{"gene":"TRIM46","run_date":"2026-04-28T21:43:00","timeline":{"discoveries":[{"year":2015,"finding":"TRIM46 specifically localizes to the newly specified axon and axon initial segment (AIS), where it forms closely spaced parallel microtubule bundles oriented with plus-end out, driving uniform microtubule polarity. Loss of TRIM46 causes all neurites to adopt a dendrite-like mixed microtubule organization, resulting in Tau missorting and altered cargo trafficking, establishing TRIM46 as instructive for neuronal polarity and axon specification.","method":"Overexpression and knockdown in cultured neurons (in vitro and in vivo), live imaging, Tau missorting readout, cargo trafficking assays","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 2 — clean KD/KO with defined cellular phenotypes, replicated in vitro and in vivo, 175 citations","pmids":["26671463"],"is_preprint":false},{"year":2019,"finding":"TRIM46 localizes to the electron-dense cross-bridges of fasciculated microtubules at the AIS. Depletion of TRIM46 causes loss of cross-bridges and increased microtubule spacing, demonstrating that TRIM46 is the structural component that forms microtubule cross-bridges and is essential for microtubule fasciculation at the AIS.","method":"Correlative light and electron microscopy (CLEM), TRIM46 depletion in cultured rat hippocampal neurons, quantitative measurement of microtubule spacing","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 1-2 — direct ultrastructural localization to cross-bridges with orthogonal loss-of-function phenotype","pmids":["30967428"],"is_preprint":false},{"year":2021,"finding":"TRIM46 interacts with GPX4 (glutathione peroxidase 4) and promotes its ubiquitination and degradation, thereby promoting ferroptosis in high-glucose-treated human retinal capillary endothelial cells. GPX4 overexpression reverses the pro-ferroptotic effects of TRIM46.","method":"Co-immunoprecipitation, ubiquitination assay, western blot, lentiviral overexpression/knockdown, ferroptosis measurement (lipid ROS, MDA, GSH)","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP confirmed interaction, multiple functional readouts, single lab","pmids":["34487731"],"is_preprint":false},{"year":2022,"finding":"TRIM46 acts as an E3 ubiquitin ligase that ubiquitinates PHLPP2 (pleckstrin homology domain leucine-rich repeat protein phosphatase 2), leading to its degradation and consequent upregulation of p-AKT and HK2, promoting glycolysis and cisplatin resistance in lung adenocarcinoma cells. A RING-domain mutant of TRIM46 loses these functions, confirming dependence on E3 ligase activity.","method":"RING-mutant overexpression, ubiquitination assay, western blot, patient-derived xenograft (PDX) model, cell proliferation and glycolysis assays","journal":"Cell death & disease","confidence":"High","confidence_rationale":"Tier 1-2 — catalytic mutant (RING) confirms E3 ligase mechanism, in vivo PDX validation, multiple orthogonal methods","pmids":["35354796"],"is_preprint":false},{"year":2021,"finding":"TRIM46 is a ubiquitin ligase that targets HDAC1 for ubiquitination and proteasomal degradation, thereby regulating genes involved in DNA replication and repair and promoting breast cancer cell proliferation and chemoresistance. The SNP rs4971059 functions as an active enhancer of TRIM46 expression.","method":"CRISPR/Cas9-mediated SNP knock-in, ubiquitination assay, co-immunoprecipitation, western blot, in vitro proliferation, in vivo tumor growth","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods including CRISPR allele swap, ubiquitination assay, and in vivo validation","pmids":["34459501"],"is_preprint":false},{"year":2020,"finding":"TRIM46 ubiquitinates DUSP1 (MAP kinase phosphatase 1), promoting activation of MAPK and NF-κB signaling pathways; TRIM46 knockdown inhibits TcdB-induced MAPK/NF-κB activation and inflammatory cytokine production. NF-κBp65 also binds the TRIM46 promoter, forming a positive feedback loop.","method":"Co-immunoprecipitation, ubiquitination assay, knockdown/overexpression, in vivo mouse model, ELISA for cytokines","journal":"Artificial cells, nanomedicine, and biotechnology","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP and ubiquitination confirmed, in vivo validation, single lab","pmids":["31918570"],"is_preprint":false},{"year":2022,"finding":"TRIM46 interacts with IκBα and promotes its ubiquitination and degradation, thereby activating NF-κB signaling and enhancing high-glucose-induced hyperpermeability and inflammatory response in human retinal capillary endothelial cells.","method":"Co-immunoprecipitation, ubiquitination assay, western blot, TEER measurement, ELISA for cytokines, overexpression/knockdown","journal":"Eye and vision","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP confirmed interaction, functional rescue by IκBα overexpression, single lab","pmids":["36064447"],"is_preprint":false},{"year":2022,"finding":"TRIM46 protein levels are controlled by two alternative splicing events: inclusion of exon 8 causes nonsense-mediated mRNA decay of Trim46 transcripts, and PTBP2-mediated exon 10 skipping produces transcripts encoding unstable TRIM46 proteins. During axonogenesis, decreased exon 8 inclusion and enhanced exon 10 inclusion converge to increase TRIM46 protein, enabling neural-specific expression. Genetic deletion of these exons confirmed TRIM46 is instructive but not always required for AnkG localization.","method":"Alternative splicing analysis, NMD assays, PTBP2 manipulation, genetic exon deletion, western blot, neuronal differentiation assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal mechanisms validated, genetic deletion experiments, strong mechanistic dissection","pmids":["35440129"],"is_preprint":false},{"year":2022,"finding":"TRIM46 promotes ubiquitination and proteasomal degradation of Axin1, a negative regulator of Wnt/β-catenin signaling, thereby activating Wnt/β-catenin signaling and driving EMT in hypoxia-treated HK2 renal tubular epithelial cells. Inhibiting β-catenin reversed TRIM46 overexpression effects.","method":"Co-immunoprecipitation, ubiquitination assay, proteasome inhibitor rescue, western blot, knockdown/overexpression, rat renal fibrosis model","journal":"Molecular and cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP and ubiquitination confirmed, in vivo rat model correlation, single