{"gene":"TRIM9","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2010,"finding":"TRIM9 functions as an E3 ubiquitin ligase collaborating with the E2 ubiquitin conjugating enzyme UbcH5b, and is localized to neurons in the brain.","method":"In vitro ubiquitin ligase assay with UbcH5b; immunohistochemistry and immunoblotting for localization","journal":"Neurobiology of disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro enzymatic assay with identified E2, plus direct localization by IHC; single lab, two orthogonal methods","pmids":["20085810"],"is_preprint":false},{"year":2016,"finding":"The short isoform of TRIM9 (TRIM9s) undergoes Lys-63-linked auto-polyubiquitination upon viral infection and acts as a scaffold bridging GSK3β to TBK1, thereby activating IRF3 signaling and enhancing type I IFN production while selectively suppressing pro-inflammatory cytokine production.","method":"Co-immunoprecipitation, ubiquitination assays (K63-linkage specific), overexpression/knockdown in cells with viral infection readouts","journal":"Cell research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP identifying GSK3β–TRIM9s–TBK1 complex, K63-ubiquitination assay, gain/loss-of-function with IFN/cytokine readouts; single lab but multiple orthogonal methods","pmids":["26915459"],"is_preprint":false},{"year":2015,"finding":"TRIM9 localizes to filopodial tips, binds the netrin receptor DCC, and ubiquitinates the barbed-end actin polymerase VASP to reduce VASP filopodial tip localization and stability; netrin stimulation causes VASP deubiquitination, promoting VASP tip localization and filopodial stability to drive axon guidance.","method":"Co-IP (TRIM9–DCC, TRIM9–VASP), in vitro ubiquitination assay, non-ubiquitinatable VASP mutant, TIRF microscopy, Trim9−/− cortical neurons, in vivo axon guidance assays","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro ubiquitination of VASP, non-ubiquitinatable mutant rescue, KO neurons with in vitro and in vivo phenotypic readouts; multiple orthogonal methods in single study","pmids":["26702829"],"is_preprint":false},{"year":2019,"finding":"TRIM9 sequesters β-TrCP from the Skp-Cullin-F-box ubiquitin ligase complex, blocking IκBα degradation and thereby dampening NF-κB-dependent proinflammatory mediator production; Trim9-deficient mice show uncontrolled neuroinflammation after ischemic stroke.","method":"Co-IP (TRIM9–β-TrCP interaction), IκBα degradation assay, Trim9−/− mouse ischemic stroke model with NF-κB pathway readouts, AAV-mediated TRIM9 rescue","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — Co-IP identifying TRIM9–β-TrCP interaction, IκBα assay, KO mouse with in vivo neuroinflammation phenotype and AAV rescue; multiple orthogonal methods","pmids":["30970257"],"is_preprint":false},{"year":2017,"finding":"TRIM9-dependent ubiquitination of DCC blocks the interaction between DCC and FAK and prevents FAK phosphorylation; upon netrin-1 stimulation TRIM9 promotes DCC multimerization but reduces DCC ubiquitination, enabling FAK activation and downstream exocytic vesicle fusion and axon branching.","method":"Co-IP (DCC–FAK), ubiquitination assays on DCC, FAK activity assays, SNARE complex assays, Trim9−/− neurons, in vitro and in vivo axon branching assays, FAK inhibitor experiments","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — direct ubiquitination of DCC demonstrated, Co-IP for DCC–FAK interaction, KO neurons with in vitro and in vivo branching readouts; multiple orthogonal methods in single study","pmids":["28701345"],"is_preprint":false},{"year":2016,"finding":"TRIM9 regulates embryonic and adult hippocampal neuron morphogenesis; Trim9 deletion causes excessive dendritic arborization and mislocalization of adult-born dentate granule neurons in vivo, associated with severe deficits in spatial learning and memory.","method":"Trim9−/− mouse KO, in vitro and in vivo morphological analysis of hippocampal neurons, behavioral testing (spatial learning/memory)","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Moderate — clean KO with defined cellular morphological phenotype in vitro and in vivo, behavioral readout; single lab but orthogonal in vitro/in vivo methods","pmids":["27147649"],"is_preprint":false},{"year":2011,"finding":"C. elegans TRIM-9 exhibits E3 ubiquitin ligase activity in vitro (RING domain-dependent) and functions in the UNC-6/netrin–UNC-40 attraction pathway upstream of MIG-10, the downstream effector of UNC-40, to regulate ventral axon guidance.","method":"In vitro ubiquitin ligase assay, C. elegans genetic epistasis analysis (trim-9 mutants, unc-6/unc-40 pathway double mutants), MIG-10 localization assay","journal":"Journal of genetics and genomics","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro E3 ligase activity confirmed, genetic epistasis placing TRIM9 upstream of MIG-10 in the UNC-40 pathway, RING domain requirement shown; orthogonal methods in single study","pmids":["21338947"],"is_preprint":false},{"year":2018,"finding":"TRIM9s promotes K63-linked ubiquitination of MKK6 at Lys82, which inhibits competing K48-linked ubiquitination at the same site to stabilize MKK6 and potentiate p38 signaling; MKK6 in turn stabilizes TRIM9s by promoting p38-dependent phosphorylation of TRIM9s at Ser76/80, blocking its proteasomal degradation—forming a positive feedback loop.","method":"Ubiquitination assays (K63- and K48-linkage specific, site-directed mutagenesis at K82), phosphorylation assays (Ser76/80 mutants), co-IP, proteasome inhibitor experiments, glioblastoma cell functional assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — site-specific mutagenesis of ubiquitination and phosphorylation sites, K63/K48-specific ubiquitination assays, reciprocal Co-IP; multiple orthogonal methods in single study","pmids":["29669288"],"is_preprint":false},{"year":2020,"finding":"TRIM9 and TRIM67 form a proximity interaction network in developing cortical neurons that includes cytoskeletal regulators (Myo16, Coro1A, MAP1B), exocytic/endocytic regulators (ExoC1), and synaptic proteins (GRIP1, PRG-1, KIF1A); knockdown of the unconventional myosin Myo16 altered growth cone filopodia density and axonal branching in a TRIM9- and netrin-1-dependent manner.","method":"BioID proximity labeling in cortical neurons, TIRF microscopy for colocalization, RNAi knockdown with morphological readouts","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — BioID interactome with subset validation and functional follow-up for Myo16; single lab, two orthogonal methods","pmids":["33378226"],"is_preprint":false},{"year":2014,"finding":"In Drosophila, Trim9 protein levels (regulated by neural activity) direct fine-scale topographic separation of presynaptic terminals of adjacent nociceptive neurons; neural activity regulates Trim9 protein levels to control axon terminal topography.","method":"Drosophila genetics (trim9 mutants, single-neuron clonal analysis), in vivo imaging of presynaptic terminals, activity manipulation experiments","journal":"Current biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO in Drosophila with single-neuron resolution in vivo readout; single lab, orthogonal genetic and imaging methods","pmids":["24746793"],"is_preprint":false},{"year":2017,"finding":"Trim9 disruption impairs macrophage chemotaxis and cellular architecture in zebrafish larvae in vivo, demonstrating a role for TRIM9 in macrophage motility beyond neurons.","method":"Zebrafish Trim9 loss-of-function model, in vivo macrophage