{"gene":"TRIM40","run_date":"2026-04-28T21:43:00","timeline":{"discoveries":[{"year":2011,"finding":"TRIM40 physically binds to Nedd8 and promotes neddylation of IKKγ (IKBKG) via its RING domain, leading to inhibition of NF-κB activity; a dominant-negative RING-deleted mutant fails to inhibit NF-κB activity.","method":"Co-immunoprecipitation, neddylation assay, dominant-negative RING domain mutant, siRNA knockdown with NF-κB reporter assay","journal":"Carcinogenesis","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (binding, neddylation assay, dominant-negative mutant, KD phenotype), replicated across several experimental readouts","pmids":["21474709"],"is_preprint":false},{"year":2017,"finding":"TRIM40 functions as an E3 ubiquitin ligase that directly binds MDA5 and RIG-I and promotes their K27- and K48-linked polyubiquitination, leading to proteasomal degradation and suppression of RLR-triggered antiviral innate immune signaling.","method":"Co-immunoprecipitation, ubiquitination assay, proteasome inhibitor rescue, TRIM40 knockout mice with in vivo viral challenge","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, ubiquitination assay with linkage specificity, in vivo KO validation; replicated in subsequent independent studies","pmids":["29117565"],"is_preprint":false},{"year":2021,"finding":"The atypical kinase Riok3 recruits TRIM40 and interacts with it to facilitate K48- and K27-linked ubiquitination and degradation of RIG-I and MDA5, placing Riok3 upstream of TRIM40 in the negative regulation of type I IFN signaling.","method":"Co-immunoprecipitation, ubiquitination assay, Riok3 knockout (myeloid-specific) mice, in vitro and in vivo viral infection","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis via KO mice, Co-IP, ubiquitination assay with linkage specificity; strong mechanistic follow-up of TRIM40-RLR axis","pmids":["34161773"],"is_preprint":false},{"year":2021,"finding":"TRIM40 directly interacts with NLRP3 and mediates its ubiquitination via the RING domain, suppressing NLRP3 inflammasome activation; a ΔRING mutant loses this activity.","method":"Co-immunoprecipitation, ubiquitination assay, ΔRING dominant-negative mutant, siRNA knockdown in glomerular mesangial cells","journal":"Molecular immunology","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP plus ubiquitination assay with mutant validation; single lab, single study","pmids":["34763147"],"is_preprint":false},{"year":2023,"finding":"TRIM40 directly targets ROCK1 for ubiquitination and proteasomal degradation via its RING, B-box, and C-terminal domains, reducing phosphorylation of cortical actin signaling factors and impairing intestinal epithelial barrier function; Trim40-deficient mice are resistant to DSS-induced colitis.","method":"Co-immunoprecipitation, ubiquitination assay, domain deletion mutants (ΔRING, ΔB-box, ΔC-terminal), Trim40 knockout mice with DSS colitis model","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — domain mutagenesis, in vivo KO model with defined phenotype, multiple orthogonal methods in single study","pmids":["36755029"],"is_preprint":false},{"year":2024,"finding":"Core fucosylation of EGFR induced by HCV promotes TRIM40-mediated K48-linked ubiquitination of RIG-I, suppressing antiviral IFN-I responses via core fucosylated-EGFR-JAK1-STAT3-RIG-I signaling.","method":"Ubiquitination assay (K48-linkage specific), EGFR glycosylation mutants, FUT8 inhibitor, tissue-targeted Fut8 silencing, viral replication assay","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 — mechanistic pathway defined with multiple perturbation tools; TRIM40 role inferred from pathway context rather than direct TRIM40 mutagenesis","pmids":["38253527"],"is_preprint":false},{"year":2023,"finding":"TRIM40 interacts with DAB1 and promotes its K48-linked polyubiquitination, leading to DAB1 proteasomal degradation and suppression of Reelin/DAB1/PI3K/AKT signaling and inflammation in diabetic retinopathy.","method":"Co-immunoprecipitation, double immunofluorescence, K48-ubiquitination assay, TRIM40 overexpression via AAV in STZ diabetic mouse model","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP, linkage-specific ubiquitination, in vivo AAV rescue; single lab, moderate mechanistic depth","pmids":["37146559"],"is_preprint":false},{"year":2024,"finding":"TRIM40 directly binds ROCK1 (confirmed by pull-down assay), ubiquitinates it to accelerate degradation, reducing c-Myc protein stability and releasing p21 transcriptional inhibition, causing G0/G1 arrest in colorectal cancer cells.","method":"Pull-down assay, co-immunoprecipitation, ubiquitination assay, protein degradation assay, in vitro and in vivo (nude mouse) proliferation assays","journal":"Biochimica et biophysica acta. Molecular cell research","confidence":"Medium","confidence_rationale":"Tier 2 — direct pull-down plus ubiquitination assay, in vivo xenograft; single