11−/− monolayers. Thus caspase-1 regulates inflammasome responses in IECs at baseline, while proinflammatory activation of IECs reveals a compensatory role for caspase-11. These results demonstrate the importance of IEC-intrinsic canonical and non-canonical inflammasomes in host defense against Salmonella., Author summary Intestinal epithelial cells (IECs) are located at the interface between the gut lumen and the mucosal immune system and form the first layer of defense against the invasive enteric pathogen Salmonella enterica serovar Typhimurium. To prevent Salmonella, and other pathogens from establishing a foothold in the gut, the host mobilizes the inflammasome to selectively eject infected/compromised IECs from the epithelial layer into the intestinal lumen. This involves the activation of the inflammatory caspases; caspase-1 and -11. The individual contributions of each caspase to intestinal host defense, as well as the importance of IEC-intrinsic inflammasomes have not been previously defined, due to the lack of Casp1−/− mice as well as appropriate IEC-intrinsic defense models. Here, we determined that both caspases contribute to controlling Salmonella pathogen burdens and IEC shedding in the mouse intestine. Caspase-1 appears to play a larger role at baseline since caspase-11 expression must be first induced through proinflammatory signalling. Our data also highlights that IEC-intrinsic caspase activation is sufficient for infection-induced cell shedding and that the intestinal epithelium is a key site for inflammasome-mediated immune defense.

We have previously provided the first genetic evidence that angiotensin converting enzyme 2 (ACE2) is the critical receptor for severe acute respiratory syndrome coronavirus (SARS-CoV), and ACE2 protects the lung from injury, providing a molecular explanation for the severe lung failure and death due to SARS-CoV infections. ACE2 has now also been identified as a key receptor for SARS-CoV-2 infections, and it has been proposed that inhibiting this interaction might be used in treating patients with COVID-19. However, it is not known whether human recombinant soluble ACE2 (hrsACE2) blocks growth of SARS-CoV-2. Here, we show that clinical grade hrsACE2 reduced SARS-CoV-2 recovery from Vero cells by a factor of 1,000– 5,000. An equivalent mouse rsACE2 had no effect. We also show that SARS-CoV-2 can directly infect engineered human blood vessel organoids and human kidney organoids, which can be inhibited by hrsACE2. These data demonstrate that hrsACE2 can significantly block early stages of SARS-CoV-2 infections.

Background and Aims Endoplasmic reticulum [ER] stress in intestinal epithelial cells [IECs] contributes to the pathogenesis of inflammatory bowel disease [IBD]. We hypothesized that ER stress changes innate signalling in human IECs, augmenting toll-like receptor [TLR] responses and inducing pro-inflammatory changes in underlying dendritic cells [DCs]. Methods Caco-2 cells and primary human colon-derived enteroid monolayers were exposed to ATP [control stressor] or thapsigargin [Tg] [ER stress inducer], and were stimulated with the TLR5 agonist flagellin. Cytokine release was measured by an enzyme immunoassay. ER stress markers CHOP, GRP78 and XBP1s/u were measured via quantitative PCR and Western blot. Monocyte-derived DCs [moDCs] were cultured with the IEC supernatants and their activation state was measured. Responses from enteroids derived from IBD patients and healthy control participants were compared. Results ER stress enhanced flagellin-induced IL-8 release from Caco-2 cells and enteroids. Moreover, conditioned media activated DCs to become pro-inflammatory, with increased expression of CD80, CD86, MHCII, IL-6, IL-15 and IL-12p70 and decreased expression of CD103 and IL-10. Flagellin-induced IL-8 production correlated with DC activation, suggesting a common stress pathway. Moreover, there were distinct differences in cytokine expression and basal ER stress between IBD and healthy subject-derived enteroid monolayers, suggesting a dysregulated ER stress pathway in IBD-derived enteroids. Conclusions Cellular stress enhances TLR5 responses in IECs, leading to increased DC activation, indicating a previously unknown mechanistic link between epithelial ER stress and immune activation in IBD. Furthermore, dysregulated ER stress may be propagated from the intestinal epithelial stem cell niche in IBD patients.