motility and morphology assays after immune stimulation","journal":"Journal of leukocyte biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean in vivo loss-of-function with defined cellular phenotype (chemotaxis, architecture); single lab, single organism model","pmids":["29021367"],"is_preprint":false},{"year":2025,"finding":"TRIM9 localizes and interacts with both the attractive netrin receptor DCC and the repulsive netrin receptor UNC5C in the growth cone; deletion of Trim9 alters both attractive and repulsive axon turning and growth cone size responses to netrin-1 and is required for netrin-1-dependent changes in surface levels of DCC and UNC5C; TRIM9 negatively regulates FAK activity in the absence of netrin-1.","method":"Co-IP (TRIM9–UNC5C, TRIM9–DCC), microfluidic netrin gradient assays, Trim9−/− cortical neurons, surface receptor quantification, FAK activity assays, pH-mScarlet UNC5C reporter","journal":"Journal of neurochemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — Co-IP for both receptors, KO neurons with in vitro axon turning and receptor surface level readouts, FAK activity assay; multiple orthogonal methods in single study","pmids":["39871643"],"is_preprint":false},{"year":2023,"finding":"TRIM9 interacts with ZEB1 and promotes ZEB1 protein degradation via the ubiquitin-proteasome pathway, suppressing esophageal cancer cell viability and invasion.","method":"Co-IP (TRIM9–ZEB1), ubiquitination blocking experiments, cell viability and invasion assays with TRIM9 overexpression/knockdown","journal":"BioMed research international","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP with functional readout; single lab, limited mechanistic follow-up","pmids":["37124931"],"is_preprint":false},{"year":2024,"finding":"TRIM9 promotes K11-linked ubiquitination and proteasomal degradation of HNRNPU in a RING domain-dependent manner in pancreatic cancer cells; TRIM9 overexpression suppressed tumor growth in vivo and was rescued by HNRNPU co-expression.","method":"In vitro and cell-based ubiquitination assays (K11-linkage), RING domain mutant, Co-IP (TRIM9–HNRNPU), overexpression/knockdown with proliferation/migration assays, in vivo xenograft rescue experiment","journal":"Frontiers in immunology","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — K11-ubiquitination with RING domain requirement, Co-IP, in vivo rescue; single lab, multiple orthogonal methods","pmids":["41050689"],"is_preprint":false},{"year":2024,"finding":"TRIM9 promotes ubiquitination of PKM2, driving its transition from tetramer to dimer and reprogramming glucose metabolism from oxidative phosphorylation to aerobic glycolysis in triple-negative breast cancer cells.","method":"Ubiquitination assay (TRIM9-mediated PKM2 ubiquitination), Co-IP, PKM2 oligomerization assay, metabolic assays (glycolysis vs. OXPHOS), TRIM9 knockdown/overexpression","journal":"Journal of cellular and molecular medicine","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, Co-IP and functional readout; limited mechanistic mutagenesis or in vitro reconstitution described in abstract","pmids":["38263865"],"is_preprint":false},{"year":2026,"finding":"TRIM9 and TRIM26 are selectively enriched in proximity to the ALS-linked UBQLN2P497H mutant (not wild-type UBQLN2 or P497S mutant), co-accumulate with UBQLN2P497H in the insoluble fraction, and mediate ubiquitination and proteasomal degradation of UBQLN2P497H; individual knockdown of TRIM9 increased the abundance of a C-terminal UBQLN2 fragment.","method":"APEX2 proximity labeling with LC-MS/MS, co-IP followed by Western blot, fractionation analysis, proteasome inhibitor treatment, TRIM9/TRIM26 siRNA knockdown","journal":"ACS chemical biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — APEX2 proximity proteomics validated by Co-IP, fractionation, and functional knockdown; single lab, multiple orthogonal methods","pmids":["41582437"],"is_preprint":false},{"year":2026,"finding":"In melanoma cells, TRIM9 interacts with VASP, alters VASP modification, localization, and dynamics, negatively regulates focal adhesion formation and mesenchymal motility; TRIM9 deletion increases actin stress fibers, focal adhesions, VASP accumulation at adhesions, and mesenchymal migration in vitro, while in vivo loss of TRIM9 slows tumor growth and alters metastasis.","method":"Co-IP (TRIM9–VASP in melanoma), TIRF microscopy, VASP modification assays, focal adhesion quantification, Trim9 KO mouse melanoma model with in vivo tumor growth and metastasis readouts","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, TIRF live imaging, KO with in vivo tumor/metastasis phenotype; preprint, single lab, multiple methods","pmids":["41889914"],"is_preprint":true}],"current_model":"TRIM9 is a brain-enriched RING-domain E3 ubiquitin ligase that ubiquitinates multiple substrates (VASP, DCC, MKK6, PKM2, HNRNPU, ZEB1, UBQLN2P497H) to regulate neuronal morphogenesis and axon guidance downstream of the netrin-1 receptors DCC and UNC5C, controls NF-κB-dependent neuroinflammation by sequestering β-TrCP, and in its short isoform bridges GSK3β to TBK1 via K63-linked auto-ubiquitination to promote antiviral type I interferon signaling."},"narrative":{"mechanistic_narrative":"TRIM9 is a brain-enriched RING-domain E3 ubiquitin ligase that controls neuronal morphogenesis and netrin-1-dependent axon guidance by ubiquitinating cytoskeletal and receptor substrates at the growth cone [PMID:20085810, PMID:26702829, PMID:27147649]. At filopodial tips it binds the netrin receptor DCC and ubiquitinates the actin polymerase VASP to limit VASP tip localization and filopodial stability; netrin stimulation reverses this, deubiquitinating VASP to promote filopodial stability and axon guidance [PMID:26702829]. TRIM9 also ubiquitinates DCC itself, blocking the DCC–FAK interaction and FAK activation until netrin-1 triggers DCC multimerization, reduced ubiquitination, FAK activity, and exocytic vesicle fusion driving axon branching [PMID:28701345]. It engages both the attractive DCC and the repulsive UNC5C receptors and is required for netrin-1-dependent changes in their surface levels and for both attractive and repulsive turning responses [PMID:39871643]. Loss of TRIM9 in mice causes excessive dendritic arborization, mislocalization of adult-born dentate granule neurons, and spatial learning deficits [PMID:27147649], and its role in the netrin/UNC-40 attraction pathway upstream of MIG-10 is conserved in C. elegans [PMID:21338947]. Beyond neurons, TRIM9 dampens NF-κB-dependent neuroinflammation by sequestering β-TrCP from the SCF complex to block IκBα degradation, with Trim9-deficient mice showing uncontrolled neuroinflammation after ischemic stroke [PMID:30970257], and its short isoform scaffolds GSK3β to TBK1 via K63-linked auto-ubiquitination to activate IRF3 and type I interferon signaling during viral infection [PMID:26915459]. In cancer settings TRIM9 ubiquitinates additional substrates including HNRNPU via K11-linkage to suppress pancreatic tumor growth [PMID:41050689] and MKK6 via K63-linkage to potentiate p38 signaling [PMID:29669288].","teleology":[{"year":2010,"claim":"Established TRIM9 as a bona fide E3 ubiquitin ligase and placed it in neurons, defining its biochemical activity and primary tissue context.","evidence":"In vitro ubiquitin ligase assay with E2 UbcH5b plus IHC localization in brain","pmids":["20085810"],"confidence":"Medium","gaps":["No substrate identified at this stage","Linkage type and