{"gene":"TRIM40","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2011,"finding":"TRIM40 physically binds Nedd8 and promotes neddylation of IKKγ (NEMO/inhibitor of NF-κB kinase subunit gamma) via its RING domain, leading to inhibition of NF-κB activity; a dominant-negative RING-deleted mutant loses this 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 / Moderate — reciprocal Co-IP, domain mutagenesis, and functional NF-κB reporter assay in single lab with multiple orthogonal methods","pmids":["21474709"],"is_preprint":false},{"year":2017,"finding":"TRIM40 acts as an E3 ubiquitin ligase that directly binds MDA5 and RIG-I and promotes their K27- and K48-linked polyubiquitination, targeting them for proteasomal degradation and thereby suppressing RLR-triggered antiviral innate immune signaling.","method":"Co-immunoprecipitation, ubiquitination assay (K27- and K48-linkage-specific), proteasome inhibitor experiments, TRIM40-deficient mice, in vivo viral challenge","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, linkage-specific ubiquitination assays, genetic knockout in vivo, replicated in subsequent studies (PMIDs 34161773, 38253527)","pmids":["29117565"],"is_preprint":false},{"year":2021,"finding":"Riok3 (an atypical kinase) recruits TRIM40 and interacts with it to facilitate TRIM40-mediated K48- and K27-linked ubiquitination of RIG-I and MDA5, promoting their degradation and negatively regulating type I IFN signaling.","method":"Co-immunoprecipitation, ubiquitination assay, Riok3 knockout mice, in vitro viral replication assay","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, linkage-specific ubiquitination, in vivo knockout model, multiple orthogonal methods in single lab","pmids":["34161773"],"is_preprint":false},{"year":2021,"finding":"TRIM40 binds NLRP3 and promotes its ubiquitination (E3 ligase activity required via RING domain), suppressing NLRP3 inflammasome activation and IgA1-induced glomerular mesangial cell proliferation; RING-deleted TRIM40 loses these effects.","method":"Co-immunoprecipitation, ubiquitination assay, dominant-negative RING-domain mutant (ΔRING), siRNA knockdown, cell proliferation assay","journal":"Molecular immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay with domain mutagenesis, single lab","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; loss of any of these domains impairs ROCK1 degradation, leading to cortical actin disruption and epithelial barrier failure in IBD.","method":"Co-immunoprecipitation, ubiquitination assay, domain-deletion mutants (ΔRING, ΔB-box, ΔC-terminal), Trim40 knockout mice (DSS-induced colitis model), barrier function assay","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, domain mutagenesis, in vivo knockout model, multiple functional readouts in single rigorous study","pmids":["36755029"],"is_preprint":false},{"year":2024,"finding":"Virus-induced FUT8 upregulation promotes core fucosylation of EGFR, which activates a JAK1-STAT3 signaling axis that enhances TRIM40-mediated K48-linked ubiquitination of RIG-I, suppressing IFN-I antiviral responses.","method":"Co-immunoprecipitation, ubiquitination assay (K48-linkage specific), FUT8 inhibitor (2FF), glycosylation site-specific EGFR mutation (Q352AT), tissue-targeted Fut8 siRNA knockdown, viral replication assay","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, mutagenesis, inhibitor), single lab, mechanistic pathway position established","pmids":["38253527"],"is_preprint":false},{"year":2023,"finding":"TRIM40 directly interacts with DAB1 and promotes its K48-linked polyubiquitination and proteasomal degradation, disrupting Reelin/DAB1 signaling and reducing downstream PI3K/AKT activation and inflammatory responses in diabetic retinopathy.","method":"Co-immunoprecipitation, double immunofluorescence, K48-linked ubiquitination assay, AAV-mediated TRIM40 overexpression in STZ-induced diabetic mice","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, linkage-specific ubiquitination assay, in vivo AAV model, single lab","pmids":["37146559"],"is_preprint":false},{"year":2024,"finding":"TRIM40 directly binds ROCK1 and promotes its ubiquitination and degradation, reducing c-Myc protein