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Schema Name NOD2 Schema for Crohn's disease
Accession MS031100031.9
Gene(s) NOD2, RICK, ATG16L1
Schema Caption Mechanism by which NOD2 1007fs variant causes increased Crohn's disease risk
Schema Description NOD2 is one of the most important loci for Crohn's disease. NOD2 have been associated with susceptibility to Crohn's disease with an odds ratio equal to 2.4 in heterozygote individuals and 17.1 in homozygotes or compound heterozygotes, representing the strongest association with CD to date (PMID:15571588). The complexity of the disease, like stricturing or fistulizing, is increased by 8% for NOD2 heterozygotes and 41% for NOD2 homozygotes or compound heterozygotes and the risk of surgery is increased by 58% with any of NOD2 mutations (PMID: 21343918). Three main variants of NOD2 gene which are associated with Crohn's disease risk, are one frameshift mutation - L1007fsC (rs2066847), and two missense SNVs - R702W (rs2066844) and G908R (rs2066845) (PMID:11385577 , PMID:11385576 , PMID:11875755). We start this mechanism schema with the frameshift single base insertion at 1007 position (rs2066847) which is most consistently associated with CD across multiple studies and population groups (PMID:15571588) with a very high relative risk of 17.6 for its homozygous genotype status as compared with wild-type controls (PMID:11385577).
Author(s) Kunal Kundu
Curator(s) John Moult
Last Modified Sun Mar 12 2023 11:01:29 GMT-0400 (Eastern Daylight Time)
Sub-state Perturbation (SSP) Annotations
Component ID: SSP1
Stage: DNA
SSP Class: IN/DEL [HOM/HET]
Other SSP Class:
Modifier: NA
Ontology:
SSP Instance: rs2066847: dupC in NOD2
Confidence Score: 5
Comment:
For Evidence: PMID:25365249, PMID:23173613, PMID:11385577
Against Evidence:
Component ID: SSP3
Stage: Protein
SSP Class: Truncated Protein
Other SSP Class:
Modifier: NA
Ontology: BAO_v20201215
SSP Instance: NP_071445: p.Leu1007fs
Confidence Score: 5
Comment: The creation of the premature stop codon causes to produce the truncated NOD2 protein loosing the last 33 amino acids of the wild-type sequence.
For Evidence: PMID:17355968, PMID:11385577
Against Evidence:
Component ID: SSP5
Stage: Protein
SSP Class: Protein Abundance
Other SSP Class:
Modifier: Decreased
Ontology: PLOSTHES_v20170921
SSP Instance: NOD2 protein at plasma membrane
Confidence Score: 5
Comment: Confocal microscopy showed that the NOD2 1007fs was only present in the cytosol. Loss of membrane targeting confirmed by the Western blot analysis after separation of cytosolic and membrane fractions. The ratio of NOD2 1007fs between membrane and cytosolic fractions was significantly decreased compared to wild type NOD2.
For Evidence: PMID:15998797
Against Evidence:
Component ID: SSP7
Stage: Cell
SSP Class: Other
Other SSP Class: Cell Product Abundance
Modifier: Decreased
Ontology:
SSP Instance: Pro-inflammatory cytokines
Confidence Score: 5
Comment: Transfection of RICK-deficient fibroblasts with constructs encoding NOD2 results in defective NF-kB activation.
For Evidence: PMID:16493424, PMID:17355968, PMID:17277144, PMID:21750585
Against Evidence:
Component ID: SSP12
Stage: Phenotype
SSP Class: Other
Other SSP Class: Disease Risk
Modifier: Increased
Ontology:
SSP Instance: Crohn's disease
Confidence Score: 5
Comment:
For Evidence:
Against Evidence:
Component ID: SSP11
Stage: Cell
SSP Class: Other
Other SSP Class: Bacterial Abundance
Modifier: Increased
Ontology:
SSP Instance: Bacteria in mucosal layer
Confidence Score: 5
Comment: It has been demonstrated that the NOD2 genotype impacts on the ileal microbiome in Crohn's disease (PMID:30818349).
For Evidence: PMID:19898471, PMID:27703457, PMID:30818349
Against Evidence:
Component ID: SSP10
Stage: Cell
SSP Class: Other
Other SSP Class: Cell Product Abundance
Modifier: Decreased
Ontology:
SSP Instance: Paneth cell defensin expression
Confidence Score: 2
Comment: Studies show that MDP-NOD2 stimulation can induce defensin HNP-1 (human neutrophil peptide 1) in Caco-2 cells and hBD2 (human ß-defensin-2) in several epithelial cells. This induction fails for the NOD21007fs mutant.