Paneth cells are a key subset of secretory epithelial cells found at the base of small intestinal crypts. Unlike intestinal goblet cells, which secrete the mucin Muc2, Paneth cells are best known for producing an array of antimicrobial factors. We unexpectedly identified Muc2 staining localized around Paneth cell granules. Electron microscopy (EM) confirmed an electron lucent halo around these granules, which was lost in Paneth cells from Muc2-deficient (−/−) mice. EM and immunostaining for lysozyme revealed that Muc2−/− Paneth cells contained larger, more densely packed granules within their cytoplasm, and we detected defects in the transcription of key antimicrobial genes in the ileal tissues of Muc2−/− mice. Enteroids derived from the small intestine of wild-type and Muc2−/− mice revealed phenotypic differences in Paneth cells similar to those seen in vivo. Moreover, lysozyme-containing granule release from Muc2−/− enteroid Paneth cells was shown to be impaired. Surprisingly, Paneth cells within human ileal and duodenal tissues were found to be Muc2 negative. Thus Muc2 plays an important role in murine Paneth cells, suggesting links in function with goblet cells; however human Paneth cells lack Muc2, highlighting that caution should be applied when linking murine to human Paneth cell functions. NEW & NOTEWORTHY We demonstrate for the first time that murine Paneth cell granules possess a halo comprised of the mucin Muc2. The presence of Muc2 exerts an impact on Paneth cell granule size and number and facilitates the release and dispersal of antimicrobials into the mucus layer. Interestingly, despite the importance of Muc2 in murine Paneth cell function, our analysis of Muc2 in human intestinal tissues revealed no trace of Muc2 expression by human Paneth cells.

Cancer cell lines have been the mainstay of intestinal epithelial experimentation for decades, due primarily to their immortality and ease of culture. However, because of the inherent biological abnormalities of cancer cell lines, many cellular biologists are currently transitioning away from these models and toward more representative primary cells. This has been particularly challenging, but recent advances in the generation of intestinal organoids have brought the routine use of primary cells within reach of most epithelial biologists. Nevertheless, even with the proliferation of publications that use primary intestinal epithelial cells, there is still a considerable amount of trial and error required for laboratories to establish a consistent and reliable method to culture three-dimensional (3D) intestinal organoids and primary epithelial monolayers. We aim to minimize the time other laboratories spend troubleshooting the technique and present a standard method for culturing primary epithelial cells. Therefore, we have described our optimized, high-yield, cost-effective protocol to grow 3D murine colonoids for more than 20 passages and our detailed methods to culture these cells as confluent monolayers for at least 14 days, enabling a wide variety of potential future experiments. By supporting and expanding on the current literature of primary epithelial culture optimization and detailed use in experiments, we hope to help enable the widespread adoption of these innovative methods and allow consistency of results obtained across laboratories and institutions. NEW & NOTEWORTHY Primary intestinal epithelial monolayers are notoriously difficult to maintain culture, even with the recent advances in the field. We describe, in detail, the protocols required to maintain three-dimensional cultures of murine colonoids and passage these primary epithelial cells to confluent monolayers in a standardized, high-yield and cost-effective manner.