lab","pmids":["35670901"],"is_preprint":false},{"year":2024,"finding":"TRIM46 knockout mice are viable with normal behavior and brain structure, demonstrating that TRIM46 is dispensable for axon specification and AIS formation in vivo, contrary to conclusions from cultured neuron knockdown studies. However, TRIM46 KO does abolish microtubule fasciculation. AnkG is required to restrict TRIM46 enrichment only to the AIS, while TRIM46 enrichment in the proximal axon (~100 μm) occurs independently of AnkG.","method":"TRIM46 knockout mice, immunohistochemistry, electron microscopy, behavioral testing, brain structure analysis","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 — constitutive knockout in vivo with multiple behavioral and structural readouts, peer-reviewed","pmids":["39251352"],"is_preprint":false},{"year":2024,"finding":"TRIM46 promotes SLC7A11 ubiquitination and decreases its stability, thereby promoting ferroptosis and inflammatory responses during H1N1 influenza virus infection in lung cells. TRIM46 knockdown suppressed viral replication and lung injury in vivo.","method":"Co-immunoprecipitation, cycloheximide stability assay, western blot, knockdown, in vivo H1N1 lung injury mouse model","journal":"Journal of bioenergetics and biomembranes","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP and stability assay confirm mechanism, in vivo validation, single lab","pmids":["39531094"],"is_preprint":false},{"year":2024,"finding":"Trim46 KO in rats impairs neuronal dendritic arbor and dendritic spine formation, shortens the AIS, and alters hippocampal levels of FKBP5, Akt phosphorylation, GABRA1, and NMDAR1. Endogenous TRIM46 was shown to interact with FKBP5 in brain tissue.","method":"CRISPR/Cas9 knockout rats, co-immunoprecipitation (TRIM46-FKBP5), western blot, behavioral testing, morphological analysis","journal":"Developmental dynamics","confidence":"Medium","confidence_rationale":"Tier 2-3 — in vivo KO with defined phenotypes, Co-IP for novel binding partner, single lab","pmids":["38193537"],"is_preprint":false},{"year":2026,"finding":"TRIM46 is specifically transported to the axon initial segment by a KIF3B-enriched, KAP3-associated kinesin-2 assembly distinct from the canonical KIF3A/B/KAP3 complex. Biochemical and structural analyses indicate preferential association of TRIM46 with this KIF3B-enriched assembly, with tail domain conformation differences underlying cargo selectivity.","method":"Biochemical fractionation, co-immunoprecipitation, structural analyses, cellular localization assays","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2 — biochemical and structural analyses with multiple orthogonal methods, single lab","pmids":["41910726"],"is_preprint":false},{"year":2025,"finding":"Loss of TRIM46 (a ubiquitin ligase with roles in microtubule organization) in non-neuronal cells causes Golgi ribbon fragmentation and enhanced TFEB-driven lysosomal biogenesis. Golgi damage triggers CASM (conjugation of Atg8 proteins to single membranes) at the trans-Golgi, and genetic inhibition of CASM in TRIM46-deficient cells exacerbates Golgi morphology defects, indicating CASM acts to preserve Golgi integrity downstream of TRIM46 loss.","method":"TRIM46 knockout cells, LC3B/GABARAP colocalization, TFEB activation assays, genetic inhibition of CASM, confocal microscopy","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 — preprint, single lab, localization and KO phenotype without full mechanistic dissection of TRIM46's direct role","pmids":["bio_10.1101_2025.09.04.674289"],"is_preprint":true}],"current_model":"TRIM46 is a RING-domain E3 ubiquitin ligase and microtubule-associated protein that, in neurons, forms plus-end-out parallel microtubule bundles and cross-bridges at the axon initial segment (required for microtubule fasciculation but dispensable for axon specification in vivo); in non-neuronal contexts it ubiquitinates and degrades multiple substrates including GPX4, HDAC1, PHLPP2, DUSP1, IκBα, Axin1, and SLC7A11 to regulate ferroptosis, NF-κB, AKT, and Wnt/β-catenin signaling, while its own protein levels are post-transcriptionally controlled by PTBP2-regulated alternative splicing coupled to NMD."},"narrative":{"teleology":[{"year":2015,"claim":"The first functional characterization of TRIM46 established it as a microtubule-organizing protein that drives uniform plus-end-out microtubule polarity at the nascent axon and AIS, framing it as a key determinant of neuronal polarity.","evidence":"Overexpression/knockdown in cultured neurons with live imaging, Tau missorting readouts, and cargo trafficking assays","pmids":["26671463"],"confidence":"High","gaps":["Whether TRIM46 directly cross-links microtubules or acts indirectly was unresolved","Whether TRIM46's role in cultured neurons reflects its requirement in vivo was untested","The E3 ligase activity of the RING domain was not examined in this neuronal context"]},{"year":2019,"claim":"Ultrastructural analysis resolved that TRIM46 is the structural component of the electron-dense cross-bridges between fasciculated microtubules at the AIS, directly answering how microtubule bundling is achieved.","evidence":"Correlative light and electron microscopy with TRIM46 depletion in cultured rat hippocampal neurons","pmids":["30967428"],"confidence":"High","gaps":["The minimal domain of TRIM46 sufficient for cross-bridge formation was not defined","Whether cross-bridge formation depends on the RING domain or a separate structural motif was unknown"]},{"year":2020,"claim":"TRIM46 was shown to function as an E3 ubiquitin ligase for DUSP1, linking it to MAPK/NF-κB inflammatory signaling and revealing substrate activities beyond microtubule organization.","evidence":"Co-IP, ubiquitination assay, knockdown/overexpression, and in vivo mouse model of TcdB-induced inflammation","pmids":["31918570"],"confidence":"Medium","gaps":["The ubiquitin chain type and RING-domain dependence were not demonstrated for DUSP1","No independent replication from a second laboratory"]},{"year":2021,"claim":"Identification of GPX4 and HDAC1 as TRIM46 ubiquitination substrates extended its E3 ligase repertoire to ferroptosis regulation and epigenetic control of DNA replication/repair, respectively, with RING-domain mutant confirmation for HDAC1.","evidence":"Co-IP, ubiquitination assays, CRISPR knock-in of enhancer SNP (HDAC1 study), western