TRIM46

TRIM46 is a microtubule-associated protein and RING-domain E3 ubiquitin ligase with distinct neuronal and non-neuronal functions. In neurons, it localizes to the newly specified axon and the axon initial segment (AIS), where it forms electron-dense cross-bridges between closely spaced, parallel, plus-end-out microtubules and organizes them into fascicles (PMID:26671463, PMID:30967428). Knockdown in cultured neurons disrupts axon specification and microtubule polarity (PMID:26671463), but in vivo knockout mice are viable with normal axon specification and AIS formation, establishing that TRIM46 is dispensable for these processes yet required for microtubule fasciculation; its proximal-axon enrichment is AnkG-independent, while AnkG restricts TRIM46 to the AIS (PMID:39251352). TRIM46 protein levels during axonogenesis are tuned post-transcriptionally through alternative cassette-exon usage, including NMD-coupled exon 8 inclusion and PTBP2-controlled exon 10 skipping (PMID:35440129), and its delivery to the AIS is mediated by a distinct KIF3B-enriched kinesin-2 assembly (PMID:41910726). In non-neuronal and cancer contexts, TRIM46 acts as an E3 ligase that ubiquitinates and degrades multiple substrates to activate downstream signaling: degradation of PHLPP2 activates AKT signaling to drive glycolysis and chemoresistance (PMID:35354796, PMID:41222281); ubiquitination of GPX4 and SLC7A11 promotes ferroptosis (PMID:34487731, PMID:39531094); degradation of IκBα and DUSP1 activates NF-κB and MAPK signaling and inflammatory responses (PMID:31918570, PMID:36064447); degradation of HDAC1 promotes proliferation and chemoresistance (PMID:34459501); and degradation of Axin1 activates Wnt/β-catenin signaling to drive epithelial-mesenchymal transition (PMID:35670901). RING-domain mutagenesis confirms these effects are E3 ligase-dependent (PMID:35354796).

1. 2015 High

   Established TRIM46 as a determinant of neuronal polarity by showing it organizes the axonal microtubule array, answering how axons acquire their characteristic uniform plus-end-out microtubule orientation.

   Evidence Knockdown in cultured neurons with live microtubule imaging, Tau localization, and cargo trafficking assays

   PMID:26671463

   Open questions at the time

   • Did not establish the molecular structure of the cross-bridges
   • Knockdown-based, leaving in vivo requirement untested
2. 2019 High

   Resolved the ultrastructural basis of TRIM46 action, showing it forms the electron-dense cross-bridges that hold AIS microtubules at defined spacing.

   Evidence Correlative light and electron microscopy with TRIM46 depletion and microtubule spacing quantification in rat hippocampal neurons

   PMID:30967428

   Open questions at the time

   • Did not define the structural domain mediating cross-bridge formation
   • In vivo relevance not yet tested
3. 2020 Medium

   First demonstrated TRIM46 as a functional E3 ligase outside neurons, ubiquitinating DUSP1 to activate MAPK/NF-κB inflammatory signaling, with NF-κB feeding back on TRIM46 expression.

   Evidence Co-IP/ubiquitination assays, siRNA knockdown, NF-κB reporter/ChIP, and an in vivo C. difficile model

   PMID:31918570

   Open questions at the time

   • Abstract-level methods, single lab
   • Direct ubiquitination linkage versus indirect effects not fully separated
4. 2021 High

   Extended TRIM46 substrate range to HDAC1 and GPX4, linking its ligase activity to proliferation/chemoresistance and to ferroptosis respectively.

   Evidence Co-IP, ubiquitination assays, CRISPR SNP knock-in, gene expression profiling, and ferroptosis readouts (lipid ROS, MDA, GSH) in breast cancer and retinal endothelial cells

   PMID:34459501 PMID:34487731

   Open questions at the time

   • RING-dependence not tested in the GPX4 study
   • Tissue-specificity of substrate selection unexplained
5. 2022 High

   Confirmed E3 ligase-dependence by RING-domain mutagenesis and broadened the substrate/pathway map to PHLPP2-AKT, IκBα-NF-κB, and Axin1-Wnt/β-catenin axes.

   Evidence RING-mutant overexpression, ubiquitination assays, rescue experiments, and in vivo PDX/fibrosis/permeability models across lung, renal, and retinal systems

   PMID:35354796 PMID:35670901 PMID:36064447

   Open questions at the time

   • What selects different substrates in different tissues is unknown
   • Direct ubiquitin chain topology not characterized
6. 2022 High

   Revealed how TRIM46 protein levels are set during axonogenesis through coupled alternative splicing, NMD, and protein-stability control.

   Evidence Alternative splicing analysis, NMD reporters, PTBP2 manipulation, cassette-exon deletion, and protein stability assays

   PMID:35440129

   Open questions at the time

   • Upstream regulators coordinating these layers not fully mapped
   • Functional consequence of the unstable exon-10-skipped isoform unclear
7. 2024 High

   In vivo knockout overturned the knockdown-based view, showing TRIM46 is dispensable for axon specification and AIS formation but required for microtubule fasciculation, and clarified its localization hierarchy with AnkG.

   Evidence TRIM46 knockout mouse with behavior, histology, EM of fasciculation, and AnkG knockout epistasis

   PMID:39251352

   Open questions at the time

   • Why knockdown and knockout phenotypes diverge not mechanistically resolved
   • Functional consequence of lost fasciculation for neuronal physiology not defined
8. 2024 Medium

   Linked TRIM46 to additional brain partners and substrates, identifying FKBP5 interaction in vivo and SLC7A11 ubiquitination promoting ferroptosis.

   Evidence CRISPR KO rat with endogenous Co-IP and morphological/behavioral analyses; Co-IP, cycloheximide chase, and lung injury models for SLC7A11

   PMID:38193537 PMID:39531094

   Open questions at the time

   • TRIM46-FKBP5 downstream signaling link is correlative in KO
   • Whether FKBP5 is a ubiquitination substrate untested
9. 2024 Low

   Proposed TRIM46 acts upstream of a Golgi damage / TFEB lysosomal biogenesis response, expanding its potential cellular roles beyond microtubules and cancer signaling.

   Evidence TRIM46 KO cell lines, CASM genetic inhibition, Golgi morphology imaging, and TFEB activation assays (preprint)

   PMID:bio_10.1101_2025.09.04.674289

   Open questions at the time

   • Preprint, not peer-reviewed; direct mechanistic role of TRIM46 in CASM/Golgi pathway not established
   • Whether the effect requires E3 ligase activity untested
10. 2026 Medium

    Identified the transport machinery delivering TRIM46 to the AIS, defining a distinct KIF3B-enriched kinesin-2 assembly with cargo selectivity.

    Evidence Biochemical fractionation, Co-IP, cellular localization, and tail-domain structural analyses

    PMID:41910726

    Open questions at the time

    • Cargo selectivity model not reconstituted in vitro
    • Structural basis of tail-domain selectivity inferred, not directly proven

• How a single E3 ligase / microtubule organizer selects among such divergent substrates and roles across neuronal and non-neuronal tissues, and whether the cancer substrate repertoire operates in vivo at physiological expression, remains unresolved.
• No unifying determinant of substrate/context selectivity identified
• Many substrate findings rest on single-lab overexpression contexts
• No human disease link established by direct genetic evidence in the corpus