stability and releasing p21 transcriptional repression, causing G0/G1 cell cycle arrest in colorectal cancer cells.","method":"Pull-down assay (direct binding), Co-immunoprecipitation, ubiquitination assay, protein degradation assay, in vitro and in vivo proliferation assays","journal":"Biochimica et biophysica acta. Molecular cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct pull-down plus Co-IP, ubiquitination assay, in vivo xenograft, single lab with multiple orthogonal methods","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 deletion and overexpression, in vivo xenograft","journal":"International immunopharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP and ubiquitination assay, single lab, single study","pmids":["38901248"],"is_preprint":false},{"year":2025,"finding":"Rnd3 facilitates the recruitment and interaction of Trim40 with Rock1 to promote Rock1 ubiquitination, preserving endothelial barrier integrity in the diabetic heart.","method":"Co-immunoprecipitation, ubiquitination assay, Rnd3 overexpression in cardiac microvascular endothelial cells, in vivo diabetic cardiomyopathy model","journal":"Diabetes","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP and functional overexpression, single lab, single study","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 manner requiring C29-dependent E3 ligase activity, leading to enhanced PKN2 phosphorylation at Ser815 and activation of downstream cardiac hypertrophy signaling.","method":"Co-immunoprecipitation, K63-linkage-specific ubiquitination assay, TRIM40 KO and cardiac-specific knockdown/overexpression mice, pharmacological PKN2 inhibition, TAC/Ang II hypertrophy models","journal":"Advanced science","confidence":"High","confidence_rationale":"Tier 2 / Moderate — domain-specific binding, linkage-specific ubiquitination, domain mutagenesis, multiple in vivo genetic models, pharmacological rescue, single lab","pmids":["41572508"],"is_preprint":false},{"year":2023,"finding":"In pteropodid (fruit bat) cells, TRIM40 is an interferon-stimulated gene (ISG) that, when knocked down, increases IFNβ and ISG expression following poly(I:C) stimulation, indicating bat TRIM40 antagonizes RIG-I-like receptor signaling as an ISG (not observed in human cells).","method":"siRNA knockdown, poly(I:C) transfection, RT-qPCR for IFNβ and ISGs, NiV infection model in bat cells","journal":"Viruses","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — siRNA knockdown with functional readout in bat cells, consistent with human TRIM40 mechanism but species-specific ISG induction not seen in human cells","pmids":["38005825"],"is_preprint":false}],"current_model":"TRIM40 is a RING domain-containing E3 ubiquitin ligase that suppresses innate immune and inflammatory signaling by directly ubiquitinating multiple substrates—including IKKγ (via neddylation), RIG-I and MDA5 (K27/K48-linked, targeting them for proteasomal degradation), NLRP3, ROCK1, DAB1, Keap1, and PKN2 (K63-linked)—with its activity dependent on an intact RING domain (or B-box for PKN2 binding), and its degradation of substrates is facilitated by interacting partners such as Riok3 and Rnd3, placing TRIM40 as a multifunctional negative regulator of NF-κB, RLR/IFN, NLRP3 inflammasome, and actin/cytoskeletal signaling pathways."},"narrative":{"mechanistic_narrative":"TRIM40 is a RING-domain E3 ubiquitin ligase that functions as a broad negative regulator of innate immune, inflammatory, and cytoskeletal signaling by ubiquitinating distinct substrates in a domain-dependent manner [PMID:21474709, PMID:29117565, PMID:36755029]. In antiviral immunity it binds the RNA sensors RIG-I and MDA5 and catalyzes K27- and K48-linked polyubiquitination that targets them for proteasomal degradation, dampening RLR-triggered type I interferon responses [PMID:29117565]; this degradation is potentiated by partner proteins, with the atypical kinase Riok3 recruiting TRIM40 to the sensors [PMID:34161773] and a FUT8/EGFR–JAK1–STAT3 axis enhancing K48-linked ubiquitination of RIG-I during infection [PMID:38253527]. TRIM40 likewise restrains NF-κB signaling by promoting RING-dependent neddylation of IKKγ/NEMO [PMID:21474709] and suppresses NLRP3 