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Co-culture of intestinal organoids with a colibactin-producing pks + E. coli strain (EcC) revealed mutational signatures also found in colorectal cancer (CRC). E. coli Nissle 1917 (EcN) remains a commonly used probiotic, despite harboring the pks operon and inducing double strand DNA breaks. We determine the mutagenicity of EcN and three CRC-derived pks + E. coli strains with an analytical framework based on sequence characteristic of colibactin-induced mutations. All strains, including EcN, display varying levels of mutagenic activity. Furthermore, a machine learning approach attributing individual mutations to colibactin reveals that patients with colibactin-induced mutations are diagnosed at a younger age and that colibactin can induce a specific APC mutation. These approaches allow the sensitive detection of colibactin-induced mutations in ∼12% of CRC genomes and even in whole exome sequencing data, representing a crucial step toward pinpointing the mutagenic activity of distinct pks + E. coli strains., Competing Interests: Declaration of interests H.C. is a full-time member of the executive board of F. Hoffmann-La Roche Ltd. as head of Pharma, Research and Early Development (pRED) in Basel, Switzerland. Additionally, H.C. is inventor on multiple organoid patents, licensed by the KNAW to the Foundation HUB in Utrecht., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Intestinal organoids are three-dimensional cultures that resemble key aspects of the epithelium of origin. Here, we describe how to differentiate human small intestinal organoids by combining growth media variations and genetic engineering. We detail the differentiation of human intestinal organoids in the presence and absence of BMP agonists to recapitulate a broader scope of functional cell states found in vivo . Using transient overexpression of the transcription factor Neurogenin-3, we describe the enhancement of differentiation toward rare enteroendocrine cells. For complete details on the use and execution of this protocol, please refer to Beumer et al. (2022)., Competing Interests: H.C. is head of Roche’s Pharma Research and Early Development in Basel, Switzerland since March 2022. J.B. and H.C. are inventors on several patents related to organoid technology. H.C.’s full disclosure is given at https://www.uu.nl/staff/JCClevers/., (© 2022 The Author(s).)

Intestinal epithelial cells derive from stem cells at the crypt base and travel along the crypt-villus axis to die at the villus tip. The two dominant villus epithelial cell types, absorptive enterocytes and mucous-secreting goblet cells, are mature when they exit crypts. Murine enterocytes switch functional cell states during migration along the villus. Here, we ask whether this zonation is driven by the bone morphogenetic protein (BMP) gradient, which increases toward the villus. Using human intestinal organoids, we show that BMP signaling controls the expression of zonated genes in enterocytes. We find that goblet cells display similar zonation involving antimicrobial genes. Using an inducible Bmpr1a knockout mouse model, we confirm that BMP controls these zonated genes in vivo. Our findings imply that local manipulation of BMP signal strength may be used to reset the enterocyte "rheostat" of carbohydrate versus lipid uptake and to control the antimicrobial response through goblet cells., Competing Interests: Declaration of interests H.C. is inventor on several patents related to organoid technology; his full disclosure is given at https://www.uu.nl/staff/JCClevers/. J.B. and H.C. are inventors on a patent related to this work (improved differentiation method, publication number 20210047618)., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

BCG vaccination can strengthen protection against pathogens through the induction of epigenetic and metabolic reprogramming of innate immune cells, a process called trained immunity. We and others recently demonstrated that mucosal or intravenous BCG better protects rhesus macaques from Mycobacterium tuberculosis infection and TB disease than standard intradermal vaccination, correlating with local adaptive immune signatures. In line with prior mouse data, here, we show in rhesus macaques that intravenous BCG enhances innate cytokine production associated with changes in H3K27 acetylation typical of trained immunity. Alternative delivery of BCG does not alter the cytokine production of unfractionated bronchial lavage cells. However, mucosal but not intradermal vaccination, either with BCG or the M. tuberculosis -derived candidate MTBVAC, enhances innate cytokine production by blood- and bone marrow-derived monocytes associated with metabolic rewiring, typical of trained immunity. These results provide support to strategies for improving TB vaccination and, more broadly, modulating innate immunity via mucosal surfaces., Competing Interests: E.R., E.P., N.A., and C.M. are co-inventors on a patent on a tuberculosis vaccine held by the University of Zaragoza and Biofabri. E.R. and E.P. are employees of Biofabri. J.T. is an employee of the TuBerculosis Vaccine Initiative and an advisor to Biofabri. M.G.N. holds a patent on the inhibition of trained immunity with nanobiologics, and a patent on the stimulation of trained immunity with nanobiologics. M.G.N. is also a scientific founder of Trained Therapeutix and Discovery (TTxD). The remaining authors of the Radboud UMC and the authors from the BPRC declare no competing interests., (© 2020 The Author(s).)

To fight tuberculosis, better vaccination strategies are needed. Live attenuated Mycobacterium tuberculosis -derived vaccine, MTBVAC, is a promising candidate in the pipeline, proven to be safe and immunogenic in humans so far. Independent studies have shown that pulmonary mucosal delivery of Bacillus Calmette-Guérin (BCG), the only tuberculosis (TB) vaccine available today, confers superior protection over standard intradermal immunization. Here we demonstrate that mucosal MTBVAC is well tolerated, eliciting polyfunctional T helper type 17 cells, interleukin-10, and immunoglobulins in the airway and yielding a broader antigenic profile than BCG in rhesus macaques. Beyond our previous work, we show that local immunoglobulins, induced by MTBVAC and BCG, bind to M. tuberculosis and enhance pathogen uptake. Furthermore, after pulmonary vaccination, but not M. tuberculosis infection, local T cells expressed high levels of mucosal homing and tissue residency markers. Our data show that pulmonary MTBVAC administration has the potential to enhance its efficacy and justifies further exploration of mucosal vaccination strategies in preclinical efficacy studies., Competing Interests: E.R., E.P., N.A., and C.M. are co-inventors on a patent-entitled tuberculosis vaccine held by the University of Zaragoza and Biofabri. E.R. and E.P. are employees of Biofabri. J.T. is an employee of TuBerculosis Vaccine Initiative and advisor to Biofabri., (© 2020 The Author(s).)

Enteroendocrine cells (EECs) sense intestinal content and release hormones to regulate gastrointestinal activity, systemic metabolism, and food intake. Little is known about the molecular make-up of human EEC subtypes and the regulated secretion of individual hormones. Here, we describe an organoid-based platform for functional studies of human EECs. EEC formation is induced in vitro by transient expression of NEUROG3. A set of gut organoids was engineered in which the major hormones are fluorescently tagged. A single-cell mRNA atlas was generated for the different EEC subtypes, and their secreted products were recorded by mass-spectrometry. We note key differences to murine EECs, including hormones, sensory receptors, and transcription factors. Notably, several hormone-like molecules were identified. Inter-EEC communication is exemplified by secretin-induced GLP-1 secretion. Indeed, individual EEC subtypes carry receptors for various EEC hormones. This study provides a rich resource to study human EEC development and function., Competing Interests: Declaration of Interests H.C. is inventor on several patents related to organoid technology; his full disclosure is given at https://www.uu.nl/staff/JCClevers/. H.C. is founder of OrganoidZ, which employs organoids for drug development. J.B., J.P., and H.C. are inventors on patents related to this work., (Copyright © 2020 Elsevier Inc. All rights reserved.)