{"gene":"DPYSL4","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2018,"finding":"DPYSL4 is a p53 transcriptional target that associates with mitochondrial supercomplexes via its dihydropyrimidinase-like domain; overexpression upregulates ATP production and oxygen consumption, while deletion of the dihydropyrimidinase-like domain abolishes both mitochondrial supercomplex association and the ability to stimulate ATP production and suppress cancer cell invasion.","method":"ChIP-seq (p53 binding), siRNA/CRISPR-Cas9 knockdown, domain-deletion mutant overexpression, ATP/oxygen consumption assays, co-fractionation with mitochondrial supercomplexes, mouse xenograft and lung-metastasis models","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (ChIP-seq, CRISPR KO, domain mutagenesis, biochemical fractionation, in vivo xenograft) in a single rigorous study","pmids":["30061407"],"is_preprint":false},{"year":2000,"finding":"CRMP3 (DPYSL4) physically associates with CRAM (a novel unc-33 family protein) when co-expressed in COS-7 cells and forms a large complex in rat brain; brain extracts show co-immunoprecipitation of CRMP3 with proteins bearing protein-tyrosine kinase activity.","method":"Co-expression in COS-7 cells with co-immunoprecipitation; immunoprecipitation of rat brain extracts followed by protein-tyrosine kinase activity assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — reciprocal co-IP in cell system and native brain extracts, single lab, two complementary methods","pmids":["10851247"],"is_preprint":false},{"year":2007,"finding":"CRMP3 (DPYSL4) is required for normal hippocampal CA1 apical and basal dendrite morphogenesis and spine formation in vivo; CRMP3-knockout mice display abnormal dendrite undulation, reduced length, altered branching, and impaired long-term potentiation.","method":"Targeted gene disruption in mice; immunohistochemistry; Golgi staining of dendrite morphology; electrophysiological LTP measurement","journal":"FASEB journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genetic KO with multiple orthogonal morphological and electrophysiological readouts","pmids":["17785607"],"is_preprint":false},{"year":2009,"finding":"Full-length CRMP3 inhibits tubulin polymerization and neurite outgrowth in mature cerebellar granule neurons; calpain-cleaved N-terminal truncated CRMP3 undergoes nuclear translocation through nuclear pores and associates with nuclear vimentin, causing nuclear condensation.","method":"Overexpression of full-length vs. truncated CRMP3 in cultured cerebellar granule neurons; in vitro tubulin polymerization assay; nuclear protein pull-down with mass spectrometry; co-localization immunofluorescence; vimentin-null neuron experiments","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro polymerization assay and pulldown/MS, single lab, multiple orthogonal methods","pmids":["19559021"],"is_preprint":false},{"year":2013,"finding":"The C-terminus of CRMP3 is necessary for its dendritogenic capacity and supports active transport in hippocampal neurons; C-terminally truncated CRMP3 phenocopies CRMP3 gene deletion and acts as a dominant-negative inhibitor. CRMP3-mediated dendritic growth requires L-type voltage-gated calcium channel activity, as L-type channel inhibitors block CRMP3-induced dendritic growth and augmented somatic Ca2+ influx.","method":"Deletional domain mapping by overexpression in hippocampal neurons; siRNA knockdown; voltage-gated calcium channel pharmacological inhibition; Ca2+ imaging","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — deletional mutagenesis combined with pharmacological and imaging approaches, single lab","pmids":["23868973"],"is_preprint":false},{"year":2022,"finding":"CRMP3 interacts with semaphorin 4C (SEMA4C) and functions as a deacetylase for α-tubulin; SEMA4C stabilizes CRMP3 to increase α-tubulin deacetylation and promote colon cancer cell motility, an effect attenuated by HDAC inhibitors.","method":"Co-immunoprecipitation (SEMA4C–CRMP3 interaction); Western blotting for tubulin acetylation; ectopic overexpression and neutralizing antibody treatment; HDAC inhibitor treatment","journal":"American journal of cancer research","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — co-IP interaction plus functional Western blot and pharmacological rescue, single lab, multiple methods but no in vitro deacetylase reconstitution","pmids":["35261797"],"is_preprint":false},{"year":2013,"finding":"Dpysl4 (CRMP3/DPYSL4) regulates dental epithelial cell proliferation, polarization, and differentiation during tooth germ morphogenesis; knockdown promotes proliferation and inhibits differentiation of inner enamel epithelial cells into pre-ameloblasts, while overexpression inhibits growth and increases Msx2 expression.","method":"Knockdown and overexpression of Dpysl4 in tooth germ; analysis of cell polarization, columnar structure formation, and ameloblast marker gene expression","journal":"International journal of biological sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss- and gain-of-function with multiple cellular