inflammasome activation through NLRP3 ubiquitination [PMID:34763147]. Beyond immunity, TRIM40 controls cytoskeletal and proliferative signaling by directing the ubiquitination and proteasomal degradation of ROCK1—requiring its RING, B-box, and C-terminal domains and facilitated by the recruiting partner Rnd3—thereby preserving epithelial and endothelial barrier integrity and imposing cell-cycle arrest via the c-Myc/p21 axis [PMID:36755029, PMID:39357549, PMID:39792251]. It further degrades DAB1 and Keap1 to modulate Reelin/PI3K-AKT and Nrf2 antioxidant signaling [PMID:37146559, PMID:38901248], and uses a B-box-dependent, C29-requiring activity to K63-ubiquitinate and activate PKN2 in cardiac hypertrophy, showing that its outputs span both degradative and non-degradative ubiquitin linkages [PMID:41572508].","teleology":[{"year":2011,"claim":"Established TRIM40 as a RING-dependent suppressor of NF-κB, the first mechanistic link between this ligase and inflammatory signaling, acting through an unusual neddylation rather than canonical ubiquitination.","evidence":"Co-IP, neddylation assay, dominant-negative ΔRING mutant, and NF-κB reporter with siRNA knockdown","pmids":["21474709"],"confidence":"High","gaps":["Did not define the structural basis for Nedd8 versus ubiquitin selectivity","Physiological context of NEMO neddylation not addressed in vivo"]},{"year":2017,"claim":"Defined TRIM40 as a brake on antiviral innate immunity by showing it ubiquitinates and degrades the RNA sensors RIG-I and MDA5, extending its negative-regulatory role from NF-κB to the RLR/IFN axis.","evidence":"Reciprocal Co-IP, K27/K48-linkage-specific ubiquitination assays, proteasome inhibition, and TRIM40-deficient mice with viral challenge","pmids":["29117565"],"confidence":"High","gaps":["Did not resolve how K27 versus K48 linkages partition functionally","Recruitment to sensors not yet explained"]},{"year":2021,"claim":"Identified Riok3 as a recruiting partner that bridges TRIM40 to RIG-I/MDA5, answering how the ligase is targeted to its antiviral substrates.","evidence":"Co-IP, ubiquitination assay, Riok3 knockout mice, and viral replication assays","pmids":["34161773"],"confidence":"High","gaps":["Whether Riok3 kinase activity is required for recruitment unclear","Does not address TRIM40 regulation in non-immune tissues"]},{"year":2021,"claim":"Extended TRIM40's anti-inflammatory role to the NLRP3 inflammasome, showing RING-dependent NLRP3 ubiquitination limits mesangial cell proliferation.","evidence":"Co-IP, ubiquitination assay, ΔRING mutant, siRNA knockdown, and proliferation assay","pmids":["34763147"],"confidence":"Medium","gaps":["Ubiquitin linkage type on NLRP3 not specified","No in vivo genetic confirmation"]},{"year":2023,"claim":"Demonstrated a cytoskeletal function distinct from immunity by showing multidomain-dependent ROCK1 degradation maintains cortical actin and epithelial barrier integrity, with loss driving IBD-like pathology.","evidence":"Co-IP, ubiquitination assay, ΔRING/ΔB-box/ΔC-terminal mutants, and Trim40 knockout mice in DSS colitis","pmids":["36755029"],"confidence":"High","gaps":["ROCK1 ubiquitin linkage type not defined","How multiple domains coordinate substrate engagement unresolved"]},{"year":2023,"claim":"Showed TRIM40 degrades DAB1 to suppress Reelin/PI3K-AKT signaling, broadening its substrate repertoire into neurodevelopmental/inflammatory signaling relevant to diabetic retinopathy.","evidence":"Co-IP, immunofluorescence, K48-linked ubiquitination assay, and AAV TRIM40 overexpression in diabetic mice","pmids":["37146559"],"confidence":"Medium","gaps":["Loss-of-function genetics not tested","Direct versus indirect DAB1 binding not fully resolved"]},{"year":2023,"claim":"Revealed species-specific deployment of TRIM40 as an interferon-stimulated gene in fruit bats that antagonizes RLR signaling, a regulatory wiring not seen in human cells.","evidence":"siRNA knockdown, poly(I:C) stimulation, RT-qPCR of IFNβ/ISGs, and NiV infection in bat cells","pmids":["38005825"],"confidence":"Medium","gaps":["Mechanistic basis of bat-specific ISG induction unknown","Substrate engagement in bat cells not biochemically mapped"]},{"year":2024,"claim":"Placed