Autophagy is an evolutionarily conserved homeostasis process through which aggregated proteins or damaged organelles are enveloped in a double-membrane structure called an autophagosome and then digested in a lysosome-dependent manner. Growing evidence suggests that malfunction of autophagy contributes to the pathogenesis of a variety of diseases, including cancer, viral infection, and neurodegeneration. However, autophagy is a complicated process, and understanding of the relevance of autophagy to disease is limited by lack of specific and potent autophagy modulators. ATG4B, a Cys-protease that cleaves ATG8 family proteins, such as LC3B, is a key protein in autophagosome formation and maturation process. A novel time-resolved fluorescence resonance energy transfer (TR-FRET) assay measuring protease activity of ATG4B was developed, validated, and adapted into a high-throughput screening (HTS) format. HTS was then conducted with a Roche focus library of 57,000 compounds. After hit confirmation and a counterscreen to filter out fluorescence interference compounds, 267 hits were confirmed, constituting a hit rate of 0.49%. Furthermore, among 65 hits with an IC50 < 50 µM, one compound mimics the LC3 peptide substrate (-TFG-). Chemistry modification based on this particular hit gave preliminary structure activity relationship (SAR) resulting in a compound with a 10-fold increase in potency. This compound forms a stable covalent bond with Cys74 of ATG4B in a 1:1 ratio as demonstrated by liquid chromatography/tandem mass spectrometry (LC/MS/MS). Furthermore, this compound displayed cellular ATG4B inhibition activity. Overall, the novel TR-FRET ATG4B protease assay plus counterscreen assay provides a robust platform to identify ATG4B inhibitors, which would help to elucidate the mechanism of the autophagy pathway and offer opportunities for drug discovery.

Background Intestinal epithelial cells (IECs) are located at the interface between the gut lumen and the underlying mucosal defense system. Here, they play a central role in the coordination of intestinal homeostasis, tempering pro-inflammatory responses but remaining rapidly responsive to noxious stimuli such as enteric pathogens. One early response mechanism by which IECs engage in immune defense is through the activation of the inflammasome which mobilizes the inflammatory caspases; caspase-1 and -11. Aims Here, we investigated the role of the inflammasome in overall mucosal defense against the enteric pathogen Salmonella enterica serovar Typhimurium. Methods Streptomycin-pretreated C57BL/6 (wildtype), Casp1/11 deficient (−/−), Casp1−/− and Casp11−/− mice were orally infected with Salmonella and burdens determined in intestinal tissues at 18h post infection (p.i.). Results Increased pathogen loads were observed for all caspase-deficient mice compared to wildtype, which correlated with increased IEC intracellular Salmonella burdens. Interestingly, despite increased bacterial loads, pathology scores for all inflammatory caspase mice were decreased, especially with regard to ‘IEC damage’ and ‘goblet cell loss’. To determine if the increased burdens were due to the loss of IEC-intrinsic inflammasomes, enteroid monolayers were derived and infected with Salmonella. This revealed significantly increased intracellular burdens in caspase-deficient monolayers as compared to wildtype, in concert with a marked decrease in IEC shedding and cell death. Peak inflammatory caspase activity was displayed in shedding wildtype IECs, suggesting the IEC-intrinsic inflammasome restricts Salmonella infection through infected IEC expulsion. The role of inflammasome signaling in acute mucosal defense was also examined. Wildtype tissue demonstrated a dramatic increase in mucus thickness (as evaluated by Muc2 immunostaining) and antimicrobial Reg3γ and β lectin transcript levels compared to caspase-deficient mice. Mucin release and Reg3 induction has been previously linked to IL-22, therefore we measured IL-22 expression and observed increased secretion in infected wildtype mice compared to Casp1/11−/−. This correlated with increased cecal infiltration of IL-22 producing ILC3 and NK T-cells. When infected mice were treated with IL-22 neutralizing antibody, this increased Salmonella burdens and decreased infection-induced mucus secretion, while no differences were observed in Casp1/11−/− treated with neutralizing antibody or isotype control. Conclusions Therefore the intestinal epithelium utilizes inflammasome signaling to coordinate multiple layers of innate defense at the gut mucosal surface to ultimately restrict enteric pathogen infections and their systemic spread. Funding Agencies CCC, CIHR, NRCUBC