phenotype readouts, single lab","pmids":["23630450"],"is_preprint":false},{"year":2025,"finding":"CRMP3 directly binds KATNA1 (katanin p60) via CRMP3's D region (residues 64–413) and KATNA1's MIT domain (residues 1–77); this interaction enhances KATNA1's microtubule-severing efficiency and promotes hippocampal neurite length and branching, with genetic knockout of either or both proteins inhibiting neurite outgrowth.","method":"GST pulldown, co-immunoprecipitation, domain-mapping mutants, microtubule-severing assays, overexpression and CRISPR knockout in cultured hippocampal neurons","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — reciprocal pulldown/co-IP with domain mapping, in vitro severing assay, and genetic KO, multiple orthogonal methods in one study","pmids":["39938451"],"is_preprint":false}],"current_model":"DPYSL4/CRMP3 is a multifunctional scaffold protein that (1) is transcriptionally induced by p53 and associates with mitochondrial supercomplexes via its dihydropyrimidinase-like domain to stimulate oxidative phosphorylation and suppress cancer invasion; (2) promotes hippocampal dendrite arborization and LTP through a C-terminal domain linked to L-type calcium channel-dependent Ca2+ influx; (3) modulates microtubule dynamics by inhibiting tubulin polymerization in its full-length form and, upon calpain cleavage, translocates to the nucleus to associate with vimentin; (4) enhances katanin p60 (KATNA1) microtubule-severing activity by direct physical interaction; (5) associates with CRAM and protein-tyrosine kinases in developing brain; and (6) acts as an α-tubulin deacetylase stabilized by SEMA4C to drive cancer cell motility."},"narrative":{"mechanistic_narrative":"DPYSL4 (CRMP3) is a multifunctional cytoskeletal regulator that links microtubule dynamics to neuronal morphogenesis and, independently, to mitochondrial energetics and cancer suppression [PMID:30061407, PMID:17785607, PMID:39938451]. In its neuronal role, DPYSL4 is required for hippocampal CA1 dendrite arborization, spine formation, and long-term potentiation [PMID:17785607], a dendritogenic activity that depends on its C-terminus and on L-type voltage-gated calcium channel-dependent Ca2+ influx [PMID:23868973]. At the molecular level it shapes the microtubule cytoskeleton through two opposing modes: full-length DPYSL4 inhibits tubulin polymerization and neurite outgrowth, whereas calpain cleavage generates an N-terminally truncated form that translocates to the nucleus and associates with vimentin to drive nuclear condensation [PMID:19559021]; it also directly binds katanin p60 (KATNA1) via its D region engaging the KATNA1 MIT domain, enhancing microtubule-severing efficiency to promote neurite length and branching [PMID:39938451]. In a distinct pathway, DPYSL4 is a p53 transcriptional target whose dihydropyrimidinase-like domain mediates association with mitochondrial supercomplexes, stimulating ATP production and oxygen consumption and suppressing cancer cell invasion and metastasis [PMID:30061407]. In a cancer-promoting context it interacts with SEMA4C, which stabilizes DPYSL4 to drive α-tubulin deacetylation and colon cancer cell motility [PMID:35261797]. DPYSL4 also regulates dental epithelial proliferation and differentiation during tooth germ morphogenesis [PMID:23630450].","teleology":[{"year":2000,"claim":"Established that CRMP3/DPYSL4 functions within protein complexes in brain, providing the first physical-partner context by linking it to a CRAM family protein and to tyrosine kinase activity.","evidence":"Co-expression and reciprocal co-IP in COS-7 cells plus IP of rat brain extracts coupled to tyrosine kinase activity assay","pmids":["10851247"],"confidence":"Medium","gaps":["Identity of the associated tyrosine kinase not resolved","Functional consequence of the CRAM complex unknown","No structural mapping of the interaction"]},{"year":2007,"claim":"Defined an in vivo neuronal requirement, showing DPYSL4 is needed for hippocampal dendrite morphogenesis, spine formation, and synaptic plasticity rather than being merely a brain-enriched marker.","evidence":"Targeted gene disruption in mice with Golgi staining, immunohistochemistry, and LTP electrophysiology","pmids":["17785607"],"confidence":"High","gaps":["Molecular pathway connecting DPYSL4 to dendrite growth not defined in this study","Mechanism of LTP impairment unresolved"]},{"year":2009,"claim":"Revealed a dual cytoskeletal mechanism in which full-length DPYSL4 inhibits tubulin polymerization while calpain cleavage redirects it to the nucleus to bind vimentin, connecting proteolytic processing to subcellular relocalization.","evidence":"In vitro tubulin polymerization assays, overexpression of full-length vs. truncated forms, nuclear pulldown/MS, and vimentin-null neuron experiments","pmids":["19559021"],"confidence":"Medium","gaps":["Trigger and physiological context for calpain cleavage unclear","Functional consequence of nuclear vimentin association beyond condensation not defined","Single lab"]},{"year":2013,"claim":"Mapped the dendritogenic activity