TRIM40 downstream of a virus-induced FUT8/EGFR/JAK1-STAT3 axis that enhances RIG-I ubiquitination, connecting glycosylation signaling to TRIM40-mediated IFN suppression.","evidence":"Co-IP, K48-linkage ubiquitination assay, FUT8 inhibitor, EGFR glycosite mutant, and Fut8 siRNA with viral replication assay","pmids":["38253527"],"confidence":"Medium","gaps":["How STAT3 signaling mechanistically boosts TRIM40 activity unclear","TRIM40 abundance versus activity contribution not separated"]},{"year":2024,"claim":"Linked ROCK1 degradation to cell-cycle control, showing TRIM40 destabilizes c-Myc and de-represses p21 to enforce G0/G1 arrest in colorectal cancer.","evidence":"Direct pull-down, Co-IP, ubiquitination and degradation assays, and in vitro/in vivo proliferation assays","pmids":["39357549"],"confidence":"Medium","gaps":["Direct versus ROCK1-dependent control of c-Myc not fully separated","Context-dependence across tumor types untested"]},{"year":2024,"claim":"Identified Keap1 as a substrate, positioning TRIM40 as an activator of Nrf2 antioxidant signaling through Keap1 degradation in esophageal cancer.","evidence":"Co-IP, ubiquitination assay, TRIM40 deletion/overexpression, and xenograft","pmids":["38901248"],"confidence":"Medium","gaps":["Ubiquitin linkage type and direct binding region undefined","Single study without independent replication"]},{"year":2025,"claim":"Generalized the recruiting-partner model to the cytoskeletal arm by showing Rnd3 bridges TRIM40 to ROCK1 to preserve endothelial barrier integrity in the diabetic heart.","evidence":"Co-IP, ubiquitination assay, Rnd3 overexpression in cardiac microvascular endothelial cells, and diabetic cardiomyopathy model","pmids":["39792251"],"confidence":"Medium","gaps":["Rnd3 versus other adaptors specificity not addressed","No loss-of-function genetics for Rnd3 in this context"]},{"year":2026,"claim":"Showed TRIM40 can activate rather than degrade a substrate, using B-box-dependent binding and C29-dependent K63-linked ubiquitination to promote PKN2 phosphorylation and cardiac hypertrophy signaling.","evidence":"Co-IP, K63-linkage ubiquitination assay, domain mutagenesis, multiple cardiac in vivo genetic models, and pharmacological PKN2 inhibition","pmids":["41572508"],"confidence":"High","gaps":["How linkage choice (K63 versus K48) is determined across substrates unknown","Structural basis for B-box-mediated substrate selection not defined"]},{"year":null,"claim":"It remains unresolved what governs TRIM40's choice of ubiquitin linkage and degradative versus non-degradative outcomes across its many substrates, and whether a unifying structural logic dictates substrate and adaptor selection.","evidence":"No timeline study directly compares linkage determinants or provides a structural model of substrate engagement","pmids":[],"confidence":"Low","gaps":["No structural model of TRIM40–substrate complexes","Determinants of K27/K48/K63 linkage selection unmapped","Adaptor specificity (Riok3 vs Rnd3) mechanism unexplained"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,3,4,6,7,8,10]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[1,4,10]}],"localization":[],"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":[1,4,6,7,8,10]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[4,6,9,10]}],"complexes":[],"partners":["RIGI","IFIH1","NLRP3","ROCK1","DAB1","KEAP1","PKN2","RIOK3"],"other_free_text":[]}},"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":112,"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":108,"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":39,"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":27,"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":"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":9,"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":4,"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":8542,"output_tokens":2961,"usd":0.035021,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10320,"output_tokens":4110,"usd":0.077175,"stage2_stop_reason":"end_turn"},"total_usd":0.112196,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2011,\n      \"finding\": \"TRIM40 physically binds Nedd8 and promotes