For Evidence: PMID:20128000, PMID:15692051, PMID:32351509
Against Evidence:
Component ID: SSP4
Stage: Cell
SSP Class: Other
Other SSP Class: Cell Product Abundance
Modifier: Altered
Ontology:
SSP Instance: Pro-inflammatory cytokines
Confidence Score: 3
Comment:
For Evidence: PMID:15220916
Against Evidence:
Component ID: SSP2
Stage: RNA
SSP Class: IN/DEL
Other SSP Class:
Modifier: NA
Ontology: NCIT_v20210125
SSP Instance: NM_022162: c.3019dup with a premature stop codon after the 1007 codon.
Confidence Score: 5
Comment: The rs2066847 variant causes the insertion of the base C after the first nucleotide of the codon 1007 followed by creation of a premature stop codon.
For Evidence:
Against Evidence:
Component ID: SSP6
Stage: Complex
SSP Class: Protein-Protein Complex Abundance
Other SSP Class:
Modifier: Decreased
Ontology: ADMO_v20200421
SSP Instance: NOD2-RICK complex at plasma membrane
Confidence Score: 3
Comment: Biochemical fractionation experiment performed in HEK293 cells showed that RICK is localized at the plasma membrane in a NOD2 dependent manner. Immunofluorescence analysis revealed that RICK is detected at the plasma membrane of the monocytic cell line THP1. Coimmunoprecipitation experiment in HEK293T cell shows that RICK and NOD2 interacts. However, there are no experiments to show that in presence of the NOD2 1007fs mutant, there is low complex abundance. Hence this step is given medium confidence.
For Evidence: PMID:11087742, PMID:17355968
Against Evidence:
Component ID: SSP8
Stage: Complex
SSP Class: Protein-Protein Complex Abundance
Other SSP Class:
Modifier: Decreased
Ontology: ADMO_v20200421
SSP Instance: NOD2-ATG16L1 complex at plasma membrane
Confidence Score: 5
Comment: Immunofluorescence of HeLa cells transfected with NOD2 and ATG16L1 showed the strong colocalization of both these proteins at the plasma membrane. NOD2 and ATG16L1 was also observed to co-localize at plasma membrane in the mouse intestinal epithelial cell line. The ATG16L1 was not localized at plasma membrane when expressed with NOD2 1007fs protein. Immunoprecipitation and immunoblot analysis of HEK293 cells transfected with NOD2 and ATG16L1 shows that they interact with each other.
For Evidence: PMID:19898471
Against Evidence:
Component ID: SSP9
Stage: Cell
SSP Class: Other
Other SSP Class: Bacterial Abundance
Modifier: Increased
Ontology:
SSP Instance: Bacteria in lamina propria
Confidence Score: 5
Comment: It has been demonstrated that the NOD2 genotype impacts on the ileal microbiome in Crohn's disease (PMID:30818349).
For Evidence: PMID:19898471, PMID:27703457, PMID:30818349
Against Evidence:
Biomarker(s) Annotations
Mechanism Module (MM) Annotations
Component ID: MM4
Mechanism Class Name:
Other Mechanism Class Name: Localization
Modifer: Altered
Ontology:
Mechanism Instance:
Confidence Score: 5
Comment: Sub-cellular localization experiments (using EGFP labeling technique in HEK and Caco-2 cells) show that NOD2 1007fs mutant cannot localize to the plasma membrane as compared to its wild type.
For Evidence: PMID:21690088, PMID:15998797
Against Evidence:
Component ID: MM5
Mechanism Class Name:
Other Mechanism Class Name: Binding of NOD2 to MDP
Modifer: Decreased
Ontology: NCIT
Mechanism Instance:
Confidence Score: 5
Comment: NOD2 activation requires its location in the vicinity of the MDP delivery site close to plasma membrane.
For Evidence: PMID:28253332
Against Evidence:
Component ID: MM6
Mechanism Class Name:
Other Mechanism Class Name: NF-κB signaling
Modifer: Decreased
Ontology:
Mechanism Instance:
Confidence Score: 5
Comment: Under wild type NOD2 state, the NOD2-RICK complex mediates the recruitment and activation of the TAK1 protein which then activates IKK complex and MAPK pathways for regulating expression of the proinflammatory cytokines. This cascade of steps are affected due to the mutant NOD2 protein. NF-kB-luciferase reporter assay shows that NOD2 1007fs has low NF-kB activity when stimulated by MDP in HEK293 cell.