blot, and in vivo tumor models","pmids":["34487731","34459501"],"confidence":"High","gaps":["Whether GPX4 ubiquitination depends on the RING domain specifically was not tested","Whether substrate selectivity among diverse targets involves different adaptor proteins was unaddressed"]},{"year":2022,"claim":"Mechanistic dissection of TRIM46 expression revealed that PTBP2-regulated alternative splicing and NMD control its neuron-specific accumulation during axonogenesis, explaining how a broadly transcribed gene achieves restricted protein expression.","evidence":"Alternative splicing analysis, NMD assays, PTBP2 manipulation, genetic exon deletion in neurons","pmids":["35440129"],"confidence":"High","gaps":["Whether additional RNA-binding proteins regulate TRIM46 splicing in non-neuronal tissues was unknown","Genetic exon deletion showed TRIM46 is instructive but not always required for AnkG localization, leaving redundant pathways unidentified"]},{"year":2022,"claim":"Additional E3 ligase substrates—PHLPP2, IκBα, and Axin1—were identified, showing TRIM46 activates AKT/glycolysis, NF-κB, and Wnt/β-catenin pathways in cancer and fibrosis contexts; RING-mutant analysis for PHLPP2 confirmed catalytic dependence.","evidence":"Co-IP, ubiquitination assays, RING-mutant overexpression, PDX models (PHLPP2), proteasome inhibitor rescue (Axin1), rat renal fibrosis model","pmids":["35354796","36064447","35670901"],"confidence":"High","gaps":["The structural basis for TRIM46 recognizing such diverse substrates is uncharacterized","Whether these non-neuronal substrates are relevant under physiological (non-pathological) conditions was not tested"]},{"year":2024,"claim":"TRIM46 knockout mice demonstrated that TRIM46 is dispensable for axon specification, AIS formation, and normal behavior in vivo—revising the prior model from cultured neurons—while confirming its requirement for microtubule fasciculation; AnkG was shown to restrict TRIM46 to the AIS.","evidence":"Constitutive TRIM46 knockout mice with immunohistochemistry, electron microscopy, and behavioral testing","pmids":["39251352"],"confidence":"High","gaps":["Compensatory mechanisms that substitute for TRIM46 in axon specification in vivo remain unidentified","Whether microtubule fasciculation loss has functional consequences under stress or aging was not tested"]},{"year":2024,"claim":"SLC7A11 was identified as a TRIM46 substrate linking it to ferroptosis and inflammation during influenza infection, and TRIM46 KO rats revealed roles in dendritic morphogenesis and interaction with FKBP5, expanding its neuronal functions beyond the AIS.","evidence":"Co-IP, cycloheximide chase, in vivo H1N1 mouse model (SLC7A11); CRISPR KO rats, Co-IP for FKBP5, morphological analysis","pmids":["39531094","38193537"],"confidence":"Medium","gaps":["SLC7A11 ubiquitination site(s) and chain linkage type not mapped","The mechanistic link between TRIM46-FKBP5 interaction and dendritic spine phenotypes is correlative","No independent replication of either finding"]},{"year":2026,"claim":"The mechanism of TRIM46 axonal delivery was resolved: a KIF3B-enriched, KAP3-associated kinesin-2 assembly distinct from the canonical KIF3A/B/KAP3 complex selectively transports TRIM46 to the AIS.","evidence":"Biochemical fractionation, co-immunoprecipitation, structural analyses, cellular localization assays","pmids":["41910726"],"confidence":"Medium","gaps":["Whether this transport mechanism is regulated during development or plasticity is unknown","Structural details of the TRIM46-kinesin-2 interface at atomic resolution are lacking"]},{"year":null,"claim":"How TRIM46 achieves substrate selectivity across its many ubiquitination targets, whether its E3 ligase and microtubule-bundling activities are coordinated or independent, and what compensatory mechanisms maintain axon specification in its absence in vivo remain open questions.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural model of TRIM46 exists to explain dual microtubule-binding and E3 ligase functions","The identity of redundant factors that compensate for TRIM46 loss in axon specification is unknown","Whether the diverse non-neuronal substrates reflect physiological or pathological roles has not been resolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[2,3,4,5,6,8,10]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,1,9]}],"localization":[{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0,1,9]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3,4]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[2,3,4,5,6,8,10]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3,5,6,8]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[2,10]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[5,6]}],"complexes":[],"partners":["GPX4","HDAC1","PHLPP2","DUSP1","NFKBIA","AXIN1","SLC7A11","FKBP5"],"other_free_text":[]},"mechanistic_narrative":"TRIM46 is a RING-domain E3 ubiquitin ligase and microtubule-associated protein that plays dual roles: organizing axonal microtubule architecture and regulating diverse signaling pathways through ubiquitin-mediated substrate degradation. In neurons, TRIM46 localizes to the axon initial segment where it forms the electron-dense cross-bridges that bundle parallel, plus-end-out microtubules; although knockout mice reveal that TRIM46 is essential for microtubule fasciculation, it is dispensable for axon specification and AIS formation in vivo [PMID:26671463, PMID:30967428, PMID:39251352]. Its neuron-specific expression is achieved through PTBP2-regulated alternative splicing coupled to nonsense-mediated mRNA decay, and its transport to the AIS depends on a KIF3B-enriched kinesin-2 complex [PMID:35440129, PMID:41910726]. Outside the nervous system, TRIM46 ubiquitinates and degrades multiple substrates—including PHLPP2, HDAC1, GPX4, IκBα, Axin1, DUSP1, and SLC7A11—thereby modulating AKT, NF-κB, Wnt/β-catenin, and ferroptosis pathways in contexts ranging from cancer chemoresistance to diabetic retinopathy and viral lung injury [PMID:35354796, PMID:34459501, PMID:34487731, PMID:36064447, PMID:35670901, PMID:39531094]."