neddylation of IKKγ (NEMO/inhibitor of NF-κB kinase subunit gamma) via its RING domain, leading to inhibition of NF-κB activity; a dominant-negative RING-deleted mutant loses this 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 / Moderate — reciprocal Co-IP, domain mutagenesis, and functional NF-κB reporter assay in single lab with multiple orthogonal methods\",\n      \"pmids\": [\"21474709\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"TRIM40 acts as an E3 ubiquitin ligase that directly binds MDA5 and RIG-I and promotes their K27- and K48-linked polyubiquitination, targeting them for proteasomal degradation and thereby suppressing RLR-triggered antiviral innate immune signaling.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay (K27- and K48-linkage-specific), proteasome inhibitor experiments, TRIM40-deficient mice, in vivo viral challenge\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, linkage-specific ubiquitination assays, genetic knockout in vivo, replicated in subsequent studies (PMIDs 34161773, 38253527)\",\n      \"pmids\": [\"29117565\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Riok3 (an atypical kinase) recruits TRIM40 and interacts with it to facilitate TRIM40-mediated K48- and K27-linked ubiquitination of RIG-I and MDA5, promoting their degradation and negatively regulating type I IFN signaling.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, Riok3 knockout mice, in vitro viral replication assay\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, linkage-specific ubiquitination, in vivo knockout model, multiple orthogonal methods in single lab\",\n      \"pmids\": [\"34161773\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TRIM40 binds NLRP3 and promotes its ubiquitination (E3 ligase activity required via RING domain), suppressing NLRP3 inflammasome activation and IgA1-induced glomerular mesangial cell proliferation; RING-deleted TRIM40 loses these effects.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, dominant-negative RING-domain mutant (ΔRING), siRNA knockdown, cell proliferation assay\",\n      \"journal\": \"Molecular immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay with domain mutagenesis, single lab\",\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; loss of any of these domains impairs ROCK1 degradation, leading to cortical actin disruption and epithelial barrier failure in IBD.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, domain-deletion mutants (ΔRING, ΔB-box, ΔC-terminal), Trim40 knockout mice (DSS-induced colitis model), barrier function assay\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, domain mutagenesis, in vivo knockout model, multiple functional readouts in single rigorous study\",\n      \"pmids\": [\"36755029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Virus-induced FUT8 upregulation promotes core fucosylation of EGFR, which activates a JAK1-STAT3 signaling axis that enhances TRIM40-mediated K48-linked ubiquitination of RIG-I, suppressing IFN-I antiviral responses.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay (K48-linkage specific), FUT8 inhibitor (2FF), glycosylation site-specific EGFR mutation (Q352AT), tissue-targeted Fut8 siRNA knockdown, viral replication assay\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, mutagenesis, inhibitor), single lab, mechanistic pathway position established\",\n      \"pmids\": [\"38253527\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TRIM40 directly interacts with DAB1 and promotes its K48-linked polyubiquitination and proteasomal degradation, disrupting Reelin/DAB1 signaling and reducing downstream PI3K/AKT activation and inflammatory responses in diabetic retinopathy.\",\n      \"method\": \"Co-immunoprecipitation, double immunofluorescence, K48-linked ubiquitination assay, AAV-mediated TRIM40 overexpression in STZ-induced diabetic mice\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, linkage-specific ubiquitination assay, in vivo AAV model, single lab\",\n      \"pmids\": [\"37146559\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM40 directly binds ROCK1 and promotes its ubiquitination and degradation, reducing c-Myc protein stability and releasing p21 transcriptional repression, causing G0/G1 cell cycle arrest in colorectal cancer cells.