to the C-terminus and tied DPYSL4-driven dendrite growth to L-type calcium channel-dependent Ca2+ influx, linking morphology to signaling.","evidence":"Deletional domain mapping, siRNA knockdown, L-type channel pharmacology, and Ca2+ imaging in hippocampal neurons","pmids":["23868973"],"confidence":"Medium","gaps":["How the C-terminus couples to calcium channels mechanistically unknown","Direct binding partners mediating Ca2+ effect not identified"]},{"year":2013,"claim":"Extended DPYSL4 function beyond neurons by showing it controls dental epithelial proliferation, polarization, and differentiation during tooth germ morphogenesis.","evidence":"Knockdown and overexpression in tooth germ with cellular phenotype and ameloblast marker analysis","pmids":["23630450"],"confidence":"Medium","gaps":["Molecular effectors in epithelium not defined","Relationship to its cytoskeletal activities untested"]},{"year":2018,"claim":"Identified a non-cytoskeletal role as a p53 target that engages mitochondrial supercomplexes through its dihydropyrimidinase-like domain to boost oxidative phosphorylation and suppress cancer invasion.","evidence":"ChIP-seq, CRISPR/siRNA knockdown, domain-deletion mutagenesis, mitochondrial co-fractionation, ATP/O2 assays, and xenograft/metastasis models","pmids":["30061407"],"confidence":"High","gaps":["Identity of the supercomplex components contacted not resolved","Mechanism by which OXPHOS stimulation suppresses invasion unclear"]},{"year":2022,"claim":"Assigned an α-tubulin deacetylase function stabilized by SEMA4C, defining a cancer-promoting axis that opposes the tumor-suppressive mitochondrial role.","evidence":"Co-IP of SEMA4C–CRMP3, tubulin acetylation Westerns, overexpression/neutralizing antibody, and HDAC inhibitor rescue in colon cancer cells","pmids":["35261797"],"confidence":"Medium","gaps":["No in vitro deacetylase reconstitution to confirm direct enzymatic activity","Reconciliation with tumor-suppressive role in other contexts unaddressed"]},{"year":2025,"claim":"Provided a direct biochemical mechanism for DPYSL4 in neurite growth by showing its D region binds the KATNA1 MIT domain to enhance microtubule-severing.","evidence":"GST pulldown, co-IP, domain-mapping mutants, in vitro microtubule-severing assays, and CRISPR knockout in hippocampal neurons","pmids":["39938451"],"confidence":"High","gaps":["How severing enhancement integrates with the tubulin-polymerization-inhibiting activity unresolved","Regulation of the DPYSL4–KATNA1 interaction unknown"]},{"year":null,"claim":"How DPYSL4's opposing molecular activities—tubulin polymerization inhibition, katanin-enhanced severing, α-tubulin deacetylation, and mitochondrial supercomplex association—are coordinated and switched between contexts remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unifying model linking cytoskeletal and mitochondrial roles","Context-dependent tumor-suppressive vs. tumor-promoting behavior unexplained","Upstream regulation of calpain processing and SEMA4C stabilization unmapped"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[3,7]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[7]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[3,7]}],"pathway":[{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[2,4]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[0,5]}],"complexes":["mitochondrial respiratory supercomplexes"],"partners":["KATNA1","SEMA4C","CRAM","VIMENTIN"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O14531","full_name":"Dihydropyrimidinase-related protein 4","aliases":["Collapsin response mediator protein 3","CRMP-3","UNC33-like phosphoprotein 4","ULIP-4"],"length_aa":572,"mass_kda":61.9,"function":"Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance, neuronal growth cone collapse and cell migration (By similarity)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/O14531/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DPYSL4","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/DPYSL4","total_profiled":1310},"omim":[{"mim_id":"608407","title":"DIHYDROPYRIMIDINASE-LIKE 4; DPYSL4","url":"https://www.omim.org/entry/608407"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Mitochondria","reliability":"Approved"},{"location":"Vesicles","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":33.8},{"tissue":"heart muscle","ntpm":33.0}],"url":"https://www.proteinatlas.org/search/DPYSL4"},"hgnc":{"alias_symbol":["ULIP4","DRP-4","CRMP3"],"prev_symbol":[]},"alphafold":{"accession":"O14531","domains":[{"cath_id":"3.20.20.140","chopping":"66-486","consensus_level":"high","plddt":97.419,"start":66,"end":486}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O14531","model_url":"https://alphafold.ebi.ac.uk/files/AF-O14531-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O14531-F1-predicted_aligned_error_v6.png","plddt_mean":90.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DPYSL4","jax_strain_url":"https://www.jax.org/strain/search?query=DPYSL4"},"sequence":{"accession":"O14531","fasta_url":"https://rest.uniprot.org/uniprotkb/O14531.