physiological target unknown"]},{"year":2011,"claim":"Showed RING-dependent E3 activity is required for TRIM9 function in netrin/UNC-40 axon guidance, genetically placing it upstream of the effector MIG-10.","evidence":"C. elegans genetic epistasis and in vitro ligase assay with RING-domain requirement","pmids":["21338947"],"confidence":"High","gaps":["Direct ubiquitination substrate in the worm not defined","Mammalian conservation of the MIG-10 axis not tested here"]},{"year":2014,"claim":"Linked activity-regulated TRIM9 protein levels to fine-scale topographic separation of presynaptic terminals, extending its role to synaptic-level wiring.","evidence":"Drosophila genetics with single-neuron clonal analysis and activity manipulation","pmids":["24746793"],"confidence":"Medium","gaps":["Substrate mediating terminal topography unknown","Mechanism coupling neural activity to TRIM9 levels not defined"]},{"year":2015,"claim":"Identified VASP as a TRIM9 substrate at filopodial tips, providing a molecular mechanism (ubiquitin-controlled actin polymerase localization) for netrin-driven filopodial dynamics and guidance.","evidence":"Co-IP, in vitro ubiquitination, non-ubiquitinatable VASP mutant, TIRF, Trim9-/- neurons and in vivo guidance assays","pmids":["26702829"],"confidence":"High","gaps":["Identity of the netrin-induced deubiquitinase not defined","Ubiquitin linkage type on VASP not specified"]},{"year":2016,"claim":"Demonstrated that loss of TRIM9 causes excessive dendritic arborization and adult-born neuron mislocalization with behavioral consequences, tying the molecular activity to hippocampal circuit function.","evidence":"Trim9-/- mouse with in vitro/in vivo morphology and spatial learning behavioral testing","pmids":["27147649"],"confidence":"High","gaps":["Substrates driving dendritic phenotype not pinned down","Cell-autonomous vs non-autonomous contribution unresolved"]},{"year":2016,"claim":"Revealed a non-degradative scaffolding role for the short isoform in innate antiviral immunity, bridging GSK3β to TBK1 through K63-linked auto-ubiquitination to boost type I IFN.","evidence":"Reciprocal Co-IP, K63-specific ubiquitination assays, gain/loss-of-function with IFN/cytokine readouts under viral infection","pmids":["26915459"],"confidence":"High","gaps":["Structural basis of the GSK3β–TRIM9s–TBK1 bridge not resolved","Relationship between neuronal and immune isoform functions unclear"]},{"year":2017,"claim":"Defined how TRIM9 gates DCC signaling: ubiquitination blocks DCC–FAK coupling, and netrin reverses this to enable FAK activation and exocytosis-dependent axon branching.","evidence":"Co-IP, DCC ubiquitination assays, FAK activity and SNARE assays, Trim9-/- neurons with in vitro/in vivo branching and FAK inhibitor experiments","pmids":["28701345"],"confidence":"High","gaps":["Spatiotemporal control of DCC deubiquitination not fully resolved","Direct ubiquitination site(s) on DCC not mapped"]},{"year":2017,"claim":"Extended TRIM9's cell-shape control to immune cells, showing it is required for macrophage chemotaxis and architecture in vivo.","evidence":"Zebrafish loss-of-function with in vivo macrophage motility and morphology assays","pmids":["29021367"],"confidence":"Medium","gaps":["Substrate driving macrophage motility not identified","Conservation to mammalian macrophages not tested here"]},{"year":2018,"claim":"Uncovered a TRIM9s–MKK6 positive feedback loop in which K63 ubiquitination outcompetes K48 ubiquitination at Lys82 to stabilize MKK6 and potentiate p38 signaling.","evidence":"Site-directed K82 and Ser76/80 mutants, K63/K48-specific ubiquitination and phosphorylation assays, reciprocal Co-IP in glioblastoma cells","pmids":["29669288"],"confidence":"High","gaps":["In vivo relevance of the feedback loop not established","Tissue specificity beyond glioblastoma unclear"]},{"year":2019,"claim":"Identified a ligase-independent mechanism whereby TRIM9 sequesters β-TrCP from the SCF complex to stabilize IκBα and restrain NF-κB neuroinflammation after stroke.","evidence":"Co-IP, IκBα degradation assay, Trim9-/- ischemic stroke mouse model with AAV rescue","pmids":["30970257"],"confidence":"High","gaps":["Whether sequestration involves ubiquitination of β-TrCP not resolved","Cell type mediating the neuroinflammatory phenotype not defined"]},{"year":2020,"claim":"Mapped a TRIM9/TRIM67 proximity interactome in cortical neurons, implicating Myo16 in TRIM9- and netrin-dependent control of filopodia and branching.","evidence":"BioID proximity labeling, TIRF colocalization, Myo16 RNAi with morphological readouts","pmids":["33378226"],"confidence":"Medium","gaps":["Most interactome members not functionally validated","Whether interactors are ubiquitination substrates unknown"]},{"year":2024,"claim":"Extended the substrate repertoire to cancer-relevant targets, with K11-linked ubiquitination of HNRNPU suppressing pancreatic tumor growth and ubiquitination of PKM2 reprogramming glycolysis in breast cancer.","evidence":"K11-linkage ubiquitination assays with RING mutant and in vivo xenograft rescue (HNRNPU); Co-IP and oligomerization/metabolic assays (PKM2)","pmids":["41050689","38263865"],"confidence":"Medium","gaps":["PKM2 ubiquitination lacks site-level and linkage mechanistic detail","How tumor-suppressive substrate selection is achieved unclear"]},{"year":2025,"claim":"Showed TRIM9 engages both attractive (DCC) and repulsive (UNC5C) netrin receptors, regulating their surface levels and bidirectional turning responses while negatively regulating FAK in the absence of netrin.","evidence":"Co-IP for both receptors, microfluidic netrin gradients, Trim9-/- neurons, surface receptor quantification, FAK assays, pH-mScarlet reporter","pmids":["39871643"],"confidence":"High","gaps":["Whether UNC5C is a direct ubiquitination substrate not established","Mechanism integrating attractive and repulsive outputs unclear"]},{"year":2026,"claim":"Implicated TRIM9 in proteostasis of disease-linked aggregating proteins, mediating degradation of the ALS-associated UBQLN2P497H mutant, and reinforced VASP-dependent control of focal adhesions and motility in melanoma.","evidence":"APEX2 proximity proteomics, Co-IP, fractionation, proteasome inhibition and siRNA (UBQLN2P497H); Co-IP, TIRF and Trim9 KO melanoma model (VASP)","pmids":["41582437","41889914"],"confidence":"Medium","gaps":["Melanoma study is a preprint (single lab)","How TRIM9 selectively recognizes the mutant UBQLN2 conformer not defined"]},{"year":null,"claim":"How TRIM9 selects among its diverse substrates and switches between degradative ubiquitination, regulatory linkage signaling, and ligase-independent sequestration across neuronal, immune, and tumor contexts remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying model for substrate/linkage selection","Isoform-specific regulation across tissues not integrated","No structural model of substrate or partner engagement"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,2,4,6,7,13]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[2,4,7,13]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,3]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3]}],"localization":[{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[2,8]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,3]}],"pathway":[{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[2,4,5,6,11]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[1,3,10]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[4,7,11]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,13,15]}],"complexes":[],"partners":["DCC","UNC5C","VASP","GSK3B","TBK1","BTRC","MKK6","HNRNPU"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9C026","full_name":"E3 