The AB5 toxins cholera toxin (CT) from Vibrio cholerae and heat-labile enterotoxin (LT) from enterotoxigenic Escherichia coli are notorious for their roles in diarrheal disease, but their effect on other intestinal bacteria remains unexplored. Another foodborne pathogen, Campylobacter jejuni, can mimic the GM1 ganglioside receptor of CT and LT. Here we demonstrate that the toxin B-subunits (CTB and LTB) inhibit C. jejuni growth by binding to GM1-mimicking lipooligosaccharides and increasing permeability of the cell membrane. Furthermore, incubation of CTB or LTB with a C. jejuni isolate capable of altering its lipooligosaccharide structure selects for variants lacking the GM1 mimic. Examining the chicken GI tract with immunofluorescence microscopy demonstrates that GM1 reactive structures are abundant on epithelial cells and commensal bacteria, further emphasizing the relevance of this mimicry. Exposure of chickens to CTB or LTB causes shifts in the gut microbial composition, providing evidence for new toxin functions in bacterial gut competition., Bacterial AB5 toxins, such as cholera toxin, bind to oligosaccharides on the host cell surface and play key roles in the pathogenesis of diarrheal disease. Here, Patry et al. show that these toxins bind also to bacterial oligosaccharides and inhibit the growth of Campylobacter jejuni and gut commensal bacteria.

BACKGROUND: Intestinal epithelial cells (IECs) are located at the interface between the gut lumen and the underlying mucosal defense system. Here, they play a central role in the coordination of intestinal homeostasis, tempering pro-inflammatory responses but remaining rapidly responsive to noxious stimuli such as an enteric pathogen. One mechanism by which IECs engage in innate immune defense is through the activation of the inflammasome which mobilizes the inflammatory caspases; Caspase-1 and -11. AIMS: Here, we investigate the role of the inflammasome in IEC and overall mucosal defense against the enteric pathogen Salmonella enterica serovar Typhimurium SL1344. METHODS: Streptomycin-pretreated wildtype C57BL/6, Casp1/11 deficient (−/−), Casp1−/− and Casp11−/− mice were orally infected and S. Typhimurium burdens determined in intestinal tissues at 18h post infection. RESULTS: Increased cecal and luminal pathogen loads were observed for all caspase-deficient mice compared to wild type, which correlated with increased IEC intracellular S. Typhimurium burdens. Interestingly, despite increased bacterial loads, cecal pathology scores for all deficient mice were decreased, especially with regard to ‘IEC damage’ and ‘goblet cell loss’. To determine if the increased burdens were due to the loss of IEC-intrinsic inflammasomes, enteroid monolayers were derived and infected. This revealed significantly increased intracellular burdens in caspase deficient monolayers as compared to wild type, in concert with a marked decrease in IEC sloughing. Peak inflammatory caspase activity was displayed in sloughing wildtype IECs, suggesting IEC-intrinsic inflammasome restricts S. Typhimurium infection through infected IEC expulsion. To examine the role of inflammasome signaling on mucosal defense, mucin layer thicknesses were evaluated by Muc2 immunostaining. After infection, wild type tissue demonstrated a dramatic increase in mucus thickness while caspase deficient mice displayed only a marginal increase. Similarly, expression of the antimicrobial lectins Reg3γ and β was dramatically increased in infected wildtype mice compared to caspase deficient mice. Since mucin release and Reg3 induction have been previously linked to the cytokine IL-22, and IL-22 expression was increased in infected wildtype mice, we tested the effects of neutralizing IL-22. This revealed increased S. Typhimurium burdens and decreased infection-induced mucin secretion, while no differences were observed in Casp1/11−/− treated with either neutralizing antibody or isotype control. CONCLUSIONS: These results thus indicate that the intestinal epithelium utilizes inflammasome signaling to coordinate multiple layers of innate defense at the gut mucosal surface to ultimately restrict enteric pathogen infections and systemic spread. FUNDING AGENCIES: CCC, CIHRNIH