},"prefetch_data":{"uniprot":{"accession":"Q7Z4K8","full_name":"Tripartite motif-containing protein 46","aliases":["Gene Y protein","GeneY","Tripartite, fibronectin type-III and C-terminal SPRY motif protein"],"length_aa":759,"mass_kda":83.4,"function":"Microtubule-associated protein that is involved in the formation of parallel microtubule bundles linked by cross-bridges in the proximal axon. Required for the uniform orientation and maintenance of the parallel microtubule fascicles, which are important for efficient cargo delivery and trafficking in axons. Thereby also required for proper axon specification, the establishment of neuronal polarity and proper neuronal migration","subcellular_location":"Cell projection, axon; Cytoplasm, cytoskeleton","url":"https://www.uniprot.org/uniprotkb/Q7Z4K8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TRIM46","classification":"Not Classified","n_dependent_lines":125,"n_total_lines":1208,"dependency_fraction":0.10347682119205298},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TRIM46","total_profiled":1310},"omim":[{"mim_id":"600986","title":"TRIPARTITE MOTIF-CONTAINING PROTEIN 46; TRIM46","url":"https://www.omim.org/entry/600986"},{"mim_id":"301121","title":"MAP7 DOMAIN-CONTAINING PROTEIN 2; MAP7D2","url":"https://www.omim.org/entry/301121"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Microtubule ends","reliability":"Approved"},{"location":"Mitotic spindle","reliability":"Approved"},{"location":"Primary cilium transition zone","reliability":"Approved"},{"location":"Cytokinetic bridge","reliability":"Additional"},{"location":"Centrosome","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"brain","ntpm":21.5}],"url":"https://www.proteinatlas.org/search/TRIM46"},"hgnc":{"alias_symbol":["FLJ23229","TRIFIC"],"prev_symbol":[]},"alphafold":{"accession":"Q7Z4K8","domains":[{"cath_id":"3.30.40.10","chopping":"28-67_123-168","consensus_level":"medium","plddt":84.8314,"start":28,"end":168},{"cath_id":"2.60.40.10","chopping":"433-524","consensus_level":"high","plddt":91.2675,"start":433,"end":524},{"cath_id":"2.60.120.920","chopping":"534-620_648-664_683-737","consensus_level":"high","plddt":89.0916,"start":534,"end":737}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z4K8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z4K8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z4K8-F1-predicted_aligned_error_v6.png","plddt_mean":79.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TRIM46","jax_strain_url":"https://www.jax.org/strain/search?query=TRIM46"},"sequence":{"accession":"Q7Z4K8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q7Z4K8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q7Z4K8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z4K8"}},"corpus_meta":[{"pmid":"26671463","id":"PMC_26671463","title":"TRIM46 Controls Neuronal Polarity and Axon Specification by Driving the Formation of Parallel Microtubule Arrays.","date":"2015","source":"Neuron","url":"https://pubmed.ncbi.nlm.nih.gov/26671463","citation_count":175,"is_preprint":false},{"pmid":"34487731","id":"PMC_34487731","title":"TRIM46 contributes to high glucose-induced ferroptosis and cell growth inhibition in human retinal capillary endothelial cells by facilitating GPX4 ubiquitination.","date":"2021","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/34487731","citation_count":123,"is_preprint":false},{"pmid":"30967428","id":"PMC_30967428","title":"TRIM46 Organizes Microtubule Fasciculation in the Axon Initial Segment.","date":"2019","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/30967428","citation_count":56,"is_preprint":false},{"pmid":"35354796","id":"PMC_35354796","title":"TRIM46 activates AKT/HK2 signaling by modifying PHLPP2 ubiquitylation to promote glycolysis and chemoresistance of lung cancer cells.","date":"2022","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/35354796","citation_count":52,"is_preprint":false},{"pmid":"34921120","id":"PMC_34921120","title":"Characterisation of TRIM46 autoantibody-associated paraneoplastic neurological syndrome.","date":"2021","source":"Journal of neurology, neurosurgery, and psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/34921120","citation_count":33,"is_preprint":false},{"pmid":"28904989","id":"PMC_28904989","title":"Antibodies to TRIM46 are associated with paraneoplastic neurological syndromes.","date":"2017","source":"Annals of clinical and translational neurology","url":"https://pubmed.ncbi.nlm.nih.gov/28904989","citation_count":30,"is_preprint":false},{"pmid":"34459501","id":"PMC_34459501","title":"SNP rs4971059 predisposes to breast carcinogenesis and chemoresistance via TRIM46-mediated HDAC1 degradation.","date":"2021","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/34459501","citation_count":28,"is_preprint":false},{"pmid":"27110773","id":"PMC_27110773","title":"Mmu-miR-1894-3p Inhibits Cell Proliferation and Migration of Breast Cancer Cells by Targeting Trim46.","date":"2016","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/27110773","citation_count":28,"is_preprint":false},{"pmid":"31918570","id":"PMC_31918570","title":"Clostridium difficile toxin B induces colonic inflammation through the TRIM46/DUSP1/MAPKs and NF-κB signalling pathway.","date":"2020","source":"Artificial cells, nanomedicine, and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/31918570","citation_count":27,"is_preprint":false},{"pmid":"33556457","id":"PMC_33556457","title":"Axonal TAU Sorting Requires the C-terminus of TAU but is Independent of ANKG and TRIM46 Enrichment at the AIS.","date":"2021","source":"Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/33556457","citation_count":27,"is_preprint":false},{"pmid":"36064447","id":"PMC_36064447","title":"TRIM46 aggravated high glucose-induced hyper permeability and inflammatory response in human retinal capillary endothelial cells by promoting IκBα ubiquitination.","date":"2022","source":"Eye and vision (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/36064447","citation_count":25,"is_preprint":false},{"pmid":"26492273","id":"PMC_26492273","title":"Aberrant MUC1-TRIM46-KRTCAP2 Chimeric RNAs in High-Grade Serous Ovarian Carcinoma.","date":"2015","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/26492273","citation_count":16,"is_preprint":false},{"pmid":"35440129","id":"PMC_35440129","title":"Multilayered regulations of alternative splicing, NMD, and protein stability control temporal induction and tissue-specific expression of TRIM46 during axon formation.","date":"2022","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/35440129","citation_count":16,"is_preprint":false},{"pmid":"35670901","id":"PMC_35670901","title":"TRIM46 