ubiquitin-protein ligase TRIM9","aliases":["RING finger protein 91","RING-type E3 ubiquitin transferase TRIM9","Tripartite motif-containing protein 9"],"length_aa":710,"mass_kda":79.2,"function":"E3 ubiquitin-protein ligase which ubiquitinates itself in cooperation with an E2 enzyme UBE2D2/UBC4 and serves as a targeting signal for proteasomal degradation. May play a role in regulation of neuronal functions and may also participate in the formation or breakdown of abnormal inclusions in neurodegenerative disorders. May act as a regulator of synaptic vesicle exocytosis by controlling the availability of SNAP25 for the SNARE complex formation","subcellular_location":"Cytoplasm; Cell projection, dendrite; Cytoplasmic vesicle, secretory vesicle, synaptic vesicle; Synapse; Cytoplasm, cytoskeleton","url":"https://www.uniprot.org/uniprotkb/Q9C026/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TRIM9","classification":"Not Classified","n_dependent_lines":72,"n_total_lines":1208,"dependency_fraction":0.059602649006622516},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TRIM9","total_profiled":1310},"omim":[{"mim_id":"610584","title":"TRIPARTITE MOTIF-CONTAINING PROTEIN 67; TRIM67","url":"https://www.omim.org/entry/610584"},{"mim_id":"606555","title":"TRIPARTITE MOTIF-CONTAINING PROTEIN 9; TRIM9","url":"https://www.omim.org/entry/606555"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":46.3},{"tissue":"retina","ntpm":21.5}],"url":"https://www.proteinatlas.org/search/TRIM9"},"hgnc":{"alias_symbol":["SPRING","RNF91"],"prev_symbol":[]},"alphafold":{"accession":"Q9C026","domains":[{"cath_id":"4.10.830.40","chopping":"165-220","consensus_level":"medium","plddt":81.8886,"start":165,"end":220},{"cath_id":"-","chopping":"280-401","consensus_level":"high","plddt":94.3293,"start":280,"end":401},{"cath_id":"2.60.40.10","chopping":"446-532","consensus_level":"high","plddt":93.2349,"start":446,"end":532},{"cath_id":"2.60.120.920","chopping":"543-709","consensus_level":"high","plddt":92.8528,"start":543,"end":709}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C026","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C026-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C026-F1-predicted_aligned_error_v6.png","plddt_mean":82.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TRIM9","jax_strain_url":"https://www.jax.org/strain/search?query=TRIM9"},"sequence":{"accession":"Q9C026","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9C026.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9C026/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C026"}},"corpus_meta":[{"pmid":"20085810","id":"PMC_20085810","title":"TRIM9, a novel brain-specific E3 ubiquitin ligase, is repressed in the brain of Parkinson's disease and dementia with Lewy bodies.","date":"2010","source":"Neurobiology of disease","url":"https://pubmed.ncbi.nlm.nih.gov/20085810","citation_count":89,"is_preprint":false},{"pmid":"26915459","id":"PMC_26915459","title":"TRIM9 short isoform preferentially promotes DNA and RNA virus-induced production of type I interferon by recruiting GSK3β to TBK1.","date":"2016","source":"Cell research","url":"https://pubmed.ncbi.nlm.nih.gov/26915459","citation_count":74,"is_preprint":false},{"pmid":"26702829","id":"PMC_26702829","title":"The E3 Ubiquitin Ligase TRIM9 Is a Filopodia Off Switch Required for Netrin-Dependent Axon Guidance.","date":"2015","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/26702829","citation_count":71,"is_preprint":false},{"pmid":"30970257","id":"PMC_30970257","title":"TRIM9-Mediated Resolution of Neuroinflammation Confers Neuroprotection upon Ischemic Stroke in Mice.","date":"2019","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/30970257","citation_count":52,"is_preprint":false},{"pmid":"27147649","id":"PMC_27147649","title":"Trim9 Deletion Alters the Morphogenesis of Developing and Adult-Born Hippocampal Neurons and Impairs Spatial Learning and Memory.","date":"2016","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/27147649","citation_count":49,"is_preprint":false},{"pmid":"30350014","id":"PMC_30350014","title":"TRIM9 and TRIM67 Are New Targets in Paraneoplastic Cerebellar Degeneration.","date":"2019","source":"Cerebellum (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/30350014","citation_count":42,"is_preprint":false},{"pmid":"28701345","id":"PMC_28701345","title":"TRIM9-dependent ubiquitination of DCC constrains kinase signaling, exocytosis, and axon branching.","date":"2017","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/28701345","citation_count":41,"is_preprint":false},{"pmid":"11960705","id":"PMC_11960705","title":"TRIM9 is specifically expressed in the embryonic and adult nervous system.","date":"2002","source":"Mechanisms of development","url":"https://pubmed.ncbi.nlm.nih.gov/11960705","citation_count":39,"is_preprint":false},{"pmid":"33378226","id":"PMC_33378226","title":"The TRIM9/TRIM67 neuronal interactome reveals novel activators of morphogenesis.","date":"2020","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/33378226","citation_count":39,"is_preprint":false},{"pmid":"29669288","id":"PMC_29669288","title":"Mutual Stabilization between TRIM9 Short Isoform and MKK6 Potentiates p38 Signaling to Synergistically Suppress Glioblastoma Progression.","date":"2018","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/29669288","citation_count":30,"is_preprint":false},{"pmid":"30910419","id":"PMC_30910419","title":"An E3 ubiquitin ligase TRIM9 is involved in WSSV infection via interaction with β-TrCP.","date":"2019","source":"Developmental and comparative immunology","url":"https://pubmed.ncbi.nlm.nih.gov/30910419","citation_count":24,"is_preprint":false},{"pmid":"26543769","id":"PMC_26543769","title":"Promoter methylation of TRIM9 as a marker for detection of circulating tumor DNA in breast cancer patients.","date":"2015","source":"SpringerPlus","url":"https://pubmed.ncbi.nlm.nih.gov/26543769","citation_count":23,"is_preprint":false},{"pmid":"32679146","id":"PMC_32679146","title":"TRIM9 overexpression promotes uterine leiomyoma cell proliferation and inhibits cell apoptosis via NF-κB signaling pathway.","date":"2020","source":"Life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/32679146","citation_count":22,"is_preprint":false},{"pmid":"24746793","id":"PMC_24746793","title":"Trim9 regulates activity-dependent fine-scale topography in Drosophila.","date":"2014","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/24746793","citation_count":22,"is_preprint":false},{"pmid":"38263865","id":"PMC_38263865","title":"METTL14/miR-29c-3p axis drives aerobic glycolysis to promote triple-negative breast cancer progression though TRIM9-mediated PKM2 ubiquitination.","date":"2024","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38263865","citation_count":18,"is_preprint":false},{"pmid":"21338947","id":"PMC_21338947","title":"TRIM-9 functions in the UNC-6/UNC-40 pathway to regulate ventral guidance.","date":"2011","source":"Journal of genetics and genomics = Yi chuan xue bao","url":"https://pubmed.ncbi.nlm.nih.gov/21338947","citation_count":18,"is_preprint":false},{"pmid":"27393236","id":"PMC_27393236","title":"The first molluscan TRIM9 is involved in the negative