a, GWAS have identified 71 risk loci in Crohn’s disease and 47 risk loci in ulcerative colitis (P value of association < 5×10⁻⁸). Of these, 28 risk loci exhibit shared associations (defined as P < 5×10⁻⁸ for either Crohn’s disease or ulcerative colitis, and P < 1×10⁻⁴ for the other form of IBD). Approximately half of the loci implicated in Crohn’s disease and ulcerative colitis are associated with cis- and/or trans-expression quantitative trait loci (eQTL) effects (left panels). Genes whose expression are affected by these variants could also be involved in IBD pathogenesis. The loci composition (right panels) shows the number of genes that either lie within or segregate in linkage disequilibrium with IBD-implicated loci (coefficient of correlation r² > 0.8). These loci are structurally heterogeneous, and are associated with widely ranging numbers of genes. Loci not associated with any genes, known as gene deserts, frequently contain non-coding transcripts or predicted open reading frames (ORFs), and can be associated with trans-eQTL effects. b, Recurring terms illustrating biological processes implicated by at least three genes represented in IBD loci; font sizes are proportional to the number of genes associated with each respective process. B_reg cells, B regulatory cells; ER, endoplasmic reticulum; GPCR, G-protein-coupled receptor; IL, interleukin; lincRNA, large intervening non-coding RNA; miRNA, microRNA; ncRNA, non-coding RNA; NF-κB, nuclear factor-κB; ROS, reactive oxygen species; T_H17 cells, T helper 17 cells; T_reg cells, T regulatory cells.

Schematic of selected signalling pathways involved in the maintenance of intestinal homeostasis, including epithelial junctional complex assembly, innate immune recognition of pathogen-associated motifs, GPCRs and immune defence, anti-inflammatory interleukin-10 (IL-10) signalling, T_H17-cell differentiation, inhibitory pathways in lymphocyte signalling, and B-cell activation and IgA antibody responses. Proteins encoded by genes identified as being in linkage disequilibrium with IBD-risk SNPs (r² > 0.8) are highlighted in red. BCR, B-cell receptor; cAMP, cyclic AMP; EGFR, epidermal growth factor receptor; ERRFI1, ERBB receptor feedback inhibitor 1; Gα₁₂, G protein subunit α₁₂; GPCR, G-protein-coupled receptor; HNF-4α, hepatocyte nuclear factor-4α; LPA, lysophosphatidic acid; MDP, muramyl dipeptide; NF-κB, nuclear factor-κB; PI(3)K, phosphatidylinositol-3-OH kinase; PLA2G2E, phospholipase A₂, group IIE; PTGER4, prostaglandin E receptor 4; SCFA, short-chain fatty acid; SIAE, sialic acid acetylesterase; ssRNA, single-stranded RNA; TCR, T-cell receptor.

Host cells have evolved processes by which they restrict the availability of intracellular permissive niches to microbes. Microbial recognition by PRRs, such as NOD proteins and TLRs, activates key immediate host programs, leading to polarized secretion of pro-inflammatory mediators (directed to either the luminal or basolateral surface). Bacteria can either be maintained in subcellular compartments such as microbe-containing vacuoles, or escape into the cytoplasm, where they can be ubiquitylated and targeted for degradation. Both subsets can be targeted by the autophagy pathway, which is also regulated by other host defence mechanisms such as oxidative stress and inflammasome activation.

Intestinal homeostasis involves the coordinated actions of epithelial, innate and adaptive immune cells. Barrier permeability permits microbial incursion, which is detected by the innate immune system, which then orchestrates appropriate tolerogenic, inflammatory and restitutive responses in part by releasing extracellular mediators that recruit other cellular components, including adaptive immune cells. Genetic variants, the microbiota and immune factors affect the balance of these signals. Genes in linkage disequilibrium (r² > 0.8) with IBD-associated single nucleotide polymorphisms (SNPs) were manually curated and classified according to their function(s) in the context of intestinal homeostasis and immunity. Text colour indicates whether the genes are linked to risk loci associated with Crohn’s disease (CD; black), ulcerative colitis (UC; blue) or both (red). Asterisk denotes corresponding coding mutations; cis-eQTL effects are underlined. G, goblet cell; P, Paneth cell.

NOD2 is activated by the bacterial peptidoglycan muramyl dipeptide (MDP). Cell-specific NOD2 functions are shown, distinguishing between those functions impaired in cells from humans with the Crohn’s-disease-associated mutation 3020insC (red), from Nod2-deficient mice (blue), or from both (black). a, In Paneth cells, Nod2 deficiency leads to attenuated antibacterial activity in the intestinal crypts and decreased expression of α-defensin 4 (encoded by Defcr4, also known as Defa4) and α-defensin-related sequence 10 (DEFCR-RS10, also known as DEFA-RS10). b, MDP-stimulated release of pro-inflammatory NF-κB-dependent cytokines (such as IL-1β, TNF-α and IL-6), as well as secretion of IL-23 (which promotes T_H17 differentiation) after co-stimulation with MDP and TLR2 ligands, is decreased in antigen-presenting cells from Nod2-deficient mice or 3020insC human donors. MDP stimulation also leads to NOD2-activated autophagy and antigen presentation. In mice, the activation of antigen-presenting cells by ssRNA or respiratory syncytial virus (RSV) stimulates secretion of type I interferon (IFN-β) in a NOD2-dependent, receptor-interacting protein-2 (RIP2)-independent fashion. In contrast to the pro-inflammatory effects, chronic NOD2 activation (right) by MDP induces both self-tolerance and cross-tolerance to IL-1β, and TLR2 and TLR4 ligands. This is dependent on IRF4 in mice and humans, and also on IL-10, TGF-β, IL-1RA and IL-1R-associated kinase M (IRAK-M) in humans. MDP-induced tolerance is lost in Nod2-deficient mice and in patients with the 3020insC variant. NOD2-dependent release of IL-10 after MDP stimulation has been demonstrated to be specific to humans and is impaired in 3020insC cells. MDP-stimulated release of several cytokines, including IL-10, IL-1β, TNF-α and IL-6, is dependent on RIP2. c, In mice, NOD2 mediates IFN-γ secretion and REL-dependent IL-2 production in T cells in response to Toxoplasma gondii infection. Also, Nod2 deficiency attenuates the ability of T cells to cause experimental colitis after transfer into Rag1-deficient hosts.