Campylobacter jejuni and Campylobacter coli are zoonotic pathogens once considered asaccharolytic, but are now known to encode pathways for glucose and fucose uptake/metabolism. For C. jejuni, strains with the fuc locus possess a competitive advantage in animal colonization models. We demonstrate that this locus is present in > 50% of genome-sequenced strains and is prevalent in livestock-associated isolates of both species. To better understand how these campylobacters sense nutrient availability, we examined biofilm formation and chemotaxis to fucose. C. jejuni NCTC11168 forms less biofilms in the presence of fucose, although its fucose permease mutant (fucP) shows no change. In a newly developed chemotaxis assay, both wild-type and the fucP mutant are chemotactic towards fucose. C. jejuni 81-176 naturally lacks the fuc locus and is unable to swim towards fucose. Transfer of the NCTC11168 locus into 81-176 activated fucose uptake and chemotaxis. Fucose chemotaxis also correlated with possession of the pathway for C. jejuni RM1221 (fuc+) and 81116 (fuc-). Systematic mutation of the NCTC11168 locus revealed that Cj0485 is necessary for fucose metabolism and chemotaxis. This study suggests that components for fucose chemotaxis are encoded within the fuc locus, but downstream signals only in fuc + strains, are involved in coordinating fucose availability with biofilm development.

We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction.

We present CSD-CrossMiner, a novel tool for pharmacophore-based searches in crystal structure databases. Intuitive pharmacophore queries describing, among others, protein-ligand interaction patterns, ligand scaffolds, or protein environments can be built and modified interactively. Matching crystal structures are overlaid onto the query and visualized as soon as they are available, enabling the researcher to quickly modify a hypothesis on the fly. We exemplify the utility of the approach by showing applications relevant to real-world drug discovery projects, including the identification of novel fragments for a specific protein environment or scaffold hopping. The ability to concurrently search protein-ligand binding sites extracted from the Protein Data Bank (PDB) and small organic molecules from the Cambridge Structural Database (CSD) using the same pharmacophore query further emphasizes the flexibility of CSD-CrossMiner. We believe that CSD-CrossMiner closes an important gap in mining structural data and will allow users to extract more value from the growing number of available crystal structures.

BACKGROUND: During periods of acute sickness, all animals including humans voluntarily decrease their food intake, a behavior known as “infection-induced anorexia”. Since infection-induced anorexia or fasting is highly conserved amongst mammals, we and others have proposed that it actually promotes host-defense. Several studies have demonstrated that fasting indeed attenuates disease during acute systemic infection or chronic inflammation. AIMS: Since the Gastrointestinal tract is the first organ to be affected by food deprivation, we investigated if fasting alters the course of infection and/or ameliorates intestinal inflammation using a mouse model of S. typhimurium-induced colitis. We furthermore examined if fasting modifies the resident gut microbiota, and whether these modifications are instrumental to alter the course of S. typhimurium infection and colitis. METHODS: S. typhimurium causes severe colitis in streptomycin pre-treated, orally infected mice as early as 12h post infection. C57BL/6 conventional as well as germfree mice were fed or fasted for 24h and orally infected with S. typhimurium, continuing the fast for another 6h to 24h. Additionally, C57BL/6 conventional mice were fed single macronutrients to gauge the effect of different nutrients on the infection. Pathology as well as Salmonella colonization, was assessed by histological and immunofluorescent staining and organ pathogen burden counts; inflammatory gene transcription was measured by qPCR. Microbiome profiling of intestinal contents was performed utilizing 16S rRNA sequencing. RESULTS: Fasting completely abrogated S. typhimurium infection and colitis in conventional C57BL/6 mice, whereas infection still proceeded, albeit in a reduced fashion in germfree mice in concert with minimal signs of inflammation. Microbiome profiles between fed and fasted groups differed greatly in terms of beta diversity with the fasting group showing a consistent increase in the genus Akkermansia. Feeding mice glucose alone was not sufficient to re-establish the infection, but preliminary results indicate that other macronutrients can partially restore Salmonella colonization. CONCLUSIONS: Taken together, our findings show that prolonged fasting dramatically protects the host against S. typhimurium infection, in part by altering the intestinal microbiome and increasing colonization resistance, likely by limiting nutrient availability for the pathogenic bacteria. Additionally our results indicate that food deprivation impairs Salmonella virulence and reduces its ability to promote an inflammatory environment independent of changes in the microbiome. FUNDING AGENCIES: CCC, CIHRNSERC