\",\n      \"method\": \"Pull-down assay (direct binding), Co-immunoprecipitation, ubiquitination assay, protein degradation assay, in vitro and in vivo proliferation assays\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct pull-down plus Co-IP, ubiquitination assay, in vivo xenograft, single lab with multiple orthogonal methods\",\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 deletion and overexpression, in vivo xenograft\",\n      \"journal\": \"International immunopharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP and ubiquitination assay, single lab, single study\",\n      \"pmids\": [\"38901248\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Rnd3 facilitates the recruitment and interaction of Trim40 with Rock1 to promote Rock1 ubiquitination, preserving endothelial barrier integrity in the diabetic heart.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, Rnd3 overexpression in cardiac microvascular endothelial cells, in vivo diabetic cardiomyopathy model\",\n      \"journal\": \"Diabetes\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP and functional overexpression, single lab, single study\",\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 manner requiring C29-dependent E3 ligase activity, leading to enhanced PKN2 phosphorylation at Ser815 and activation of downstream cardiac hypertrophy signaling.\",\n      \"method\": \"Co-immunoprecipitation, K63-linkage-specific ubiquitination assay, TRIM40 KO and cardiac-specific knockdown/overexpression mice, pharmacological PKN2 inhibition, TAC/Ang II hypertrophy models\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain-specific binding, linkage-specific ubiquitination, domain mutagenesis, multiple in vivo genetic models, pharmacological rescue, single lab\",\n      \"pmids\": [\"41572508\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In pteropodid (fruit bat) cells, TRIM40 is an interferon-stimulated gene (ISG) that, when knocked down, increases IFNβ and ISG expression following poly(I:C) stimulation, indicating bat TRIM40 antagonizes RIG-I-like receptor signaling as an ISG (not observed in human cells).\",\n      \"method\": \"siRNA knockdown, poly(I:C) transfection, RT-qPCR for IFNβ and ISGs, NiV infection model in bat cells\",\n      \"journal\": \"Viruses\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — siRNA knockdown with functional readout in bat cells, consistent with human TRIM40 mechanism but species-specific ISG induction not seen in human cells\",\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 directly ubiquitinating multiple substrates—including IKKγ (via neddylation), RIG-I and MDA5 (K27/K48-linked, targeting them for proteasomal degradation), NLRP3, ROCK1, DAB1, Keap1, and PKN2 (K63-linked)—with its activity dependent on an intact RING domain (or B-box for PKN2 binding), and its degradation of substrates is facilitated by interacting partners such as Riok3 and Rnd3, placing TRIM40 as a multifunctional negative regulator of NF-κB, RLR/IFN, NLRP3 inflammasome, and actin/cytoskeletal signaling pathways.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TRIM40 is a RING-domain E3 ubiquitin ligase that functions as a broad negative regulator of innate immune, inflammatory, and cytoskeletal signaling by ubiquitinating distinct substrates in a domain-dependent manner [#0, #1, #4]. In antiviral immunity it binds the RNA sensors RIG-I and MDA5 and catalyzes K27- and K48-linked polyubiquitination that targets them for proteasomal degradation, dampening RLR-triggered type I interferon responses [#1]; this degradation is potentiated by partner proteins, with the atypical kinase Riok3 recruiting TRIM40 to the sensors [#2] and a FUT8/EGFR\\u2013JAK1\\u2013STAT3 axis enhancing K48-linked ubiquitination of RIG-I during infection [#5]. TRIM40 likewise restrains NF-\\u03baB signaling by promoting RING-dependent neddylation of IKK\\u03b3/NEMO [#0] and suppresses NLRP3 inflammasome activation through NLRP3 ubiquitination [#3]. Beyond immunity, TRIM40 controls cytoskeletal and proliferative signaling by directing the ubiquitination and proteasomal degradation of ROCK1\\u2014requiring its RING, B-box, and C-terminal domains and facilitated by the recruiting partner Rnd3\\u2014thereby preserving epithelial and endothelial barrier integrity and imposing cell-cycle arrest via the c-Myc/p21 axis [#4, #7, #9]. It further degrades DAB1 and Keap1 to modulate Reelin/PI3K-AKT and Nrf2 antioxidant signaling [#6, #8], and uses a B-box-dependent, C29-requiring activity to K63-ubiquitinate and activate PKN2 in cardiac hypertrophy, showing that its outputs span both degradative and non-degradative ubiquitin linkages [#10].