regulation of NF-κB activity in the Hong Kong oyster, Crassostrea hongkongensis.","date":"2016","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/27393236","citation_count":16,"is_preprint":false},{"pmid":"37632288","id":"PMC_37632288","title":"Detection of High-Risk Paraneoplastic Antibodies against TRIM9 and TRIM67 Proteins.","date":"2023","source":"Annals of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/37632288","citation_count":10,"is_preprint":false},{"pmid":"29021367","id":"PMC_29021367","title":"Disruption of Trim9 function abrogates macrophage motility in vivo.","date":"2017","source":"Journal of leukocyte biology","url":"https://pubmed.ncbi.nlm.nih.gov/29021367","citation_count":10,"is_preprint":false},{"pmid":"37124931","id":"PMC_37124931","title":"TRIM9 Interacts with ZEB1 to Suppress Esophageal Cancer by Promoting ZEB1 Protein Degradation via the UPP Pathway.","date":"2023","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/37124931","citation_count":10,"is_preprint":false},{"pmid":"35281067","id":"PMC_35281067","title":"A Novel TRIM9 Protein Promotes NF-κB Activation Through Interacting With LvIMD in Shrimp During WSSV Infection.","date":"2022","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/35281067","citation_count":9,"is_preprint":false},{"pmid":"30703767","id":"PMC_30703767","title":"MicroRNA-653 Inhibits Thymocyte Proliferation and Induces Thymocyte Apoptosis in Mice with Autoimmune Myasthenia Gravis by Downregulating TRIM9.","date":"2019","source":"Neuroimmunomodulation","url":"https://pubmed.ncbi.nlm.nih.gov/30703767","citation_count":9,"is_preprint":false},{"pmid":"39580859","id":"PMC_39580859","title":"Exercise-induced upregulation of TRIM9 attenuates neuroinflammation in Alzheimer's disease-like rat.","date":"2024","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/39580859","citation_count":7,"is_preprint":false},{"pmid":"33636432","id":"PMC_33636432","title":"TRIM9 is involved in facilitating Vibrio parahaemolyticus infection by inhibition of relish pathway in Penaeus monodon.","date":"2021","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/33636432","citation_count":6,"is_preprint":false},{"pmid":"36889762","id":"PMC_36889762","title":"Targeting TRIM9 by miR-218-5p Restricts Cell Proliferation and Epithelial-Mesenchymal Transition in Non-Small Cell Lung Cancer.","date":"2023","source":"Annals of clinical and laboratory science","url":"https://pubmed.ncbi.nlm.nih.gov/36889762","citation_count":5,"is_preprint":false},{"pmid":"34676875","id":"PMC_34676875","title":"Knockdown of TRIM9 attenuates irinotecan‑induced intestinal mucositis in IEC‑6 cells by regulating DUSP6 expression via the P38 pathway.","date":"2021","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/34676875","citation_count":5,"is_preprint":false},{"pmid":"34925522","id":"PMC_34925522","title":"miR-181a Ameliorates the Progression of Myasthenia Gravis by Regulating TRIM9.","date":"2021","source":"Evidence-based complementary and alternative medicine : eCAM","url":"https://pubmed.ncbi.nlm.nih.gov/34925522","citation_count":5,"is_preprint":false},{"pmid":"39871643","id":"PMC_39871643","title":"TRIM9 Controls Growth Cone Responses to Netrin Through DCC and UNC5C.","date":"2025","source":"Journal of neurochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/39871643","citation_count":3,"is_preprint":false},{"pmid":"38765979","id":"PMC_38765979","title":"TRIM9 controls growth cone responses to netrin through DCC and UNC5C.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38765979","citation_count":2,"is_preprint":false},{"pmid":"37792226","id":"PMC_37792226","title":"TRIM9 promotes Müller cell-derived retinal stem cells to differentiate into retinal ganglion cells by regulating Atoh7.","date":"2023","source":"In vitro cellular & developmental biology. Animal","url":"https://pubmed.ncbi.nlm.nih.gov/37792226","citation_count":2,"is_preprint":false},{"pmid":"39706432","id":"PMC_39706432","title":"Explorations of novel MDR-related hub genes and the potential roles TRIM9 played in drug-resistant hepatocellular carcinoma.","date":"2024","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/39706432","citation_count":2,"is_preprint":false},{"pmid":"41050689","id":"PMC_41050689","title":"Single-cell and multi-omics analysis identifies TRIM9 as a key ubiquitination regulator in pancreatic cancer.","date":"2025","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/41050689","citation_count":1,"is_preprint":false},{"pmid":"40145576","id":"PMC_40145576","title":"[Retracted] Knockdown of TRIM9 attenuates irinotecan‑induced intestinal mucositis in IEC‑6 cells by regulating DUSP6 expression via the P38 pathway.","date":"2025","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/40145576","citation_count":1,"is_preprint":false},{"pmid":"38432885","id":"PMC_38432885","title":"Trim9 regulates the directional differentiation of retinal Müller cells to retinal ganglion cells.","date":"2023","source":"Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38432885","citation_count":0,"is_preprint":false},{"pmid":"41582437","id":"PMC_41582437","title":"TRIM9 and TRIM26 Interact with UBQLN2P497H to Modulate Its Proteasomal Degradation.","date":"2026","source":"ACS chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/41582437","citation_count":0,"is_preprint":false},{"pmid":"41889914","id":"PMC_41889914","title":"TRIM9 switches the morphological phenotype of melanoma cells.","date":"2026","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41889914","citation_count":0,"is_preprint":false},{"pmid":"41146861","id":"PMC_41146861","title":"Correction to \"TRIM9 Interacts with ZEB1 to Suppress Esophageal Cancer by Promoting ZEB1 Protein Degradation via the UPP Pathway\".","date":"2025","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/41146861","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":19718,"output_tokens":4456,"usd":0.062997,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12593,"output_tokens":4640,"usd":0.089483,"stage2_stop_reason":"end_turn"},"total_usd":0.15248,"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\": 2010,\n      \"finding\": \"TRIM9 functions as an E3 ubiquitin ligase collaborating with the E2 ubiquitin conjugating enzyme UbcH5b, and is localized to neurons in the brain.\",\n      \"method\": \"In vitro ubiquitin ligase assay with UbcH5b; immunohistochemistry and immunoblotting for localization\",\n      \"journal\": \"Neurobiology of disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro enzymatic assay with identified E2, plus direct localization by IHC; single lab, two orthogonal methods\",\n      \"pmids\": [\"20085810\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The short isoform of TRIM9 (TRIM9s) undergoes Lys-63-linked auto-polyubiquitination upon viral infection and acts as a scaffold bridging GSK3β to TBK1, thereby activating IRF3 signaling and enhancing type I IFN production while selectively suppressing pro-inflammatory cytokine production.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays (K63-linkage specific), overexpression/knockdown in cells with viral infection readouts\",\n      \"journal\": \"Cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP identifying GSK3β–TRIM9s–TBK1 complex, K63-ubiquitination assay, gain/loss-of-function with IFN/cytokine readouts; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"26915459\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"TRIM9 localizes to filopodial tips, binds the netrin receptor DCC, and ubiquitinates the barbed-end actin polymerase VASP to reduce VASP filopodial tip localization and stability; netrin stimulation causes VASP deubiquitination, promoting VASP tip localization and filopodial stability to drive axon guidance.