BACKGROUND: Campylobacter jejuni is the most common cause of bacterial gastroenteritis in the developed world, often rivaling the total number of E.coli and Salmonella infections combined. Furthermore, even after the initial infection has been cleared, C. jejuni infection has been strongly linked to the development of Guillain Barre syndrome. Despite this, many aspects of its colonization and infection of the gut remain poorly defined. One cryptic aspect of its pathogenesis is C. jejuni’s’s ability to invade intestinal epithelial cells as it colonizes and infects the host intestine. Our previous work has illustrated that C. jejuni has the capacity to invade intestinal epithelial cells in the mammalian gut near the apical ends of intestinal crypts, where it resides within LAMP-1 positive vesicles. AIMS: The aim of this study is the characterize the role of the epithelial cell inflammasome in defending against cell invasion by C. jejuni in vivo and to describe the impact of inflammasome activation and cell invasion on the immune response to C. jejuni infection. METHODS: Using a combination of knockout mouse models and an in vitro primary epithelial cell model, we can now illustrate the role of epithelial cell intrinsic inflammasomes in controlling Campylobacter cell invasion during the course of infection. We infected mice lacking key inflammasome components, including Asc, Caspase 1, and relevant nod-like receptors, along with knockout mice in relevant inflammasome-linked cytokines, including IL18. We also used primary epithelial cells, derived from human and murine sources, and cultivated as organoid cultures, do create monolayer cultures we could infect with C. jejuni. This allowed us to model C. jejuni cell invasion of the intestinal epithelium in vitro. RESULTS: Mice lacking key inflammasome components lose much of their ability to limit C. jejuni invasion and replication inside of intestinal epithelial cells. This allows C. jejuni to replicate to large numbers inside of these LAMP1 positive vesicles, from where they can be released back into the intestinal lumen and infect additional epithelial cells. The consequences of impaired inflammasome function include increased pathogen burdens, a prolonged course of infection and significantly increased pathology in infected mice. Conversely, mice with functional epithelial cell inflammasomes effectively control the number of intracellular bacteria and exhibit only moderate infection induced pathology and pathophysiology. CONCLUSIONS: Although much remains to be discovered regarding the role of epithelial cell invasion in C. jejuni pathogenesis, these findings highlight the importance of epithelial cells as an active player in combating this important enteric pathogen. FUNDING AGENCIES: CAG, CCC, CIHR

Medicinal chemistry has always been closer to the arts than other disciplines in the natural sciences. Instead of searching for natural laws, medicinal chemistry creates new molecular entities entailing desired pharmaceutical characteristics. While the productive output of medicinal chemistry is comprehensively documented, the epistemic paths of the creative process are less well described. Here we show how such paths could be visualized and how these visualizations relate to images developed in the history and philosophy of science. Based on the discussion of these visualizations, we argue that there is a need for a new language of creativity that can be employed during the very course of research, as opposed to its retrospective analysis. This language should be able to reflect both the status and directions in highly complex research processes that may have a clear goal, yet must remain open to unexpected moments of serendipity.