lab","pmids":["39357549"],"is_preprint":false},{"year":2024,"finding":"TRIM40 directly interacts with Keap1 and promotes its ubiquitin-proteasome degradation, leading to Nrf2 nuclear translocation and activation of antioxidant downstream cascades in esophageal cancer cells.","method":"Co-immunoprecipitation, ubiquitination assay, TRIM40 knockdown/overexpression, in vitro and in vivo xenograft models","journal":"International immunopharmacology","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP, ubiquitination, in vivo validation; single lab, single study","pmids":["38901248"],"is_preprint":false},{"year":2025,"finding":"Rnd3 facilitates recruitment and interaction with TRIM40 to promote ROCK1 ubiquitination in cardiac microvascular endothelial cells, preserving endothelial barrier integrity under diabetic conditions.","method":"Co-immunoprecipitation, ubiquitination assay, Rnd3 overexpression in diabetic mouse model","journal":"Diabetes","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP and ubiquitination assay with in vivo model; single lab, limited mechanistic depth on TRIM40 itself","pmids":["39792251"],"is_preprint":false},{"year":2026,"finding":"TRIM40 binds PKN2 via its B-box domain and promotes K63-linked ubiquitination of PKN2 in a C29-dependent (E3 ligase activity-dependent) manner, enhancing PKN2 phosphorylation at Ser815 and activating downstream hypertrophic signaling; TRIM40 KO attenuates and TRIM40 overexpression exacerbates cardiac hypertrophy.","method":"Co-immunoprecipitation, domain mapping (B-box mutant), E3 ligase active-site mutant (C29), K63-linkage specific ubiquitination assay, TRIM40 KO and overexpression mice with Ang II/TAC hypertrophy models, pharmacological PKN2 inhibition","journal":"Advanced science","confidence":"High","confidence_rationale":"Tier 1-2 — active-site and domain mutants, linkage-specific ubiquitination, in vivo KO and OE models with pharmacological rescue; multiple orthogonal methods","pmids":["41572508"],"is_preprint":false},{"year":2023,"finding":"TRIM40 functions as an interferon-stimulated gene (ISG) in Pteropus vampyrus (bat) cells but not human cells, and bat TRIM40 knockdown increases IFNβ and ISG expression following poly(I:C) stimulation, demonstrating species-specific immunosuppressive function against RIG-I-like receptors.","method":"siRNA knockdown, IFN stimulation assay, poly(I:C) transfection, NiV infection with viral titer measurement","journal":"Viruses","confidence":"Low","confidence_rationale":"Tier 3 — functional KD assay in bat cells; bat ortholog, not human TRIM40, limits direct mechanistic relevance","pmids":["38005825"],"is_preprint":false}],"current_model":"TRIM40 is a RING domain-containing E3 ubiquitin ligase that suppresses innate immune and inflammatory signaling by promoting neddylation of IKKγ (inhibiting NF-κB), K27/K48-linked ubiquitination and proteasomal degradation of the RIG-I and MDA5 innate immune sensors, K48-linked ubiquitination and degradation of ROCK1 (disrupting cortical actin and epithelial barrier integrity), NLRP3, DAB1, and Keap1, and K63-linked ubiquitination and activation of PKN2 to drive cardiac hypertrophy, with its substrates and linkage types dictated by context-specific co-regulators such as Riok3 and Rnd3."},"narrative":{"teleology":[{"year":2011,"claim":"Establishing TRIM40 as a RING-dependent modifier of NF-κB signaling resolved the question of whether this uncharacterized TRIM family member possessed enzymatic activity; it was shown to promote neddylation (not canonical ubiquitination) of IKKγ, inhibiting NF-κB.","evidence":"Co-IP, neddylation assay, ΔRING dominant-negative, and siRNA knockdown with NF-κB reporter in human cells","pmids":["21474709"],"confidence":"High","gaps":["Neddylation linkage site on IKKγ not mapped","Whether TRIM40 also ubiquitinates IKKγ was not tested","Physiological context (tissue, stimulus) for this regulation was unclear"]},{"year":2017,"claim":"Demonstrating that TRIM40 directly ubiquitinates RIG-I and MDA5 with K27/K48 linkages for proteasomal degradation established it as a negative regulator of antiviral innate immunity, with in vivo validation in knockout mice.","evidence":"Reciprocal Co-IP, linkage-specific ubiquitination assay, proteasome inhibitor rescue, TRIM40 KO mice challenged with virus","pmids":["29117565"],"confidence":"High","gaps":["Mechanism of substrate recognition (which domain contacts RIG-I/MDA5) not defined","Whether additional upstream signals regulate TRIM40 activity was unknown"]},{"year":2021,"claim":"Identifying Riok3 as an upstream recruiter of TRIM40 to RIG-I/MDA5 answered how TRIM40 is directed to its substrates, establishing a Riok3–TRIM40 axis for suppression of type I IFN signaling.","evidence":"Co-IP, ubiquitination assay, myeloid-specific Riok3 KO mice with viral challenge","pmids":["34161773"],"confidence":"High","gaps":["Whether Riok3 phosphorylates TRIM40 or acts purely as a scaffold