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Established TRIM40 as a RING-dependent suppressor of NF-\\u03baB, the first mechanistic link between this ligase and inflammatory signaling, acting through an unusual neddylation rather than canonical ubiquitination.\",\n      \"evidence\": \"Co-IP, neddylation assay, dominant-negative \\u0394RING mutant, and NF-\\u03baB reporter with siRNA knockdown\",\n      \"pmids\": [\"21474709\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the structural basis for Nedd8 versus ubiquitin selectivity\", \"Physiological context of NEMO neddylation not addressed in vivo\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined TRIM40 as a brake on antiviral innate immunity by showing it ubiquitinates and degrades the RNA sensors RIG-I and MDA5, extending its negative-regulatory role from NF-\\u03baB to the RLR/IFN axis.\",\n      \"evidence\": \"Reciprocal Co-IP, K27/K48-linkage-specific ubiquitination assays, proteasome inhibition, and TRIM40-deficient mice with viral challenge\",\n      \"pmids\": [\"29117565\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve how K27 versus K48 linkages partition functionally\", \"Recruitment to sensors not yet explained\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified Riok3 as a recruiting partner that bridges TRIM40 to RIG-I/MDA5, answering how the ligase is targeted to its antiviral substrates.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, Riok3 knockout mice, and viral replication assays\",\n      \"pmids\": [\"34161773\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Riok3 kinase activity is required for recruitment unclear\", \"Does not address TRIM40 regulation in non-immune tissues\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extended TRIM40's anti-inflammatory role to the NLRP3 inflammasome, showing RING-dependent NLRP3 ubiquitination limits mesangial cell proliferation.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, \\u0394RING mutant, siRNA knockdown, and proliferation assay\",\n      \"pmids\": [\"34763147\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitin linkage type on NLRP3 not specified\", \"No in vivo genetic confirmation\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrated a cytoskeletal function distinct from immunity by showing multidomain-dependent ROCK1 degradation maintains cortical actin and epithelial barrier integrity, with loss driving IBD-like pathology.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, \\u0394RING/\\u0394B-box/\\u0394C-terminal mutants, and Trim40 knockout mice in DSS colitis\",\n      \"pmids\": [\"36755029\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"ROCK1 ubiquitin linkage type not defined\", \"How multiple domains coordinate substrate engagement unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showed TRIM40 degrades DAB1 to suppress Reelin/PI3K-AKT signaling, broadening its substrate repertoire into neurodevelopmental/inflammatory signaling relevant to diabetic retinopathy.\",\n      \"evidence\": \"Co-IP, immunofluorescence, K48-linked ubiquitination assay, and AAV TRIM40 overexpression in diabetic mice\",\n      \"pmids\": [\"37146559\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Loss-of-function genetics not tested\", \"Direct versus indirect DAB1 binding not fully resolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Revealed species-specific deployment of TRIM40 as an interferon-stimulated gene in fruit bats that antagonizes RLR signaling, a regulatory wiring not seen in human cells.