Abstract Background Endoscopic healing (EH) is the major long-term treatment target for inflammatory bowel diseases (IBD) in adults and paediatric patients. However, EH may not represent disease clearance. Hence, risk of relapse remains high and treatment discontinuation after reaching EH often results in disease exacerbation. We aimed to identify persistent cellular, molecular and microbial drivers of IBD under EH and longitudinally collected endoscopic biopsies from paediatric patients for analysis of single T-cell and bulk transcriptomics as well as mucosa-associated microbiota. Methods We followed disease trajectories of paediatric IBD patients treated according to international guidelines and collected mucosal biopsies from the terminal ileum (TI) and sigmoid colon (SC) at baseline (T1) and after approximately 3-12 months (T2) to assess EH. Non-IBD controls showed no macroscopic or histologic signs of inflammation. Host RNA and bacterial DNA were simultaneously extracted from single biopsies for bulk RNA-seq, and 16S rRNA seq. A second biopsy was used for isolation of lamina propria mononuclear cells (LPMCs), followed by CD45+, CD3+ cell sorting and single T-cell analysis (10X Genomics). Data were quality controlled and integrated. Results 217 biopsies (135 simultaneous extraction of host RNA and bacterial DNA; 82 single T-cell analysis) from 32 paediatric IBD patients (mean age 13 ± 3.5 years, 21 Crohn’s disease [CD], 11 ulcerative colitis [UC]; T1 = 32, T2 = 32, T > 2 = 6) and 5 non-IBD controls were analysed. Time between T1 and T2 averages 40 ± 22 weeks. At baseline, 15 patients (14 CD, 1 UC) were newly diagnosed and 31/32 patients had active mucosal inflammation. Twenty-two patients (71%) achieved EH at T2 (SES-CED ≤2 and absence of ulcerations), mostly on anti-TNF therapy. One patient (EH at T1) experienced relapsing disease within 10 weeks after discontinuing medication. In the bulk RNA-seq, we identified 299 differential expressed genes (DEGs; corrected p-value <0.05, FC >2.0), such as DUOX2, SAA2-SAA4, FCGR3B and NOS2, that are associated with active IBD and remained upregulated in EH in contrast to non-IBD controls. In addition single cell analysis revealed an IBD-specific pathogenic Th17 cluster that continued to exist in EH and showed high correlation with top DEGs after data integration. 16S rRNA gene seq highlighted highly individual mucosa-associated bacterial profiles and a reduced α-diversity in active and EH compared to non-IBD controls. Conclusion A persisting IBD signature in EH reflects ongoing cellular, molecular and microbial activity in comparison to non-IBD controls despite EH and mucosal regeneration. These markers may provide targets for future or sequential therapies.

Abstract Background Exclusive enteral nutrition (EEN) is a first-line induction therapy for paediatric Crohn’s disease (CD). Although the protective mechanisms remain unclear, previous studies showed substantial changes in microbiome composition in response to EEN. We aim to assess the protective function of EEN and its impact on gut microbiome signatures in paediatric CD. Methods We prospectively followed, 15 newly diagnosed paediatric CD patients aged, 3–18 years between, 01/2019 –, 08/2021. Patients were treated according to international guidelines including EEN therapy for, 6–8 weeks, followed by a gradual re-introduction of solid food and concomitant start of maintenance treatment. Disease activity and inflammatory biomarkers were monitored during, 12-months follow-up. 16S rRNA gene sequencing and targeted/untargeted metabolomics was performed from stool samples collected weekly during EEN and monthly thereafter (n = 261). Dietary modulation and clinical activity of patient-derived stool microbiota were studied by ex-vivo faecal fermentation and after faecal microbiota transplantation (FMT) into germ free (GF) IL10-/- mice. Results All patients achieved remission with EEN therapy but, 6/15 had resuming CD activity within, 6 months. Longitudinal microbial and metabolite profiling of stool samples showed highly individualized responses to EEN without coherent signatures. Integrated multi-omics data analysis showed an enrichment of long-chain fatty acids in patients under EEN, which correlated with a reduced abundance of Lachnospiraceae, compared to patients under regular diet. Faecal microbiota from CD patients with active disease (baseline or relapse) or inactive disease (EEN-induced remission) were exposed to EEN-like or dietary control formulations in continuous ex-vivo cultures. EEN-like formulation induced protective changes in the patient-derived baseline microbiota confirmed by the absence of disease activity after FMT in GF IL10-/- mice. Mice colonized with baseline microbiota after ex-vivo EEN exposure showed a decreased abundance of Bacteroides, Akkermansia, Blautia and an increase of Lachnoclostridium and Parabacteroides in comparison to those colonized directly with patient’s baseline microbiota. In contrast, EEN-like diet failed to mitigate the aggressive behaviour of relapse microbiota when transferred into GF IL10-/- mice which was in line with an inability to cause significant compositional changes. Conclusion Our data show that clinical efficacy of EEN in paediatric CD is accompanied by temporal and individual gut microbial and metabolite changes. The combined findings of continuous culture and gnotobiotic mouse models point towards a direct protective role of EEN-modulated patient microbiomes in regulating intestinal inflammation.

BACKGROUND & AIMS:The major drawback of plastic stents for biliary drainage is the occlusion by sludge. Sludge is accrued because the stent surface allows for the adherence of proteins, glycoproteins, or bacteria and the bile flow is insufficient to clean the surface. In this study, experience from nanotechnology to achieve a clean surface by improved soil-release characteristics is used to optimize biliary stent surface. The aim of this study was to examine sludge accumulation in relation to surface characteristics designed by nanotechnology. METHODS:A variety of inorganic-organic sol-gel-coated stents were incubated in sterilized human bile and enzyme-active Escherichia coli for 35 days. Materials were Teflon (DuPont, Wilmington, DE) coated with hydrophobic Clearcoat (NTC, Tholey, Germany), Teflon with sol-gel coating synthesized of organic epoxides of 190 g/mol or 500 g/mol, and propylaminosilane without or with fluorsilanes for increased hydrophobicity. Scanning electron microscopy and semiquantitative analysis, blinded to the type of coating, were used to determine the amount of sludge accumulated on the surface. RESULTS:Sludge deposition was reduced on the designed surfaces as compared with uncoated Teflon and Clearcoat. The performance of high molecular (500 g/mol) was superior to that of low molecular (190 g/mol) epoxide ligand. However, increasing hydrophobicity by adding fluoraminosilanes resulted in increased adherence of sludge. Less than a micrometer-thin sol-gel coating is inexpensive because very little coating material is required. This is the first published data comparing systematically modified surfaces of biliary stents using nanotechnology. CONCLUSIONS:Optimized soil release by sol-gel nanocoating of plastic stents may prevent biliary plastic stents from clogging.

The various strains of mouse hepatitis virus exhibit distinct organ tropisms. MHV-4(JHM) and MHV-3 are predominantly neurotropic and hepatotropic respectively. Studies on the mechanisms involved in organ specific infection of mouse hepatitis virus (MHV) have focused on several factors such as dose, route of administration, age and strain of experimental animals1. Another potential mechanism for regulation of tissue specific spread of virus is the ability of organ specific endothelial cells to selectively support the replication of different strains of MHV. Endothelial cells form an interface between circulating blood and organs and thus could serve as a barrier to infection by viruses. Endothelial cells are also heterogeneous in different organs and may exhibit selectivity in permitting viral entry, thus influencing their tissue tropism2.