upregulates Wnt/β-catenin signaling by inhibiting Axin1 to mediate hypoxia-induced epithelial-mesenchymal transition in HK2 cells.","date":"2022","source":"Molecular and cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/35670901","citation_count":13,"is_preprint":false},{"pmid":"38795848","id":"PMC_38795848","title":"Oxymatrine induces apoptosis in non-small cell lung cancer cells by downregulating TRIM46.","date":"2024","source":"Toxicon : official journal of the International Society on Toxinology","url":"https://pubmed.ncbi.nlm.nih.gov/38795848","citation_count":9,"is_preprint":false},{"pmid":"33717417","id":"PMC_33717417","title":"Trim46 contributes to the midbrain development via Sonic Hedgehog signaling pathway in zebrafish embryos.","date":"2021","source":"Animal cells and systems","url":"https://pubmed.ncbi.nlm.nih.gov/33717417","citation_count":8,"is_preprint":false},{"pmid":"34881275","id":"PMC_34881275","title":"Identification TRIM46 as a Potential Biomarker and Therapeutic Target for Clear Cell Renal Cell Carcinoma Through Comprehensive Bioinformatics Analyses.","date":"2021","source":"Frontiers in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34881275","citation_count":6,"is_preprint":false},{"pmid":"39251352","id":"PMC_39251352","title":"TRIM46 Is Required for Microtubule Fasciculation In Vivo But Not Axon Specification or Axon Initial Segment Formation.","date":"2024","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/39251352","citation_count":5,"is_preprint":false},{"pmid":"39937005","id":"PMC_39937005","title":"Enhanced Expression of TRIM46 in Ovarian Cancer Cells Induced by Tumor-Associated Macrophages Promotes Invasion via the Wnt/β-Catenin Pathway.","date":"2025","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/39937005","citation_count":5,"is_preprint":false},{"pmid":"38193537","id":"PMC_38193537","title":"Trim46 knockout impaired neuronal architecture and caused hypoactive behavior in rats.","date":"2024","source":"Developmental dynamics : an official publication of the American Association of Anatomists","url":"https://pubmed.ncbi.nlm.nih.gov/38193537","citation_count":5,"is_preprint":false},{"pmid":"39531094","id":"PMC_39531094","title":"TRIM46 accelerates H1N1 influenza virus-induced ferroptosis and inflammatory response by regulating SLC7A11 ubiquitination.","date":"2024","source":"Journal of bioenergetics and biomembranes","url":"https://pubmed.ncbi.nlm.nih.gov/39531094","citation_count":3,"is_preprint":false},{"pmid":"41222281","id":"PMC_41222281","title":"TRIM46 promotes chemoresistance of ovarian cancer via activating PHLPP2/PI3K/AKT pathway.","date":"2025","source":"Biochemistry and cell biology = Biochimie et biologie cellulaire","url":"https://pubmed.ncbi.nlm.nih.gov/41222281","citation_count":2,"is_preprint":false},{"pmid":"39553213","id":"PMC_39553213","title":"Comprehensive analysis of ferroptosis-related genes indicates that TRIM46 is a novel biomarker and promotes the progression of ovarian cancer via modulating ferroptosis and Wnt signaling pathway.","date":"2024","source":"American journal of cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/39553213","citation_count":2,"is_preprint":false},{"pmid":"40154001","id":"PMC_40154001","title":"ONECUT3 activates the TRIM46-NF-κB pathway to promote the development of pancreatic cancer.","date":"2025","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/40154001","citation_count":1,"is_preprint":false},{"pmid":"38826451","id":"PMC_38826451","title":"TRIM46 is not required for axon specification or axon initial segment formation in vivo.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38826451","citation_count":1,"is_preprint":false},{"pmid":"40590258","id":"PMC_40590258","title":"Autoantibodies against TRIM46 identified in a dog suffering from suspected meningoencephalomyelitis of unknown origin.","date":"2025","source":"The Journal of small animal practice","url":"https://pubmed.ncbi.nlm.nih.gov/40590258","citation_count":0,"is_preprint":false},{"pmid":"41910726","id":"PMC_41910726","title":"The KIF3B/B/KAP3 tail domain specifically facilitates TRIM46 transport to the axon initial segment.","date":"2026","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/41910726","citation_count":0,"is_preprint":false},{"pmid":"41614410","id":"PMC_41614410","title":"TRIM46 deficiency‑induced DNA damage enhances the sensitivity of cisplatin in non‑small cell lung cancer by regulating the Akt signaling pathway.","date":"2026","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/41614410","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.09.04.674289","title":"A role for CASM in the repair of damaged Golgi architecture","date":"2025-09-04","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.04.674289","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.05.23.595556","title":"TRIM46 is not required for axon specification or axon initial segment formation<i>in vivo</i>","date":"2024-05-23","source":"bioRxiv","url":"https://doi.org/10.1101/2024.05.23.595556","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15929,"output_tokens":3551,"usd":0.050526},"stage2":{"model":"claude-opus-4-6","input_tokens":6986,"output_tokens":2890,"usd":0.16077},"total_usd":0.211296,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"TRIM46 specifically localizes to the newly specified axon and axon initial segment (AIS), where it forms closely spaced parallel microtubule bundles oriented with plus-end out, driving uniform microtubule polarity. Loss of TRIM46 causes all neurites to adopt a dendrite-like mixed microtubule organization, resulting in Tau missorting and altered cargo trafficking, establishing TRIM46 as instructive for neuronal polarity and axon specification.\",\n      \"method\": \"Overexpression and knockdown in cultured neurons (in vitro and in vivo), live imaging, Tau missorting readout, cargo trafficking assays\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KD/KO with defined cellular phenotypes, replicated in vitro and in vivo, 175 citations\",\n      \"pmids\": [\"26671463\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TRIM46 localizes to the electron-dense cross-bridges of fasciculated microtubules at the AIS. Depletion of TRIM46 causes loss of cross-bridges and increased microtubule spacing, demonstrating that TRIM46 is the structural component that forms microtubule cross-bridges and is essential for microtubule fasciculation at the AIS.