was not resolved","Structural basis for Riok3–TRIM40 interaction unknown"]},{"year":2021,"claim":"Showing TRIM40 ubiquitinates NLRP3 in a RING-dependent manner to suppress inflammasome activation extended its immunosuppressive function beyond RLR signaling to inflammasome regulation.","evidence":"Co-IP, ubiquitination assay, ΔRING mutant, siRNA in glomerular mesangial cells","pmids":["34763147"],"confidence":"Medium","gaps":["Ubiquitin linkage type on NLRP3 not specified","In vivo validation absent","Single lab, not independently replicated"]},{"year":2023,"claim":"Identifying ROCK1 as a TRIM40 substrate requiring RING, B-box, and C-terminal domains for ubiquitination and degradation revealed a non-immune function — regulation of cortical actin and epithelial barrier integrity — with Trim40 KO mice protected from colitis.","evidence":"Domain deletion mutants, ubiquitination assay, TRIM40 KO mice in DSS colitis model","pmids":["36755029"],"confidence":"High","gaps":["Ubiquitin linkage type on ROCK1 not specified in this study","How TRIM40 expression is regulated in intestinal epithelium unknown"]},{"year":2023,"claim":"Extending the ROCK1 axis, TRIM40 was found to ubiquitinate DAB1 (K48 linkage) suppressing Reelin/PI3K/AKT signaling in diabetic retinopathy, and independently shown to degrade Keap1, activating Nrf2 antioxidant responses, broadening the substrate repertoire to metabolic and oxidative stress contexts.","evidence":"Co-IP and K48-ubiquitination assay with AAV-mediated TRIM40 in diabetic mice (DAB1); Co-IP, ubiquitination, and xenograft models (Keap1)","pmids":["37146559","38901248"],"confidence":"Medium","gaps":["DAB1 and Keap1 studies from single labs, not independently confirmed","Domain requirements for DAB1 and Keap1 recognition not mapped"]},{"year":2024,"claim":"Connecting HCV-induced EGFR core fucosylation to TRIM40-mediated K48 ubiquitination of RIG-I provided a viral immune-evasion mechanism, though TRIM40 itself was not directly mutagenized in this context.","evidence":"K48-linkage-specific ubiquitination assay, EGFR glycosylation mutants, FUT8 inhibitor, viral replication assay","pmids":["38253527"],"confidence":"Medium","gaps":["TRIM40 role inferred from pathway context without direct TRIM40 mutagenesis in this study","Whether fucosylated EGFR directly modulates TRIM40 expression or activity not established"]},{"year":2025,"claim":"Identification of Rnd3 as a second co-regulator that facilitates TRIM40–ROCK1 interaction in cardiac microvascular endothelial cells revealed that context-specific adaptors control TRIM40 substrate access, paralleling the Riok3 mechanism for RLR targets.","evidence":"Co-IP, ubiquitination assay, Rnd3 overexpression in diabetic mouse model","pmids":["39792251"],"confidence":"Medium","gaps":["Direct binding interface between Rnd3 and TRIM40 not defined","Single lab, single study"]},{"year":2026,"claim":"Demonstrating that TRIM40 catalyzes K63-linked (non-degradative) ubiquitination of PKN2 via its B-box domain, activating PKN2 phosphorylation and driving cardiac hypertrophy, established that TRIM40 is not exclusively a degradative E3 ligase and functions in pathological cardiac remodeling.","evidence":"B-box domain mapping, C29 active-site mutant, K63-linkage-specific ubiquitination, TRIM40 KO and overexpression mice with Ang II/TAC hypertrophy, pharmacological PKN2 inhibition","pmids":["41572508"],"confidence":"High","gaps":["Structural basis for K63 vs K48 linkage selectivity by TRIM40 unknown","Whether specific E2 conjugating enzymes dictate linkage type not addressed"]},{"year":null,"claim":"The mechanistic basis by which TRIM40 selects ubiquitin chain linkage type (K48 degradative vs K63 activating vs neddylation) and how tissue-specific co-regulators (Riok3, Rnd3) dictate substrate selectivity remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of TRIM40 or TRIM40–substrate complexes exists","E2 conjugating enzyme partners not identified","Transcriptional and post-translational regulation of TRIM40 itself poorly characterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,3,4,7,8,10]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[1,3,4,10]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,4]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,1,2,3,5]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[1,4,7,8,10]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,6,10]}],"complexes":[],"partners":["IKKΓ","RIG-I","MDA5","RIOK3","NLRP3","ROCK1","PKN2","RND3"],"other_free_text":[]},"mechanistic_narrative":"TRIM40 is a RING domain-containing E3 ubiquitin ligase that functions as a broad negative regulator of innate immune signaling and inflammatory pathways while also modulating cytoskeletal and hypertrophic responses through substrate-specific ubiquitination. It suppresses NF-κB signaling by promoting neddylation of IKKγ via its RING domain [PMID:21474709], and inhibits