Background Therapy for HCV-infected patients after orthotopic liver transplantation (OLT) is based on interferon (IFN) as the gold standard, but sustained virologic response (SVR) and safety profiles of the IFN-based therapies are very unsatisfactory. The aim of this continuing analysis is evaluation of the impact of an IFN-free sofosbuvir (SOF)-based therapy in HCV-infected liver transplant recipients. Material and methods Post-OLT patients with a proven recurrence of HCV were treated with SOF and ribavirin (RBV) for 24 weeks (n=10). Laboratory parameters and FibroScan® are continuously evaluated at weeks 0, 12, 24, and 36. A retrospectively analyzed HCV patient cohort who received antiviral therapy with pegylated INF and RBV± telaprevir (TLV) were used as a control group. Results All patients who finished their treatment with SOF/RBV at least 12 weeks ago showed an SVR. The SOF-based therapy showed a significantly higher rate of rapid virologic response (RVR) and sustained virologic response (SVR) compared to the IFN-based therapies (RVR: p=0.007; SVR: p=0.009). According to temporary data on FibroScan® analysis, regression of fibrosis was observed in 8 patients treated with SOF/RBV. No premature termination of SOF became necessary. Conclusions In this small group of patients, the preliminary results indicate that a regression of fibrosis is achievable within 24 weeks of therapy with SOF after OLT. SOF seems to be effective and safe in the treatment of OLT patients infected with HCV and will likely improve patient and transplant survival.

Goblet cells (GCs) are the predominant secretory epithelial cells lining the luminal surface of the mammalian gastrointestinal (GI) tract. Best known for their apical release of mucin 2 (Muc2), which is critical for the formation of the intestinal mucus barrier, GCs have often been overlooked for their active contributions to intestinal protection and host defense. In part, this oversight reflects the limited tools available to study their function but also because GCs have long been viewed as relatively passive players in promoting intestinal homeostasis and host defense. In light of recent studies, this perspective has shifted, as current evidence suggests that Muc2 as well as other GC mediators are actively released into the lumen to defend the host when the GI tract is challenged by noxious stimuli. The ability of GCs to sense and respond to danger signals, such as bacterial pathogens, has recently been linked to inflammasome signaling, potentially intrinsic to the GCs themselves. Moreover, further work suggests that GCs release Muc2, as well as other mediators, to modulate the composition of the gut microbiome, leading to both the expansion as well as the depletion of specific gut microbes. This review will focus on the mechanisms by which GCs actively defend the host from noxious stimuli, as well as describe advanced technologies and new approaches by which their responses can be addressed. Taken together, we will highlight current insights into this understudied, yet critical, aspect of intestinal mucosal protection and its role in promoting gut defense and homeostasis.

Enteropathogenic Escherichia coli (EPEC)-induced diarrhea is often associated with disruption of intestinal epithelial tight junctions. Although studies have shown alterations in the expression and localization of bicellular tight junction proteins during EPEC infections, little is known about whether tricellular tight junction proteins (tTJs) are affected. Using Caco-2 cell monolayers, we investigated if EPEC is capable of targeting the tTJ protein tricellulin. Our results demonstrated that at 4 h postinfection, EPEC induced a significant reduction in tricellulin levels, accompanied by a significant loss of transepithelial resistance (TEER) and a corresponding increase in paracellular permeability. Conversely, cells overexpressing tricellulin were highly resistant to EPEC-induced barrier disruption. Confocal microscopy revealed the distribution of tricellulin into the plasma membrane of infected epithelial cells and confirmed the localization of EPEC aggregates in close proximity to tTJs. Moreover, infections with EPEC strains lacking genes encoding specific type III secreted effector proteins demonstrated a crucial role for the effector EspG1 in modulating tricellulin expression. Complementation studies suggest that the EspG-induced depletion of tricellulin is microtubule dependent. Overall, our results show that EPEC-induced epithelial barrier dysfunction is mediated in part by EspG1-induced microtubule-dependent depletion of tricellulin.