\",\n      \"method\": \"Correlative light and electron microscopy (CLEM), TRIM46 depletion in cultured rat hippocampal neurons, quantitative measurement of microtubule spacing\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — direct ultrastructural localization to cross-bridges with orthogonal loss-of-function phenotype\",\n      \"pmids\": [\"30967428\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TRIM46 interacts with GPX4 (glutathione peroxidase 4) and promotes its ubiquitination and degradation, thereby promoting ferroptosis in high-glucose-treated human retinal capillary endothelial cells. GPX4 overexpression reverses the pro-ferroptotic effects of TRIM46.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, western blot, lentiviral overexpression/knockdown, ferroptosis measurement (lipid ROS, MDA, GSH)\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP confirmed interaction, multiple functional readouts, single lab\",\n      \"pmids\": [\"34487731\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TRIM46 acts as an E3 ubiquitin ligase that ubiquitinates PHLPP2 (pleckstrin homology domain leucine-rich repeat protein phosphatase 2), leading to its degradation and consequent upregulation of p-AKT and HK2, promoting glycolysis and cisplatin resistance in lung adenocarcinoma cells. A RING-domain mutant of TRIM46 loses these functions, confirming dependence on E3 ligase activity.\",\n      \"method\": \"RING-mutant overexpression, ubiquitination assay, western blot, patient-derived xenograft (PDX) model, cell proliferation and glycolysis assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — catalytic mutant (RING) confirms E3 ligase mechanism, in vivo PDX validation, multiple orthogonal methods\",\n      \"pmids\": [\"35354796\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TRIM46 is a ubiquitin ligase that targets HDAC1 for ubiquitination and proteasomal degradation, thereby regulating genes involved in DNA replication and repair and promoting breast cancer cell proliferation and chemoresistance. The SNP rs4971059 functions as an active enhancer of TRIM46 expression.\",\n      \"method\": \"CRISPR/Cas9-mediated SNP knock-in, ubiquitination assay, co-immunoprecipitation, western blot, in vitro proliferation, in vivo tumor growth\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods including CRISPR allele swap, ubiquitination assay, and in vivo validation\",\n      \"pmids\": [\"34459501\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TRIM46 ubiquitinates DUSP1 (MAP kinase phosphatase 1), promoting activation of MAPK and NF-κB signaling pathways; TRIM46 knockdown inhibits TcdB-induced MAPK/NF-κB activation and inflammatory cytokine production. NF-κBp65 also binds the TRIM46 promoter, forming a positive feedback loop.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, knockdown/overexpression, in vivo mouse model, ELISA for cytokines\",\n      \"journal\": \"Artificial cells, nanomedicine, and biotechnology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP and ubiquitination confirmed, in vivo validation, single lab\",\n      \"pmids\": [\"31918570\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TRIM46 interacts with IκBα and promotes its ubiquitination and degradation, thereby activating NF-κB signaling and enhancing high-glucose-induced hyperpermeability and inflammatory response in human retinal capillary endothelial cells.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, western blot, TEER measurement, ELISA for cytokines, overexpression/knockdown\",\n      \"journal\": \"Eye and vision\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP confirmed interaction, functional rescue by IκBα overexpression, single lab\",\n      \"pmids\": [\"36064447\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TRIM46 protein levels are controlled by two alternative splicing events: inclusion of exon 8 causes nonsense-mediated mRNA decay of Trim46 transcripts, and PTBP2-mediated exon 10 skipping produces transcripts encoding unstable TRIM46 proteins. During axonogenesis, decreased exon 8 inclusion and enhanced exon 10 inclusion converge to increase TRIM46 protein, enabling neural-specific expression. Genetic deletion of these exons confirmed TRIM46 is instructive but not always required for AnkG localization.\",\n      \"method\": \"Alternative splicing analysis, NMD assays, PTBP2 manipulation, genetic exon deletion, western blot, neuronal differentiation assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal mechanisms validated, genetic deletion experiments, strong mechanistic dissection\",\n      \"pmids\": [\"35440129\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TRIM46 promotes ubiquitination and proteasomal degradation of Axin1, a negative regulator of Wnt/β-catenin signaling, thereby activating Wnt/β-catenin signaling and driving EMT in hypoxia-treated HK2 renal tubular epithelial cells. Inhibiting β-catenin reversed TRIM46 overexpression effects.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, proteasome inhibitor rescue, western blot, knockdown/overexpression, rat renal fibrosis model\",\n      \"journal\": \"Molecular and cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP and ubiquitination confirmed, in vivo rat model correlation, single lab\",\n      \"pmids\": [\"35670901\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM46 knockout mice are viable with normal behavior and brain structure, demonstrating that TRIM46 is dispensable for axon specification and AIS formation in vivo, contrary to conclusions from cultured neuron knockdown studies. However, TRIM46 KO does abolish microtubule fasciculation. AnkG is required to restrict TRIM46 enrichment only to the AIS, while TRIM46 enrichment in the proximal axon (~100 μm) occurs independently of AnkG.\",\n      \"method\": \"TRIM46 knockout mice, immunohistochemistry, electron microscopy, behavioral testing, brain structure analysis\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — constitutive knockout in vivo with multiple behavioral and structural readouts, peer-reviewed\",\n      \"pmids\": [\"39251352\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM46 promotes SLC7A11 ubiquitination and decreases its stability, thereby promoting ferroptosis and inflammatory responses during H1N1 influenza virus infection in lung cells. TRIM46 knockdown suppressed viral replication and lung injury in vivo.