\",\n      \"evidence\": \"siRNA knockdown, poly(I:C) stimulation, RT-qPCR of IFN\\u03b2/ISGs, and NiV infection in bat cells\",\n      \"pmids\": [\"38005825\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic basis of bat-specific ISG induction unknown\", \"Substrate engagement in bat cells not biochemically mapped\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placed TRIM40 downstream of a virus-induced FUT8/EGFR/JAK1-STAT3 axis that enhances RIG-I ubiquitination, connecting glycosylation signaling to TRIM40-mediated IFN suppression.\",\n      \"evidence\": \"Co-IP, K48-linkage ubiquitination assay, FUT8 inhibitor, EGFR glycosite mutant, and Fut8 siRNA with viral replication assay\",\n      \"pmids\": [\"38253527\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How STAT3 signaling mechanistically boosts TRIM40 activity unclear\", \"TRIM40 abundance versus activity contribution not separated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Linked ROCK1 degradation to cell-cycle control, showing TRIM40 destabilizes c-Myc and de-represses p21 to enforce G0/G1 arrest in colorectal cancer.\",\n      \"evidence\": \"Direct pull-down, Co-IP, ubiquitination and degradation assays, and in vitro/in vivo proliferation assays\",\n      \"pmids\": [\"39357549\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct versus ROCK1-dependent control of c-Myc not fully separated\", \"Context-dependence across tumor types untested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified Keap1 as a substrate, positioning TRIM40 as an activator of Nrf2 antioxidant signaling through Keap1 degradation in esophageal cancer.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, TRIM40 deletion/overexpression, and xenograft\",\n      \"pmids\": [\"38901248\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitin linkage type and direct binding region undefined\", \"Single study without independent replication\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Generalized the recruiting-partner model to the cytoskeletal arm by showing Rnd3 bridges TRIM40 to ROCK1 to preserve endothelial barrier integrity in the diabetic heart.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, Rnd3 overexpression in cardiac microvascular endothelial cells, and diabetic cardiomyopathy model\",\n      \"pmids\": [\"39792251\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Rnd3 versus other adaptors specificity not addressed\", \"No loss-of-function genetics for Rnd3 in this context\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Showed TRIM40 can activate rather than degrade a substrate, using B-box-dependent binding and C29-dependent K63-linked ubiquitination to promote PKN2 phosphorylation and cardiac hypertrophy signaling.\",\n      \"evidence\": \"Co-IP, K63-linkage ubiquitination assay, domain mutagenesis, multiple cardiac in vivo genetic models, and pharmacological PKN2 inhibition\",\n      \"pmids\": [\"41572508\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How linkage choice (K63 versus K48) is determined across substrates unknown\", \"Structural basis for B-box-mediated substrate selection not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved what governs TRIM40's choice of ubiquitin linkage and degradative versus non-degradative outcomes across its many substrates, and whether a unifying structural logic dictates substrate and adaptor selection.\",\n      \"evidence\": \"No timeline study directly compares linkage determinants or provides a structural model of substrate engagement\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of TRIM40\\u2013substrate complexes\", \"Determinants of K27/K48/K63 linkage selection unmapped\", \"Adaptor specificity (Riok3 vs Rnd3) mechanism unexplained\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 3, 4, 6, 7, 8, 10]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [1, 4, 10]}\n    ],\n    \"localization\": [],\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, 6, 7, 8, 10]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [4, 6, 9, 10]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RIGI\", \"IFIH1\", \"NLRP3\", \"ROCK1\", \"DAB1\", \"KEAP1\", \"PKN2\", \"RIOK3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":5,"faith_pct":80.0}}