\",\n      \"method\": \"Co-IP (TRIM9–DCC, TRIM9–VASP), in vitro ubiquitination assay, non-ubiquitinatable VASP mutant, TIRF microscopy, Trim9−/− cortical neurons, in vivo axon guidance assays\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro ubiquitination of VASP, non-ubiquitinatable mutant rescue, KO neurons with in vitro and in vivo phenotypic readouts; multiple orthogonal methods in single study\",\n      \"pmids\": [\"26702829\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TRIM9 sequesters β-TrCP from the Skp-Cullin-F-box ubiquitin ligase complex, blocking IκBα degradation and thereby dampening NF-κB-dependent proinflammatory mediator production; Trim9-deficient mice show uncontrolled neuroinflammation after ischemic stroke.\",\n      \"method\": \"Co-IP (TRIM9–β-TrCP interaction), IκBα degradation assay, Trim9−/− mouse ischemic stroke model with NF-κB pathway readouts, AAV-mediated TRIM9 rescue\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP identifying TRIM9–β-TrCP interaction, IκBα assay, KO mouse with in vivo neuroinflammation phenotype and AAV rescue; multiple orthogonal methods\",\n      \"pmids\": [\"30970257\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"TRIM9-dependent ubiquitination of DCC blocks the interaction between DCC and FAK and prevents FAK phosphorylation; upon netrin-1 stimulation TRIM9 promotes DCC multimerization but reduces DCC ubiquitination, enabling FAK activation and downstream exocytic vesicle fusion and axon branching.\",\n      \"method\": \"Co-IP (DCC–FAK), ubiquitination assays on DCC, FAK activity assays, SNARE complex assays, Trim9−/− neurons, in vitro and in vivo axon branching assays, FAK inhibitor experiments\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — direct ubiquitination of DCC demonstrated, Co-IP for DCC–FAK interaction, KO neurons with in vitro and in vivo branching readouts; multiple orthogonal methods in single study\",\n      \"pmids\": [\"28701345\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"TRIM9 regulates embryonic and adult hippocampal neuron morphogenesis; Trim9 deletion causes excessive dendritic arborization and mislocalization of adult-born dentate granule neurons in vivo, associated with severe deficits in spatial learning and memory.\",\n      \"method\": \"Trim9−/− mouse KO, in vitro and in vivo morphological analysis of hippocampal neurons, behavioral testing (spatial learning/memory)\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined cellular morphological phenotype in vitro and in vivo, behavioral readout; single lab but orthogonal in vitro/in vivo methods\",\n      \"pmids\": [\"27147649\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"C. elegans TRIM-9 exhibits E3 ubiquitin ligase activity in vitro (RING domain-dependent) and functions in the UNC-6/netrin–UNC-40 attraction pathway upstream of MIG-10, the downstream effector of UNC-40, to regulate ventral axon guidance.\",\n      \"method\": \"In vitro ubiquitin ligase assay, C. elegans genetic epistasis analysis (trim-9 mutants, unc-6/unc-40 pathway double mutants), MIG-10 localization assay\",\n      \"journal\": \"Journal of genetics and genomics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro E3 ligase activity confirmed, genetic epistasis placing TRIM9 upstream of MIG-10 in the UNC-40 pathway, RING domain requirement shown; orthogonal methods in single study\",\n      \"pmids\": [\"21338947\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TRIM9s promotes K63-linked ubiquitination of MKK6 at Lys82, which inhibits competing K48-linked ubiquitination at the same site to stabilize MKK6 and potentiate p38 signaling; MKK6 in turn stabilizes TRIM9s by promoting p38-dependent phosphorylation of TRIM9s at Ser76/80, blocking its proteasomal degradation—forming a positive feedback loop.\",\n      \"method\": \"Ubiquitination assays (K63- and K48-linkage specific, site-directed mutagenesis at K82), phosphorylation assays (Ser76/80 mutants), co-IP, proteasome inhibitor experiments, glioblastoma cell functional assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — site-specific mutagenesis of ubiquitination and phosphorylation sites, K63/K48-specific ubiquitination assays, reciprocal Co-IP; multiple orthogonal methods in single study\",\n      \"pmids\": [\"29669288\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TRIM9 and TRIM67 form a proximity interaction network in developing cortical neurons that includes cytoskeletal regulators (Myo16, Coro1A, MAP1B), exocytic/endocytic regulators (ExoC1), and synaptic proteins (GRIP1, PRG-1, KIF1A); knockdown of the unconventional myosin Myo16 altered growth cone filopodia density and axonal branching in a TRIM9- and netrin-1-dependent manner.\",\n      \"method\": \"BioID proximity labeling in cortical neurons, TIRF microscopy for colocalization, RNAi knockdown with morphological readouts\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — BioID interactome with subset validation and functional follow-up for Myo16; single lab, two orthogonal methods\",\n      \"pmids\": [\"33378226\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In Drosophila, Trim9 protein levels (regulated by neural activity) direct fine-scale topographic separation of presynaptic terminals of adjacent nociceptive neurons; neural activity regulates Trim9 protein levels to control axon terminal topography.\",\n      \"method\": \"Drosophila genetics (trim9 mutants, single-neuron clonal analysis), in vivo imaging of presynaptic terminals, activity manipulation experiments\",\n      \"journal\": \"Current biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO in Drosophila with single-neuron resolution in vivo readout; single lab, orthogonal genetic and imaging methods\",\n      \"pmids\": [\"24746793\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Trim9 disruption impairs macrophage chemotaxis and cellular architecture in zebrafish larvae in vivo, demonstrating a role for TRIM9 in macrophage motility beyond neurons.\",\n      \"method\": \"Zebrafish Trim9 loss-of-function model, in vivo macrophage motility and morphology assays after immune stimulation\",\n      \"journal\": \"Journal of leukocyte biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean in vivo loss-of-function with defined cellular phenotype (chemotaxis, architecture); single lab, single organism model\",\n      \"pmids\": [\"29021367\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TRIM9 localizes and interacts with both the attractive netrin receptor DCC and the repulsive netrin receptor UNC5C in the growth cone; deletion of Trim9 alters both attractive and repulsive axon turning and growth cone size responses to netrin-1 and is required for netrin-1-dependent changes in surface levels of DCC and UNC5C; TRIM9 negatively regulates FAK activity in the absence of netrin-1.