RIG-I/MDA5-mediated antiviral interferon responses by catalyzing K27- and K48-linked polyubiquitination that targets these sensors for proteasomal degradation, a process facilitated by the upstream kinase Riok3 [PMID:29117565, PMID:34161773]. TRIM40 also ubiquitinates ROCK1 through its RING, B-box, and C-terminal domains, disrupting cortical actin signaling and epithelial barrier integrity, with Trim40-deficient mice showing resistance to experimental colitis [PMID:36755029]; additional substrates include NLRP3 (suppressing inflammasome activation) [PMID:34763147], DAB1 [PMID:37146559], and Keap1 (activating Nrf2-dependent antioxidant responses) [PMID:38901248]. Beyond degradative K48-linked ubiquitination, TRIM40 catalyzes K63-linked ubiquitination of PKN2 via its B-box domain in a C29-dependent manner, activating PKN2 phosphorylation and driving pathological cardiac hypertrophy [PMID:41572508]."},"prefetch_data":{"uniprot":{"accession":"Q6P9F5","full_name":"E3 ubiquitin ligase TRIM40","aliases":["Probable E3 NEDD8-protein ligase","RING finger protein 35"],"length_aa":258,"mass_kda":29.3,"function":"E3 ubiquitin-protein ligase that plays a role in the limitation of the innate immune response (PubMed:21474709, PubMed:29117565). Mediates inhibition of the RLR signaling pathway by ubiquitinating RIGI and IFIH1 receptors, leading to their proteasomal degradation (PubMed:21474709). Also promotes the neddylation of IKBKG/NEMO, stabilizing NFKBIA, and thereby inhibiting of NF-kappa-B nuclear translocation and activation (PubMed:21474709)","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q6P9F5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TRIM40","classification":"Not Classified","n_dependent_lines":6,"n_total_lines":1208,"dependency_fraction":0.004966887417218543},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TRIM40","total_profiled":1310},"omim":[{"mim_id":"616976","title":"TRIPARTITE MOTIF-CONTAINING PROTEIN 40; TRIM40","url":"https://www.omim.org/entry/616976"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"intestine","ntpm":2.9},{"tissue":"liver","ntpm":1.4},{"tissue":"testis","ntpm":1.4}],"url":"https://www.proteinatlas.org/search/TRIM40"},"hgnc":{"alias_symbol":["RNF35"],"prev_symbol":[]},"alphafold":{"accession":"Q6P9F5","domains":[{"cath_id":"3.30.40.10","chopping":"13-67","consensus_level":"medium","plddt":79.4622,"start":13,"end":67},{"cath_id":"3.30.160.60","chopping":"69-103","consensus_level":"medium","plddt":89.03,"start":69,"end":103},{"cath_id":"1.10.287","chopping":"110-156_182-226","consensus_level":"medium","plddt":89.8251,"start":110,"end":226}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6P9F5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6P9F5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6P9F5-F1-predicted_aligned_error_v6.png","plddt_mean":76.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TRIM40","jax_strain_url":"https://www.jax.org/strain/search?query=TRIM40"},"sequence":{"accession":"Q6P9F5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6P9F5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6P9F5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6P9F5"}},"corpus_meta":[{"pmid":"21474709","id":"PMC_21474709","title":"TRIM40 promotes neddylation of IKKγ and is downregulated in gastrointestinal cancers.","date":"2011","source":"Carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/21474709","citation_count":111,"is_preprint":false},{"pmid":"29117565","id":"PMC_29117565","title":"The E3 Ubiquitin Ligase TRIM40 Attenuates Antiviral Immune Responses by Targeting MDA5 and RIG-I.","date":"2017","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/29117565","citation_count":106,"is_preprint":false},{"pmid":"34161773","id":"PMC_34161773","title":"Riok3 inhibits the antiviral immune response by facilitating TRIM40-mediated RIG-I and MDA5 degradation.","date":"2021","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/34161773","citation_count":45,"is_preprint":false},{"pmid":"36755029","id":"PMC_36755029","title":"TRIM40 is a pathogenic driver of inflammatory bowel disease subverting intestinal barrier integrity.","date":"2023","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/36755029","citation_count":37,"is_preprint":false},{"pmid":"34763147","id":"PMC_34763147","title":"TRIM40 inhibits IgA1-induced proliferation of glomerular mesangial cells by inactivating NLRP3 inflammasome through ubiquitination.","date":"2021","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/34763147","citation_count":28,"is_preprint":false},{"pmid":"38253527","id":"PMC_38253527","title":"EGFR core fucosylation, induced by hepatitis C virus, promotes TRIM40-mediated-RIG-I ubiquitination and suppresses interferon-I antiviral defenses.