For Evidence: PMID:25526305, PMID:17355968, PMID:15998797, PMID:12527755
Against Evidence:
Component ID: MM7
Mechanism Class Name:
Other Mechanism Class Name: Xenophagy
Modifer: Decreased
Ontology:
Mechanism Instance:
Confidence Score: 5
Comment: HeLa cells expressing NOD2 1007fs and ATG16L1 protein when infected with S. flexneri did not show any colocalization of ATG16L1 protein with the invading bacteria at the plasma membrane. The number of LC3+ bacteria in GFP-LC3-transduced Nod2 1007fs BMDMs from mice infected with S. flexneri was much lower than that in wild-type BMDMs.
For Evidence: PMID:19898471
Against Evidence:
Component ID: MM3
Mechanism Class Name:
Other Mechanism Class Name: Regulation of TLR-mediated NF-κB signaling
Modifer: Altered
Ontology:
Mechanism Instance:
Confidence Score: 3
Comment: It is not clear mechanistically how Nod2 and Toll-like regulate inflammatory responses. Different models have been proposed to describe the collaboration between NOD2 and TLRs such as synergistic production of TNF-alpha between NOD2 - TLR4, activation of the inflammasome by NOD2 to produce IL-1beta or MDP dose-dependent TNF-alpha production by NOD2-TLR2. There is a need to design experiments for testing how the existing models behave in response to the NOD21007fs mutation. Because of the lack of evidence this path is given low confidence.
For Evidence: PMID:17850483, PMID:15220916, PMID:18340358, PMID:26153766
Against Evidence:
Component ID: MM8
Mechanism Class Name:
Other Mechanism Class Name: Bactericidal activity
Modifer: Decreased
Ontology:
Mechanism Instance:
Confidence Score: 5
Comment:
For Evidence: PMID:18973303
Against Evidence:
Component ID: MM1
Mechanism Class Name:
Other Mechanism Class Name:
Modifer: NA
Ontology:
Mechanism Instance: Transcription
Confidence Score: 5
Comment:
For Evidence:
Against Evidence:
Component ID: MM2
Mechanism Class Name:
Other Mechanism Class Name:
Modifer: NA
Ontology: GO
Mechanism Instance: Translation
Confidence Score: 5
Comment:
For Evidence:
Against Evidence:
Component ID: MM10
Mechanism Class Name:
Other Mechanism Class Name: Activation of immune response
Modifer: Altered
Ontology:
Mechanism Instance:
Confidence Score: 5
Comment:
For Evidence: PMID:22408345, PMID:17277144, PMID:21750585, PMID:29483781
Against Evidence:
Component ID: MM9
Mechanism Class Name:
Other Mechanism Class Name: Bacterial influx to epithelium
Modifer: Increased
Ontology:
Mechanism Instance:
Confidence Score: 5
Comment:
For Evidence:
Against Evidence:
Unknown Mechanism Module (MM) Annotations
Component ID: MM11
Comment: There are conflicting evidence regarding the association between NOD2 and defensin production. Experimental evidence shows that MDP-NOD2 stimulation induced defensin HNP-1 (human neutrophil peptide 1) in Caco-2 cells and that NOD2 1007fs protein fails to induce the production of defensin hBD2 (human β-defensin-2) in several epithelial cells. On the other hand, in two out of four CD cohort studies [PMID: 16330776, 18305068, 26891258], and in NOD2 deficient mouse organoids [PMID: 25118165], the association between NOD2 and defensin is not reproduced. Thus, the mechanism of regulation of Paneth cell defensin expression in humans by NOD2 is not yet resolved.
For Evidence: PMID:32351509
Against Evidence:
Environmental Factor Annotations
Component ID: EF2
Annotation Text: PAMPs
Comment: Pathogen-associated molecular patterns (PAMPs) such as lipopolysaccharide (LPS), or muramyl dipeptide (MDP) activates TLRs and NOD sensors to trigger immune response.
For Evidence: PMID:18029230
Against Evidence:
Component ID: EF1
Annotation Text: MDP
Comment: Muramyl dipeptide (MDP), an immunostimulatory fragment of bacterial cell wall, binds to NOD2 to trigger the innate immune response.
For Evidence: PMID:22857257
Against Evidence:
Therapeutic Interventions Annotations