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The mammalian intestinal tract is colonized by trillions of beneficial commensal bacteria that are anatomically restricted to specific niches. However, the mechanisms that regulate anatomical containment remain unclear. Here we identify that interleukin (IL)-22-producing innate lymphoid cells (ILCs) are present in intestinal tissues of healthy mammals. Depletion of ILCs resulted in peripheral dissemination of commensal bacteria and systemic inflammation, which was prevented by administration of IL-22. Disseminating bacteria were identified as Alcaligenes species originating from host lymphoid tissues. Alcaligenes was sufficient to promote systemic inflammation following ILC-depletion in mice, and Alcaligenes-specific systemic immune responses were associated with Crohn's disease and progressive HCV infection in patients. Collectively, these data indicate that ILCs regulate selective containment of lymphoid-resident bacteria to prevent systemic inflammation associated with chronic diseases.

Clinical benefits of cytokine blockade in ileal Crohn's disease (iCD) are limited to a subset of patients. Here, we applied single-cell technologies to iCD lesions to address whether cellular heterogeneity contributes to treatment resistance. We found that a subset of patients expressed a unique cellular module in inflamed tissues that consisted of IgG plasma cells, inflammatory mononuclear phagocytes, activated T cells, and stromal cells, which we named the GIMATS module. Analysis of ligand-receptor interaction pairs identified a distinct network connectivity that likely drives the GIMATS module. Strikingly, the GIMATS module was also present in a subset of patients in four independent iCD cohorts (n = 441), and its presence at diagnosis correlated with failure to achieve durable corticosteroid-free remission upon anti-TNF therapy. These results emphasize the limitations of current diagnostic assays and the potential for single-cell mapping tools to identify novel bio-markers of treatment response and tailored therapeutic opportunities.

The specification of the vertebrate liver is thought to occur in a two-step process, beginning with the establishment of competence within the foregut endoderm for responding to organ-specific signals, followed by the induction of liver-specific genes. On the basis of expression and in vitro studies, it has been proposed that the Foxa transcription factors establish competence by opening compacted chromatin structures within liver-specific target genes. Here we show that Foxa1 and Foxa2 (forkhead box proteins A1 and A2) are required in concert for hepatic specification in mouse. In embryos deficient for both genes in the foregut endoderm, no liver bud is evident and expression of the hepatoblast marker alpha-fetoprotein (Afp) is lost. Furthermore, Foxa1/Foxa2-deficient endoderm cultured in the presence of exogenous fibroblast growth factor 2 (FGF2) fails to initiate expression of the liver markers albumin and transthyretin. Thus, Foxa1 and Foxa2 are required for the establishment of competence within the foregut endoderm and the onset of hepatogenesis.

The Foxa subfamily of winged helix/forkhead box (Fox) transcription factors has been the subject of genetic and biochemical study for over 15 years. During this time its three members, Foxa1, Foxa2 and Foxa3, have been found to play important roles in multiple stages of mammalian life, beginning with early development, continuing during organogenesis, and finally in metabolism and homeostasis in the adult. Foxa2 is required for the formation of the node and notochord, and in its absence severe defects in gastrulation, neural tube patterning, and gut morphogenesis result in embryonic lethality. Foxa1 and Foxa2 cooperate to establish competence in foregut endoderm and are required for normal development of endoderm-derived organs such as the liver, pancreas, lungs, and prostate. In post-natal life, members of the Foxa family control glucose metabolism through the regulation of multiple target genes in the liver, pancreas, and adipose tissue. Insight into the unique molecular basis of Foxa function has been obtained from recent genetic and genomic data, which identify the Foxa proteins as 'pioneer factors' whose binding to promoters and enhancers enable chromatin access for other tissue-specific transcription factors.

SUMMARY Type 2 diabetes mellitus (T2DM) is a complex disease characterized by the inability of the insulin-producing β-cells in the endocrine pancreas to overcome insulin resistance in peripheral tissues. To determine if microRNAs are involved in the pathogenesis of human T2DM, we sequenced the small RNAs of human islets from diabetic and non-diabetic organ donors. We identified a cluster of miRNAs in an imprinted locus on human chromosome 14q32 that is highly and specifically expressed in human β-cells and dramatically down-regulated in islets from T2DM organ donors. The down-regulation of this locus strongly correlates with hyper-methylation of its promoter. Using HITS-CLIP for the essential RISC-component Argonaute, we identified disease-relevant targets of the chromosome 14q32 microRNAs, such as IAPP and TP53INP1 that cause increased β-cell apoptosis upon over-expression in human islets. Our results support a role for microRNAs and their epigenetic control by DNA methylation in the pathogenesis of T2DM.