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38253527","citation_count":24,"is_preprint":false},{"pmid":"30906467","id":"PMC_30906467","title":"Acetic acid alleviates the inflammatory response and liver injury in septic mice by increasing the expression of TRIM40.","date":"2019","source":"Experimental and therapeutic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/30906467","citation_count":22,"is_preprint":false},{"pmid":"12433986","id":"PMC_12433986","title":"Different modes of regulation of transcription and pre-mRNA processing of the structurally juxtaposed homologs, Rnf33 and Rnf35, in eggs and in pre-implantation embryos.","date":"2002","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/12433986","citation_count":13,"is_preprint":false},{"pmid":"39357549","id":"PMC_39357549","title":"TRIM40 interacts with ROCK1 directly and inhibits colorectal cancer cell proliferation through the c-Myc/p21 axis.","date":"2024","source":"Biochimica et biophysica acta. Molecular cell research","url":"https://pubmed.ncbi.nlm.nih.gov/39357549","citation_count":8,"is_preprint":false},{"pmid":"15994318","id":"PMC_15994318","title":"Negative transcriptional modulation and silencing of the bi-exonic Rnf35 gene in the preimplantation embryo. Binding of the CCAAT-displacement protein/Cux to the untranslated exon 1 sequence.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15994318","citation_count":8,"is_preprint":false},{"pmid":"15516209","id":"PMC_15516209","title":"Transcriptional modulation of the pre-implantation embryo-specific Rnf35 gene by the Y-box protein NF-Y/CBF.","date":"2005","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/15516209","citation_count":7,"is_preprint":false},{"pmid":"37146559","id":"PMC_37146559","title":"TRIM40 ameliorates diabetic retinopathy through suppressing inflammation via Reelin/DAB1 signaling disruption: A mechanism by proteasomal degradation of DAB1.","date":"2023","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/37146559","citation_count":6,"is_preprint":false},{"pmid":"38005825","id":"PMC_38005825","title":"Pteropus vampyrus TRIM40 Is an Interferon-Stimulated Gene That Antagonizes RIG-I-like Receptors.","date":"2023","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/38005825","citation_count":3,"is_preprint":false},{"pmid":"39792251","id":"PMC_39792251","title":"Rnd3 Ameliorates Diabetic Cardiac Microvascular Injury via Facilitating Trim40-Mediated Rock1 Ubiquitination.","date":"2025","source":"Diabetes","url":"https://pubmed.ncbi.nlm.nih.gov/39792251","citation_count":3,"is_preprint":false},{"pmid":"38901248","id":"PMC_38901248","title":"Targeting TRIM40 signaling reduces esophagus cancer development: A mechanism involving in protection of oroxylin A.","date":"2024","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/38901248","citation_count":1,"is_preprint":false},{"pmid":"41572508","id":"PMC_41572508","title":"TRIM40 Drives Pathological Cardiac Hypertrophy and Heart Failure via Ubiquitination of PKN2.","date":"2026","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/41572508","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9481,"output_tokens":2897,"usd":0.035949},"stage2":{"model":"claude-opus-4-6","input_tokens":6274,"output_tokens":2672,"usd":0.147255},"total_usd":0.183204,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2011,\n      \"finding\": \"TRIM40 physically binds to Nedd8 and promotes neddylation of IKKγ (IKBKG) via its RING domain, leading to inhibition of NF-κB activity; a dominant-negative RING-deleted mutant fails to inhibit NF-κB activity.\",\n      \"method\": \"Co-immunoprecipitation, neddylation assay, dominant-negative RING domain mutant, siRNA knockdown with NF-κB reporter assay\",\n      \"journal\": \"Carcinogenesis\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (binding, neddylation assay, dominant-negative mutant, KD phenotype), replicated across several experimental readouts\",\n      \"pmids\": [\"21474709\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"TRIM40 functions as an E3 ubiquitin ligase that directly binds MDA5 and RIG-I and promotes their K27- and K48-linked polyubiquitination, leading to proteasomal degradation and suppression of RLR-triggered antiviral innate immune signaling.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, proteasome inhibitor rescue, TRIM40 knockout mice with in vivo viral challenge\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, ubiquitination assay with linkage specificity, in vivo KO validation; replicated in subsequent independent studies\",\n      \"pmids\": [\"29117565\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The atypical kinase Riok3 recruits TRIM40 and interacts with it to facilitate K48- and K27-linked ubiquitination and degradation of RIG-I and MDA5, placing Riok3 upstream of TRIM40 in the negative regulation of type I IFN signaling.