\",\n      \"method\": \"Co-IP (TRIM9–UNC5C, TRIM9–DCC), microfluidic netrin gradient assays, Trim9−/− cortical neurons, surface receptor quantification, FAK activity assays, pH-mScarlet UNC5C reporter\",\n      \"journal\": \"Journal of neurochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for both receptors, KO neurons with in vitro axon turning and receptor surface level readouts, FAK activity assay; multiple orthogonal methods in single study\",\n      \"pmids\": [\"39871643\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TRIM9 interacts with ZEB1 and promotes ZEB1 protein degradation via the ubiquitin-proteasome pathway, suppressing esophageal cancer cell viability and invasion.\",\n      \"method\": \"Co-IP (TRIM9–ZEB1), ubiquitination blocking experiments, cell viability and invasion assays with TRIM9 overexpression/knockdown\",\n      \"journal\": \"BioMed research international\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP with functional readout; single lab, limited mechanistic follow-up\",\n      \"pmids\": [\"37124931\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM9 promotes K11-linked ubiquitination and proteasomal degradation of HNRNPU in a RING domain-dependent manner in pancreatic cancer cells; TRIM9 overexpression suppressed tumor growth in vivo and was rescued by HNRNPU co-expression.\",\n      \"method\": \"In vitro and cell-based ubiquitination assays (K11-linkage), RING domain mutant, Co-IP (TRIM9–HNRNPU), overexpression/knockdown with proliferation/migration assays, in vivo xenograft rescue experiment\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — K11-ubiquitination with RING domain requirement, Co-IP, in vivo rescue; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"41050689\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM9 promotes ubiquitination of PKM2, driving its transition from tetramer to dimer and reprogramming glucose metabolism from oxidative phosphorylation to aerobic glycolysis in triple-negative breast cancer cells.\",\n      \"method\": \"Ubiquitination assay (TRIM9-mediated PKM2 ubiquitination), Co-IP, PKM2 oligomerization assay, metabolic assays (glycolysis vs. OXPHOS), TRIM9 knockdown/overexpression\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, Co-IP and functional readout; limited mechanistic mutagenesis or in vitro reconstitution described in abstract\",\n      \"pmids\": [\"38263865\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"TRIM9 and TRIM26 are selectively enriched in proximity to the ALS-linked UBQLN2P497H mutant (not wild-type UBQLN2 or P497S mutant), co-accumulate with UBQLN2P497H in the insoluble fraction, and mediate ubiquitination and proteasomal degradation of UBQLN2P497H; individual knockdown of TRIM9 increased the abundance of a C-terminal UBQLN2 fragment.\",\n      \"method\": \"APEX2 proximity labeling with LC-MS/MS, co-IP followed by Western blot, fractionation analysis, proteasome inhibitor treatment, TRIM9/TRIM26 siRNA knockdown\",\n      \"journal\": \"ACS chemical biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — APEX2 proximity proteomics validated by Co-IP, fractionation, and functional knockdown; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"41582437\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"In melanoma cells, TRIM9 interacts with VASP, alters VASP modification, localization, and dynamics, negatively regulates focal adhesion formation and mesenchymal motility; TRIM9 deletion increases actin stress fibers, focal adhesions, VASP accumulation at adhesions, and mesenchymal migration in vitro, while in vivo loss of TRIM9 slows tumor growth and alters metastasis.\",\n      \"method\": \"Co-IP (TRIM9–VASP in melanoma), TIRF microscopy, VASP modification assays, focal adhesion quantification, Trim9 KO mouse melanoma model with in vivo tumor growth and metastasis readouts\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, TIRF live imaging, KO with in vivo tumor/metastasis phenotype; preprint, single lab, multiple methods\",\n      \"pmids\": [\"41889914\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"TRIM9 is a brain-enriched RING-domain E3 ubiquitin ligase that ubiquitinates multiple substrates (VASP, DCC, MKK6, PKM2, HNRNPU, ZEB1, UBQLN2P497H) to regulate neuronal morphogenesis and axon guidance downstream of the netrin-1 receptors DCC and UNC5C, controls NF-κB-dependent neuroinflammation by sequestering β-TrCP, and in its short isoform bridges GSK3β to TBK1 via K63-linked auto-ubiquitination to promote antiviral type I interferon signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TRIM9 is a brain-enriched RING-domain E3 ubiquitin ligase that controls neuronal morphogenesis and netrin-1-dependent axon guidance by ubiquitinating cytoskeletal and receptor substrates at the growth cone [#0, #2, #5]. At filopodial tips it binds the netrin receptor DCC and ubiquitinates the actin polymerase VASP to limit VASP tip localization and filopodial stability; netrin stimulation reverses this, deubiquitinating VASP to promote filopodial stability and axon guidance [#2]. TRIM9 also ubiquitinates DCC itself, blocking the DCC–FAK interaction and FAK activation until netrin-1 triggers DCC multimerization, reduced ubiquitination, FAK activity, and exocytic vesicle fusion driving axon branching [#4]. It engages both the attractive DCC and the repulsive UNC5C receptors and is required for netrin-1-dependent changes in their surface levels and for both attractive and repulsive turning responses [#11]. Loss of TRIM9 in mice causes excessive dendritic arborization, mislocalization of adult-born dentate granule neurons, and spatial learning deficits [#5], and its role in the netrin/UNC-40 attraction pathway upstream of MIG-10 is conserved in C. elegans [#6]. Beyond neurons, TRIM9 dampens NF-κB-dependent neuroinflammation by sequestering β-TrCP from the SCF complex to block IκBα degradation, with Trim9-deficient mice showing uncontrolled neuroinflammation after ischemic stroke [#3], and its short isoform scaffolds GSK3β to TBK1 via K63-linked auto-ubiquitination to activate IRF3 and type I interferon signaling during viral infection [#1]. In cancer settings TRIM9 ubiquitinates additional substrates including HNRNPU via K11-linkage to suppress pancreatic tumor growth [#13] and MKK6 via K63-linkage to potentiate p38 signaling [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established TRIM9 as a bona fide E3 ubiquitin ligase and placed it in neurons, defining its biochemical activity and primary tissue context.\",\n      \"evidence\": \"In vitro ubiquitin ligase assay with E2 UbcH5b plus IHC localization in brain\",\n      \"pmids\": [\"20085810\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No substrate identified at this stage\", \"Linkage type and physiological target unknown\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Showed RING-dependent E3 activity is required for TRIM9 function in netrin/UNC-40 axon guidance, genetically placing it upstream of the effector MIG-10.\",\n      \"evidence\": \"C. elegans genetic epistasis and in vitro ligase assay with RING-domain requirement\",\n      \"pmids\": [\"21338947\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct ubiquitination substrate in the worm not defined\", \"Mammalian conservation of the MIG-10 axis not tested here\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Linked activity-regulated TRIM9 protein levels to fine-scale topographic separation of presynaptic terminals, extending its role to synaptic-level wiring.\",\n      \"evidence\": \"Drosophila genetics with single-neuron clonal analysis and activity manipulation\",\n      \"pmids\": [\"24746793\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Substrate mediating terminal topography unknown\", \"Mechanism coupling neural activity to TRIM9 levels not defined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identified VASP as a TRIM9 substrate at filopodial tips, providing a molecular mechanism (ubiquitin-controlled actin polymerase localization) for netrin-driven filopodial dynamics and guidance.