The onset of pancreas development in the foregut endoderm is marked by activation of the homeobox gene Pdx1 (IPF1). Pdx1 is essential for the expansion of the pancreatic primordium and the development of endocrine islets. The control of Pdx1 expression has been only partially elucidated. We demonstrate here that the winged-helix transcription factors Foxa1 and Foxa2 co-occupy multiple regulatory domains in the Pdx1 gene. Compound conditional ablation of both Foxa1 and Foxa2 in the pancreatic primordium results in complete loss of Pdx1 expression and severe pancreatic hypoplasia. Mutant mice exhibit hyperglycemia with severely disrupted acinar and islet development, and die shortly after birth. Assessment of developmental markers in the mutant pancreas revealed a failure in the expansion of the pancreatic anlage, a blockage of exocrine and endocrine cell differentiation, and an arrest at the primitive duct stage. Comparing their relative developmental activity, we find that Foxa2 is the major regulator in promoting pancreas development and cell differentiation. Using chromatin immunoprecipitations (ChIP) and ChIP sequencing (ChIPSeq) of fetal pancreas and islet chromatin, we demonstrate that Foxa1 and Foxa2 predominantly occupy a distal enhancer at −6.4 kb relative to the transcriptional start site in the Pdx1 gene. In addition, occupancy of the well-characterized proximal Pdx1 enhancer by Foxa1 and Foxa2 is developmental stage-dependent. Thus, the regulation of Pdx1 expression by Foxa1 and Foxa2 is a key early event controlling the expansion and differentiation of the pancreatic primordia.[Keywords: Pancreas; development; Pdx1; Foxa1; Foxa2; conditional gene ablation] Supplemental material is available at http://www.genesdev.org. Received June 27, 2008; revised version accepted October 17, 2008. Mouse pancreas development begins on embryonic day 8.5-9.0 (E8.5-E9.0) when two epithelial buds emerge from the ventral and dorsal surfaces of the posterior foregut endoderm. These rudimentary buds undergo branching morphogenesis to form a ductal tree consisting primarily of undifferentiated ductal epithelia or pancreatic cords. By E13.5-E14.5, intensive epithelial cell proliferation and differentiation initiates in what has been termed the "secondary transition," and by E16.5, exocrine acinar cells separate from the central ducts while endocrine cells begin to cluster into islet-like structures. Additional islet remodeling and maturation is completed 3 wk after birth, resulting in a mature functional pancreas (Jorgensen et al. 2007).These early morphogenetic processes coincide with extensive migration and differentiation of epithelial cell lineages, whose fate can be traced through the dynamic expression of several key transcription factors. For instance, the initial expression of Pdx1 (E8.5-E9.0) highlights the prospective pancreatic domain even before the pancreatic buds can be distinguished morphologically. The initial broad expression of Pdx1 becomes restricted to differentiated ␤-and ␦-cells upon the completion ...

Background and Aims While the importance of miRNA for the development and maintenance of several tissues is well established, its role in the intestine is unknown. Our aims were to determine the entire miRNA expression profile of the mammalian small intestine in a quantitative manner and to determine the contribution of miRNAs to intestinal development and homeostasis using genetic means. Methods We determined the complete miRNA transcriptome of the mouse intestinal epithelium using ultra-high throughput sequencing. We employed gene ablation of Dicer1 to generate mice deficient for all miRNAs in the mouse intestine. Results miRNA abundance varies over a large dynamic range in the mammalian small intestine, from one read per million to 250,000. Of the 453 miRNA families identified, mmu-miR-192 and mmu-let-7 are the most highly expressed. Morphologically, the epithelium of Dicer1loxP/loxP; Villin-Cre mutants mice is disorganized in both the small and large intestine, with a four-fold decrease in goblet cells in the colon and a dramatic increase in apoptosis in the crypts of both the large and small intestine. Furthermore, intestinal barrier function is dependent on the presence of miRNAs, and consequently Dicer1 deficient mice display intestinal inflammation with lymphocyte and neutrophil infiltration. Conclusion We have identified all intestinal miRNAs and shown using gene ablation of Dicer1 that miRNAs play a vital role in the differentiation and function of the intestinal epithelium.