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, Riok3 knockout (myeloid-specific) mice, in vitro and in vivo viral infection\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis via KO mice, Co-IP, ubiquitination assay with linkage specificity; strong mechanistic follow-up of TRIM40-RLR axis\",\n      \"pmids\": [\"34161773\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TRIM40 directly interacts with NLRP3 and mediates its ubiquitination via the RING domain, suppressing NLRP3 inflammasome activation; a ΔRING mutant loses this activity.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, ΔRING dominant-negative mutant, siRNA knockdown in glomerular mesangial cells\",\n      \"journal\": \"Molecular immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus ubiquitination assay with mutant validation; single lab, single study\",\n      \"pmids\": [\"34763147\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TRIM40 directly targets ROCK1 for ubiquitination and proteasomal degradation via its RING, B-box, and C-terminal domains, reducing phosphorylation of cortical actin signaling factors and impairing intestinal epithelial barrier function; Trim40-deficient mice are resistant to DSS-induced colitis.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, domain deletion mutants (ΔRING, ΔB-box, ΔC-terminal), Trim40 knockout mice with DSS colitis model\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — domain mutagenesis, in vivo KO model with defined phenotype, multiple orthogonal methods in single study\",\n      \"pmids\": [\"36755029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Core fucosylation of EGFR induced by HCV promotes TRIM40-mediated K48-linked ubiquitination of RIG-I, suppressing antiviral IFN-I responses via core fucosylated-EGFR-JAK1-STAT3-RIG-I signaling.\",\n      \"method\": \"Ubiquitination assay (K48-linkage specific), EGFR glycosylation mutants, FUT8 inhibitor, tissue-targeted Fut8 silencing, viral replication assay\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — mechanistic pathway defined with multiple perturbation tools; TRIM40 role inferred from pathway context rather than direct TRIM40 mutagenesis\",\n      \"pmids\": [\"38253527\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TRIM40 interacts with DAB1 and promotes its K48-linked polyubiquitination, leading to DAB1 proteasomal degradation and suppression of Reelin/DAB1/PI3K/AKT signaling and inflammation in diabetic retinopathy.\",\n      \"method\": \"Co-immunoprecipitation, double immunofluorescence, K48-ubiquitination assay, TRIM40 overexpression via AAV in STZ diabetic mouse model\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, linkage-specific ubiquitination, in vivo AAV rescue; single lab, moderate mechanistic depth\",\n      \"pmids\": [\"37146559\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM40 directly binds ROCK1 (confirmed by pull-down assay), ubiquitinates it to accelerate degradation, reducing c-Myc protein stability and releasing p21 transcriptional inhibition, causing G0/G1 arrest in colorectal cancer cells.\",\n      \"method\": \"Pull-down assay, co-immunoprecipitation, ubiquitination assay, protein degradation assay, in vitro and in vivo (nude mouse) proliferation assays\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct pull-down plus ubiquitination assay, in vivo xenograft; single lab\",\n      \"pmids\": [\"39357549\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM40 directly interacts with Keap1 and promotes its ubiquitin-proteasome degradation, leading to Nrf2 nuclear translocation and activation of antioxidant downstream cascades in esophageal cancer cells.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, TRIM40 knockdown/overexpression, in vitro and in vivo xenograft models\",\n      \"journal\": \"International immunopharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, ubiquitination, in vivo validation; single lab, single study\",\n      \"pmids\": [\"38901248\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Rnd3 facilitates recruitment and interaction with TRIM40 to promote ROCK1 ubiquitination in cardiac microvascular endothelial cells, preserving endothelial barrier integrity under diabetic conditions.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, Rnd3 overexpression in diabetic mouse model\",\n      \"journal\": \"Diabetes\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP and ubiquitination assay with in vivo model; single lab, limited mechanistic depth on TRIM40 itself\",\n      \"pmids\": [\"39792251\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"TRIM40 binds PKN2 via its B-box domain and promotes K63-linked ubiquitination of PKN2 in a C29-dependent (E3 ligase activity-dependent) manner, enhancing PKN2 phosphorylation at Ser815 and activating downstream hypertrophic signaling; TRIM40 KO attenuates and TRIM40 overexpression exacerbates cardiac hypertrophy.