\",\n      \"evidence\": \"Co-IP, in vitro ubiquitination, non-ubiquitinatable VASP mutant, TIRF, Trim9-/- neurons and in vivo guidance assays\",\n      \"pmids\": [\"26702829\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the netrin-induced deubiquitinase not defined\", \"Ubiquitin linkage type on VASP not specified\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Demonstrated that loss of TRIM9 causes excessive dendritic arborization and adult-born neuron mislocalization with behavioral consequences, tying the molecular activity to hippocampal circuit function.\",\n      \"evidence\": \"Trim9-/- mouse with in vitro/in vivo morphology and spatial learning behavioral testing\",\n      \"pmids\": [\"27147649\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Substrates driving dendritic phenotype not pinned down\", \"Cell-autonomous vs non-autonomous contribution unresolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Revealed a non-degradative scaffolding role for the short isoform in innate antiviral immunity, bridging GSK3β to TBK1 through K63-linked auto-ubiquitination to boost type I IFN.\",\n      \"evidence\": \"Reciprocal Co-IP, K63-specific ubiquitination assays, gain/loss-of-function with IFN/cytokine readouts under viral infection\",\n      \"pmids\": [\"26915459\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the GSK3β–TRIM9s–TBK1 bridge not resolved\", \"Relationship between neuronal and immune isoform functions unclear\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined how TRIM9 gates DCC signaling: ubiquitination blocks DCC–FAK coupling, and netrin reverses this to enable FAK activation and exocytosis-dependent axon branching.\",\n      \"evidence\": \"Co-IP, DCC ubiquitination assays, FAK activity and SNARE assays, Trim9-/- neurons with in vitro/in vivo branching and FAK inhibitor experiments\",\n      \"pmids\": [\"28701345\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Spatiotemporal control of DCC deubiquitination not fully resolved\", \"Direct ubiquitination site(s) on DCC not mapped\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Extended TRIM9's cell-shape control to immune cells, showing it is required for macrophage chemotaxis and architecture in vivo.\",\n      \"evidence\": \"Zebrafish loss-of-function with in vivo macrophage motility and morphology assays\",\n      \"pmids\": [\"29021367\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Substrate driving macrophage motility not identified\", \"Conservation to mammalian macrophages not tested here\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Uncovered a TRIM9s–MKK6 positive feedback loop in which K63 ubiquitination outcompetes K48 ubiquitination at Lys82 to stabilize MKK6 and potentiate p38 signaling.\",\n      \"evidence\": \"Site-directed K82 and Ser76/80 mutants, K63/K48-specific ubiquitination and phosphorylation assays, reciprocal Co-IP in glioblastoma cells\",\n      \"pmids\": [\"29669288\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo relevance of the feedback loop not established\", \"Tissue specificity beyond glioblastoma unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified a ligase-independent mechanism whereby TRIM9 sequesters β-TrCP from the SCF complex to stabilize IκBα and restrain NF-κB neuroinflammation after stroke.\",\n      \"evidence\": \"Co-IP, IκBα degradation assay, Trim9-/- ischemic stroke mouse model with AAV rescue\",\n      \"pmids\": [\"30970257\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether sequestration involves ubiquitination of β-TrCP not resolved\", \"Cell type mediating the neuroinflammatory phenotype not defined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Mapped a TRIM9/TRIM67 proximity interactome in cortical neurons, implicating Myo16 in TRIM9- and netrin-dependent control of filopodia and branching.\",\n      \"evidence\": \"BioID proximity labeling, TIRF colocalization, Myo16 RNAi with morphological readouts\",\n      \"pmids\": [\"33378226\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Most interactome members not functionally validated\", \"Whether interactors are ubiquitination substrates unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended the substrate repertoire to cancer-relevant targets, with K11-linked ubiquitination of HNRNPU suppressing pancreatic tumor growth and ubiquitination of PKM2 reprogramming glycolysis in breast cancer.\",\n      \"evidence\": \"K11-linkage ubiquitination assays with RING mutant and in vivo xenograft rescue (HNRNPU); Co-IP and oligomerization/metabolic assays (PKM2)\",\n      \"pmids\": [\"41050689\", \"38263865\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"PKM2 ubiquitination lacks site-level and linkage mechanistic detail\", \"How tumor-suppressive substrate selection is achieved unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed TRIM9 engages both attractive (DCC) and repulsive (UNC5C) netrin receptors, regulating their surface levels and bidirectional turning responses while negatively regulating FAK in the absence of netrin.\",\n      \"evidence\": \"Co-IP for both receptors, microfluidic netrin gradients, Trim9-/- neurons, surface receptor quantification, FAK assays, pH-mScarlet reporter\",\n      \"pmids\": [\"39871643\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether UNC5C is a direct ubiquitination substrate not established\", \"Mechanism integrating attractive and repulsive outputs unclear\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Implicated TRIM9 in proteostasis of disease-linked aggregating proteins, mediating degradation of the ALS-associated UBQLN2P497H mutant, and reinforced VASP-dependent control of focal adhesions and motility in melanoma.\",\n      \"evidence\": \"APEX2 proximity proteomics, Co-IP, fractionation, proteasome inhibition and siRNA (UBQLN2P497H); Co-IP, TIRF and Trim9 KO melanoma model (VASP)\",\n      \"pmids\": [\"41582437\", \"41889914\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Melanoma study is a preprint (single lab)\", \"How TRIM9 selectively recognizes the mutant UBQLN2 conformer not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TRIM9 selects among its diverse substrates and switches between degradative ubiquitination, regulatory linkage signaling, and ligase-independent sequestration across neuronal, immune, and tumor contexts remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying model for substrate/linkage selection\", \"Isoform-specific regulation across tissues not integrated\", \"No structural model of substrate or partner engagement\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 2, 4, 6, 7, 13]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [2, 4, 7, 13]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [2, 8]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [2, 4, 5, 6, 11]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [1, 3, 10]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [4, 7, 11]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 13, 15]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"DCC\", \"UNC5C\", \"VASP\", \"GSK3B\", \"TBK1\", \"BTRC\", \"MKK6\", \"HNRNPU\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}