BACKGROUND: Attaching and effacing (A/E) pathogens such as Enterohemorrhagic E. coli (EHEC) are important causes of diarrheal disease worldwide. Interestingly, little is known about how these bacteria obtain key nutrients, and whether these nutrients modulate pathogen colonization and gut infection. For example, fucose is an important sugar and bacterial food source cleaved from host glycans found on the intestinal mucosal surface via the actions of commensal microbes expressing fucosidase enzymes. Interestingly, although the mouse A/E pathogen Citrobacter rodentium does not itself express a fucosidase, recent studies have found that it and EHEC use a fucose sensing system to modulate their pathogenicity in vitro. At present, it is unclear what role fucose metabolism may play in A/E pathogen virulence and metabolism in vivo. To address this, we focused on C. rodentium enzyme L-fuculose kinase (encoded by the fucK gene), which plays a key role in the L-fucose metabolic pathway and fucose utilization as a food source. AIMS: We investigated the roles of fucose and the enzyme L-fuculose kinase in controlling C. rodentium pathogenesis. METHODS: Wildtype (WT) and ΔfucK C. rodentium were used for in vitro assays (type three secretion, growth and adhesion assays) and for in vivo infection. C57Bl/6 mice were infected either separately, or with both C. rodentium strains at a dose of 10^8 colony forming units. In some infections, mice were pretreated with streptomycin (20mg 24h pre-infection) or were fed fucose (200ul of 25mM L-fucose 2x/day). Bacterial burdens, pathology score and competitive assay were assessed on day 6 post-infection. RESULTS: In vitro virulence assays identified no significant differences between ΔfucK and WT C. rodentium regarding type three secretion, growth or adherence to cultured epithelial cells. Moreover, both WT and ΔfucK C. rodentium readily colonized the intestines of mice either pretreated (or not), with streptomycin, with pathogen burdens, localisation and histological pathology scores similar between the two strains. In contrast, simultaneous infection by both strains (competitive assay) within the same mice revealed the ΔfucK strain was significantly impaired when competing with WT C. rodentium (no streptomycin). In contrast, ΔfucK was able to equally compete with WT C. rodentium when streptomycin pretreatment was given to deplete commensal bacteria. Feeding fucose to these streptomycin treated mice again reduced the ability of the ΔfucK strain to compete with WT C. rodentium. CONCLUSIONS: These results indicate that the fucK-dependent fucose metabolic pathway promotes but is not essential to C. rodentium pathogenesis. Moreover these findings suggest that commensal microbes play a key role in controlling fucose availability in the gut, and thereby impact A/E pathogen metabolism and virulence. FUNDING AGENCIES: CCC, CIHRNSERC, FRQS

Crystal structure databases offer ample opportunities to derive small molecule conformation preferences, but the derived knowledge is not systematically applied in drug discovery research. We address this gap by a comprehensive and extendable expert system enabling quick assessment of the probability of a given conformation to occur. It is based on a hierarchical system of torsion patterns that cover a large part of druglike chemical space. Each torsion pattern has associated frequency histograms generated from CSD and PDB data and, derived from the histograms, traffic-light rules for frequently observed, rare, and highly unlikely torsion ranges. Structures imported into the corresponding software are annotated according to these rules. We present the concept behind the tree of torsion patterns, the design of an intuitive user interface for the management and usage of the torsion library, and we illustrate how the system helps analyze and understand conformation properties of substructures widely used in medicinal chemistry.

TARGETING PPIS: A novel strategy for designing libraries targeting protein-protein interfaces enabled us to identify diverse chemical entry points to interact with therapeutic targets for which conventional screening libraries delivered no or only few hit structures. The concept was experimentally validated by early hit evaluation in biochemical screens and early ADMET profiling.

Relevant animal models for Campylobacter jejuni infection have been difficult to establish due to C. jejuni's inability to cause disease in many common animal research models. Fortunately, recent work has proven successful in developing several new and relevant mouse models of C. jejuni infection, including the SIGIRR-deficient mouse strain that develops acute enterocolitis in response to C. jejuni. Here we describe how to properly infect mice with C. jejuni, as well as a number of accompanying histological techniques to aid in studying C. jejuni colonization and infection in mice.