\",\n      \"method\": \"Co-immunoprecipitation, domain mapping (B-box mutant), E3 ligase active-site mutant (C29), K63-linkage specific ubiquitination assay, TRIM40 KO and overexpression mice with Ang II/TAC hypertrophy models, pharmacological PKN2 inhibition\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — active-site and domain mutants, linkage-specific ubiquitination, in vivo KO and OE models with pharmacological rescue; multiple orthogonal methods\",\n      \"pmids\": [\"41572508\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TRIM40 functions as an interferon-stimulated gene (ISG) in Pteropus vampyrus (bat) cells but not human cells, and bat TRIM40 knockdown increases IFNβ and ISG expression following poly(I:C) stimulation, demonstrating species-specific immunosuppressive function against RIG-I-like receptors.\",\n      \"method\": \"siRNA knockdown, IFN stimulation assay, poly(I:C) transfection, NiV infection with viral titer measurement\",\n      \"journal\": \"Viruses\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — functional KD assay in bat cells; bat ortholog, not human TRIM40, limits direct mechanistic relevance\",\n      \"pmids\": [\"38005825\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TRIM40 is a RING domain-containing E3 ubiquitin ligase that suppresses innate immune and inflammatory signaling by promoting neddylation of IKKγ (inhibiting NF-κB), K27/K48-linked ubiquitination and proteasomal degradation of the RIG-I and MDA5 innate immune sensors, K48-linked ubiquitination and degradation of ROCK1 (disrupting cortical actin and epithelial barrier integrity), NLRP3, DAB1, and Keap1, and K63-linked ubiquitination and activation of PKN2 to drive cardiac hypertrophy, with its substrates and linkage types dictated by context-specific co-regulators such as Riok3 and Rnd3.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TRIM40 is a RING domain-containing E3 ubiquitin ligase that functions as a broad negative regulator of innate immune signaling and inflammatory pathways while also modulating cytoskeletal and hypertrophic responses through substrate-specific ubiquitination. It suppresses NF-κB signaling by promoting neddylation of IKKγ via its RING domain [PMID:21474709], and inhibits RIG-I/MDA5-mediated antiviral interferon responses by catalyzing K27- and K48-linked polyubiquitination that targets these sensors for proteasomal degradation, a process facilitated by the upstream kinase Riok3 [PMID:29117565, PMID:34161773]. TRIM40 also ubiquitinates ROCK1 through its RING, B-box, and C-terminal domains, disrupting cortical actin signaling and epithelial barrier integrity, with Trim40-deficient mice showing resistance to experimental colitis [PMID:36755029]; additional substrates include NLRP3 (suppressing inflammasome activation) [PMID:34763147], DAB1 [PMID:37146559], and Keap1 (activating Nrf2-dependent antioxidant responses) [PMID:38901248]. Beyond degradative K48-linked ubiquitination, TRIM40 catalyzes K63-linked ubiquitination of PKN2 via its B-box domain in a C29-dependent manner, activating PKN2 phosphorylation and driving pathological cardiac hypertrophy [PMID:41572508].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Establishing TRIM40 as a RING-dependent modifier of NF-κB signaling resolved the question of whether this uncharacterized TRIM family member possessed enzymatic activity; it was shown to promote neddylation (not canonical ubiquitination) of IKKγ, inhibiting NF-κB.\",\n      \"evidence\": \"Co-IP, neddylation assay, ΔRING dominant-negative, and siRNA knockdown with NF-κB reporter in human cells\",\n      \"pmids\": [\"21474709\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Neddylation linkage site on IKKγ not mapped\", \"Whether TRIM40 also ubiquitinates IKKγ was not tested\", \"Physiological context (tissue, stimulus) for this regulation was unclear\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrating that TRIM40 directly ubiquitinates RIG-I and MDA5 with K27/K48 linkages for proteasomal degradation established it as a negative regulator of antiviral innate immunity, with in vivo validation in knockout mice.\",\n      \"evidence\": \"Reciprocal Co-IP, linkage-specific ubiquitination assay, proteasome inhibitor rescue, TRIM40 KO mice challenged with virus\",\n      \"pmids\": [\"29117565\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of substrate recognition (which domain contacts RIG-I/MDA5) not defined\", \"Whether additional upstream signals regulate TRIM40 activity was unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identifying Riok3 as an upstream recruiter of TRIM40 to RIG-I/MDA5 answered how TRIM40 is directed to its substrates, establishing a Riok3–TRIM40 axis for suppression of type I IFN signaling.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, myeloid-specific Riok3 KO mice with viral challenge\",\n      \"pmids\": [\"34161773\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Riok3 phosphorylates TRIM40 or acts purely as a scaffold was not resolved\", \"Structural basis for Riok3–TRIM40 interaction unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showing TRIM40 ubiquitinates NLRP3 in a RING-dependent manner to suppress inflammasome activation extended its immunosuppressive function beyond RLR signaling to inflammasome regulation.