\",\n      \"method\": \"Co-immunoprecipitation, cycloheximide stability assay, western blot, knockdown, in vivo H1N1 lung injury mouse model\",\n      \"journal\": \"Journal of bioenergetics and biomembranes\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP and stability assay confirm mechanism, in vivo validation, single lab\",\n      \"pmids\": [\"39531094\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Trim46 KO in rats impairs neuronal dendritic arbor and dendritic spine formation, shortens the AIS, and alters hippocampal levels of FKBP5, Akt phosphorylation, GABRA1, and NMDAR1. Endogenous TRIM46 was shown to interact with FKBP5 in brain tissue.\",\n      \"method\": \"CRISPR/Cas9 knockout rats, co-immunoprecipitation (TRIM46-FKBP5), western blot, behavioral testing, morphological analysis\",\n      \"journal\": \"Developmental dynamics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — in vivo KO with defined phenotypes, Co-IP for novel binding partner, single lab\",\n      \"pmids\": [\"38193537\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"TRIM46 is specifically transported to the axon initial segment by a KIF3B-enriched, KAP3-associated kinesin-2 assembly distinct from the canonical KIF3A/B/KAP3 complex. Biochemical and structural analyses indicate preferential association of TRIM46 with this KIF3B-enriched assembly, with tail domain conformation differences underlying cargo selectivity.\",\n      \"method\": \"Biochemical fractionation, co-immunoprecipitation, structural analyses, cellular localization assays\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — biochemical and structural analyses with multiple orthogonal methods, single lab\",\n      \"pmids\": [\"41910726\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Loss of TRIM46 (a ubiquitin ligase with roles in microtubule organization) in non-neuronal cells causes Golgi ribbon fragmentation and enhanced TFEB-driven lysosomal biogenesis. Golgi damage triggers CASM (conjugation of Atg8 proteins to single membranes) at the trans-Golgi, and genetic inhibition of CASM in TRIM46-deficient cells exacerbates Golgi morphology defects, indicating CASM acts to preserve Golgi integrity downstream of TRIM46 loss.\",\n      \"method\": \"TRIM46 knockout cells, LC3B/GABARAP colocalization, TFEB activation assays, genetic inhibition of CASM, confocal microscopy\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — preprint, single lab, localization and KO phenotype without full mechanistic dissection of TRIM46's direct role\",\n      \"pmids\": [\"bio_10.1101_2025.09.04.674289\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"TRIM46 is a RING-domain E3 ubiquitin ligase and microtubule-associated protein that, in neurons, forms plus-end-out parallel microtubule bundles and cross-bridges at the axon initial segment (required for microtubule fasciculation but dispensable for axon specification in vivo); in non-neuronal contexts it ubiquitinates and degrades multiple substrates including GPX4, HDAC1, PHLPP2, DUSP1, IκBα, Axin1, and SLC7A11 to regulate ferroptosis, NF-κB, AKT, and Wnt/β-catenin signaling, while its own protein levels are post-transcriptionally controlled by PTBP2-regulated alternative splicing coupled to NMD.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TRIM46 is a RING-domain E3 ubiquitin ligase and microtubule-associated protein that plays dual roles: organizing axonal microtubule architecture and regulating diverse signaling pathways through ubiquitin-mediated substrate degradation. In neurons, TRIM46 localizes to the axon initial segment where it forms the electron-dense cross-bridges that bundle parallel, plus-end-out microtubules; although knockout mice reveal that TRIM46 is essential for microtubule fasciculation, it is dispensable for axon specification and AIS formation in vivo [PMID:26671463, PMID:30967428, PMID:39251352]. Its neuron-specific expression is achieved through PTBP2-regulated alternative splicing coupled to nonsense-mediated mRNA decay, and its transport to the AIS depends on a KIF3B-enriched kinesin-2 complex [PMID:35440129, PMID:41910726]. Outside the nervous system, TRIM46 ubiquitinates and degrades multiple substrates—including PHLPP2, HDAC1, GPX4, IκBα, Axin1, DUSP1, and SLC7A11—thereby modulating AKT, NF-κB, Wnt/β-catenin, and ferroptosis pathways in contexts ranging from cancer chemoresistance to diabetic retinopathy and viral lung injury [PMID:35354796, PMID:34459501, PMID:34487731, PMID:36064447, PMID:35670901, PMID:39531094].\",\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"The first functional characterization of TRIM46 established it as a microtubule-organizing protein that drives uniform plus-end-out microtubule polarity at the nascent axon and AIS, framing it as a key determinant of neuronal polarity.\",\n      \"evidence\": \"Overexpression/knockdown in cultured neurons with live imaging, Tau missorting readouts, and cargo trafficking assays\",\n      \"pmids\": [\"26671463\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether TRIM46 directly cross-links microtubules or acts indirectly was unresolved\",\n        \"Whether TRIM46's role in cultured neurons reflects its requirement in vivo was untested\",\n        \"The E3 ligase activity of the RING domain was not examined in this neuronal context\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Ultrastructural analysis resolved that TRIM46 is the structural component of the electron-dense cross-bridges between fasciculated microtubules at the AIS, directly answering how microtubule bundling is achieved.\",\n      \"evidence\": \"Correlative light and electron microscopy with TRIM46 depletion in cultured rat hippocampal neurons\",\n      \"pmids\": [\"30967428\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The minimal domain of TRIM46 sufficient for cross-bridge formation was not defined\",\n        \"Whether cross-bridge formation depends on the RING domain or a separate structural motif was unknown\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"TRIM46 was shown to function as an E3 ubiquitin ligase for DUSP1, linking it to MAPK/NF-κB inflammatory signaling and revealing substrate activities beyond microtubule organization.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, knockdown/overexpression, and in vivo mouse model of TcdB-induced inflammation\",\n      \"pmids\": [\"31918570\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The ubiquitin chain type and RING-domain dependence were not demonstrated for DUSP1\",\n        \"No independent replication from a second laboratory\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identification of GPX4 and HDAC1 as TRIM46 ubiquitination substrates extended its E3 ligase repertoire to ferroptosis regulation and epigenetic control of DNA replication/repair, respectively, with RING-domain mutant confirmation for HDAC1.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, CRISPR knock-in of enhancer SNP (HDAC1 study), western blot, and in vivo tumor models\",\n      \"pmids\": [\"34487731\", \"34459501\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether GPX4 ubiquitination depends on the RING domain specifically was not tested\",\n        \"Whether substrate selectivity among diverse targets involves different adaptor proteins was unaddressed\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Mechanistic dissection of TRIM46 expression revealed that PTBP2-regulated alternative splicing and NMD control its neuron-specific accumulation during axonogenesis, explaining how a broadly transcribed gene achieves restricted protein expression.\",\n      \"evidence\": \"Alternative splicing analysis, NMD assays, PTBP2 manipulation, genetic exon deletion in neurons\",\n      \"pmids\": [\"35440129\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether additional RNA-binding proteins regulate TRIM46 splicing in non-neuronal tissues was unknown\",\n        \"Genetic exon deletion showed TRIM46 is instructive but not always required for AnkG localization, leaving redundant pathways unidentified\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Additional E3 ligase substrates—PHLPP2, IκBα, and Axin1—were identified, showing TRIM46 activates AKT/glycolysis, NF-κB, and Wnt/β-catenin pathways in cancer and fibrosis contexts; RING-mutant analysis for PHLPP2 confirmed catalytic dependence.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, RING-mutant overexpression, PDX models (PHLPP2), proteasome inhibitor rescue (Axin1), rat renal fibrosis model\",\n      \"pmids\": [\"35354796\", \"36064447\", \"35670901\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The structural basis for TRIM46 recognizing such diverse substrates is uncharacterized\",\n        \"Whether these non-neuronal substrates are relevant under physiological (non-pathological) conditions was not tested\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"TRIM46 knockout mice demonstrated that TRIM46 is dispensable for axon specification, AIS formation, and normal behavior in vivo—revising the prior model from cultured neurons—while confirming its requirement for microtubule fasciculation; AnkG was shown to restrict TRIM46 to the AIS.\",\n      \"evidence\": \"Constitutive TRIM46 knockout mice with immunohistochemistry, electron microscopy, and behavioral testing\",\n      \"pmids\": [\"39251352\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Compensatory mechanisms that substitute for TRIM46 in axon specification in vivo remain unidentified\",\n        \"Whether microtubule fasciculation loss has functional consequences under stress or aging was not tested\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"SLC7A11 was identified as a TRIM46 substrate linking it to ferroptosis and inflammation during influenza infection, and TRIM46 KO rats revealed roles in dendritic morphogenesis and interaction with FKBP5, expanding its neuronal functions beyond the AIS.\",\n      \"evidence\": \"Co-IP, cycloheximide chase, in vivo H1N1 mouse model (SLC7A11); CRISPR KO rats, Co-IP for FKBP5, morphological analysis\",\n      \"pmids\": [\"39531094\", \"38193537\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"SLC7A11 ubiquitination site(s) and chain linkage type not mapped\",\n        \"The mechanistic link between TRIM46-FKBP5 interaction and dendritic spine phenotypes is correlative\",\n        \"No independent replication of either finding\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"The mechanism of TRIM46 axonal delivery was resolved: a KIF3B-enriched, KAP3-associated kinesin-2 assembly distinct from the canonical KIF3A/B/KAP3 complex selectively transports TRIM46 to the AIS.\",\n      \"evidence\": \"Biochemical fractionation, co-immunoprecipitation, structural analyses, cellular localization assays\",\n      \"pmids\": [\"41910726\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether this transport mechanism is regulated during development or plasticity is unknown\",\n        \"Structural details of the TRIM46-kinesin-2 interface at atomic resolution are lacking\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TRIM46 achieves substrate selectivity across its many ubiquitination targets, whether its E3 ligase and microtubule-bundling activities are coordinated or independent, and what compensatory mechanisms maintain axon specification in its absence in vivo remain open questions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No structural model of TRIM46 exists to explain dual microtubule-binding and E3 ligase functions\",\n        \"The identity of redundant factors that compensate for TRIM46 loss in axon specification is unknown\",\n        \"Whether the diverse non-neuronal substrates reflect physiological or pathological roles has not been resolved\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [2, 3, 4, 5, 6, 8, 10]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 1, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0, 1, 9]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": []},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [2, 3, 4, 5, 6, 8, 10]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3, 5, 6, 8]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [2, 10]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [5, 6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"GPX4\",\n      \"HDAC1\",\n      \"PHLPP2\",\n      \"DUSP1\",\n      \"NFKBIA\",\n      \"AXIN1\",\n      \"SLC7A11\",\n      \"FKBP5\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}