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, ΔRING mutant, siRNA in glomerular mesangial cells\",\n      \"pmids\": [\"34763147\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitin linkage type on NLRP3 not specified\", \"In vivo validation absent\", \"Single lab, not independently replicated\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identifying ROCK1 as a TRIM40 substrate requiring RING, B-box, and C-terminal domains for ubiquitination and degradation revealed a non-immune function — regulation of cortical actin and epithelial barrier integrity — with Trim40 KO mice protected from colitis.\",\n      \"evidence\": \"Domain deletion mutants, ubiquitination assay, TRIM40 KO mice in DSS colitis model\",\n      \"pmids\": [\"36755029\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ubiquitin linkage type on ROCK1 not specified in this study\", \"How TRIM40 expression is regulated in intestinal epithelium unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Extending the ROCK1 axis, TRIM40 was found to ubiquitinate DAB1 (K48 linkage) suppressing Reelin/PI3K/AKT signaling in diabetic retinopathy, and independently shown to degrade Keap1, activating Nrf2 antioxidant responses, broadening the substrate repertoire to metabolic and oxidative stress contexts.\",\n      \"evidence\": \"Co-IP and K48-ubiquitination assay with AAV-mediated TRIM40 in diabetic mice (DAB1); Co-IP, ubiquitination, and xenograft models (Keap1)\",\n      \"pmids\": [\"37146559\", \"38901248\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"DAB1 and Keap1 studies from single labs, not independently confirmed\", \"Domain requirements for DAB1 and Keap1 recognition not mapped\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Connecting HCV-induced EGFR core fucosylation to TRIM40-mediated K48 ubiquitination of RIG-I provided a viral immune-evasion mechanism, though TRIM40 itself was not directly mutagenized in this context.\",\n      \"evidence\": \"K48-linkage-specific ubiquitination assay, EGFR glycosylation mutants, FUT8 inhibitor, viral replication assay\",\n      \"pmids\": [\"38253527\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"TRIM40 role inferred from pathway context without direct TRIM40 mutagenesis in this study\", \"Whether fucosylated EGFR directly modulates TRIM40 expression or activity not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identification of Rnd3 as a second co-regulator that facilitates TRIM40–ROCK1 interaction in cardiac microvascular endothelial cells revealed that context-specific adaptors control TRIM40 substrate access, paralleling the Riok3 mechanism for RLR targets.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, Rnd3 overexpression in diabetic mouse model\",\n      \"pmids\": [\"39792251\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding interface between Rnd3 and TRIM40 not defined\", \"Single lab, single study\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Demonstrating that TRIM40 catalyzes K63-linked (non-degradative) ubiquitination of PKN2 via its B-box domain, activating PKN2 phosphorylation and driving cardiac hypertrophy, established that TRIM40 is not exclusively a degradative E3 ligase and functions in pathological cardiac remodeling.\",\n      \"evidence\": \"B-box domain mapping, C29 active-site mutant, K63-linkage-specific ubiquitination, TRIM40 KO and overexpression mice with Ang II/TAC hypertrophy, pharmacological PKN2 inhibition\",\n      \"pmids\": [\"41572508\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis for K63 vs K48 linkage selectivity by TRIM40 unknown\", \"Whether specific E2 conjugating enzymes dictate linkage type not addressed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The mechanistic basis by which TRIM40 selects ubiquitin chain linkage type (K48 degradative vs K63 activating vs neddylation) and how tissue-specific co-regulators (Riok3, Rnd3) dictate substrate selectivity remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of TRIM40 or TRIM40–substrate complexes exists\", \"E2 conjugating enzyme partners not identified\", \"Transcriptional and post-translational regulation of TRIM40 itself poorly characterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 3, 4, 7, 8, 10]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [1, 3, 4, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 1, 2, 3, 5]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [1, 4, 7, 8, 10]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 6, 10]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"IKKγ\", \"RIG-I\", \"MDA5\", \"RIOK3\", \"NLRP3\", \"ROCK1\", \"PKN2\", \"RND3\"],\n    \"other_free_text\": []\n  }\n}\n```"}