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O14531/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O14531"}},"corpus_meta":[{"pmid":"10851247","id":"PMC_10851247","title":"Identification of CRAM, a novel unc-33 gene family protein that associates with CRMP3 and protein-tyrosine kinase(s) in the developing rat brain.","date":"2000","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10851247","citation_count":84,"is_preprint":false},{"pmid":"17785607","id":"PMC_17785607","title":"CRMP3 is required for hippocampal CA1 dendritic organization and plasticity.","date":"2007","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/17785607","citation_count":66,"is_preprint":false},{"pmid":"30061407","id":"PMC_30061407","title":"p53-inducible DPYSL4 associates with mitochondrial supercomplexes and regulates energy metabolism in adipocytes and cancer cells.","date":"2018","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/30061407","citation_count":51,"is_preprint":false},{"pmid":"17403058","id":"PMC_17403058","title":"Antibodies to CRMP3-4 associated with limbic encephalitis and thymoma.","date":"2007","source":"Clinical and experimental immunology","url":"https://pubmed.ncbi.nlm.nih.gov/17403058","citation_count":30,"is_preprint":false},{"pmid":"19559021","id":"PMC_19559021","title":"Characterization of the role of full-length CRMP3 and its calpain-cleaved product in inhibiting microtubule polymerization and neurite outgrowth.","date":"2009","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/19559021","citation_count":25,"is_preprint":false},{"pmid":"23868973","id":"PMC_23868973","title":"Mapping CRMP3 domains involved in dendrite morphogenesis and voltage-gated calcium channel regulation.","date":"2013","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/23868973","citation_count":22,"is_preprint":false},{"pmid":"35261797","id":"PMC_35261797","title":"Semaphorin 4C promotes motility and immunosuppressive activity of cancer cells via CRMP3 and PD-L1.","date":"2022","source":"American journal of cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/35261797","citation_count":7,"is_preprint":false},{"pmid":"23630450","id":"PMC_23630450","title":"Dpysl4 is involved in tooth germ morphogenesis through growth regulation, polarization and differentiation of dental epithelial cells.","date":"2013","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/23630450","citation_count":7,"is_preprint":false},{"pmid":"39938451","id":"PMC_39938451","title":"The interaction between KATNA1 and CRMP3 modulates microtubule dynamics and neurite outgrowth.","date":"2025","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/39938451","citation_count":3,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6515,"output_tokens":2248,"usd":0.026632,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9326,"output_tokens":3333,"usd":0.064977,"stage2_stop_reason":"end_turn"},"total_usd":0.091609,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"DPYSL4 is a p53 transcriptional target that associates with mitochondrial supercomplexes via its dihydropyrimidinase-like domain; overexpression upregulates ATP production and oxygen consumption, while deletion of the dihydropyrimidinase-like domain abolishes both mitochondrial supercomplex association and the ability to stimulate ATP production and suppress cancer cell invasion.\",\n      \"method\": \"ChIP-seq (p53 binding), siRNA/CRISPR-Cas9 knockdown, domain-deletion mutant overexpression, ATP/oxygen consumption assays, co-fractionation with mitochondrial supercomplexes, mouse xenograft and lung-metastasis models\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (ChIP-seq, CRISPR KO, domain mutagenesis, biochemical fractionation, in vivo xenograft) in a single rigorous study\",\n      \"pmids\": [\"30061407\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"CRMP3 (DPYSL4) physically associates with CRAM (a novel unc-33 family protein) when co-expressed in COS-7 cells and forms a large complex in rat brain; brain extracts show co-immunoprecipitation of CRMP3 with proteins bearing protein-tyrosine kinase activity.\",\n      \"method\": \"Co-expression in COS-7 cells with co-immunoprecipitation; immunoprecipitation of rat brain extracts followed by protein-tyrosine kinase activity assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — reciprocal co-IP in cell system and native brain extracts, single lab, two complementary methods\",\n      \"pmids\": [\"10851247\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"CRMP3 (DPYSL4) is required for normal hippocampal CA1 apical and basal dendrite morphogenesis and spine formation in vivo; CRMP3-knockout mice display abnormal dendrite undulation, reduced length, altered branching, and impaired long-term potentiation.\",\n      \"method\": \"Targeted gene disruption in mice; immunohistochemistry; Golgi staining of dendrite morphology; electrophysiological LTP measurement\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genetic KO with multiple orthogonal morphological and electrophysiological readouts\",\n      \"pmids\": [\"17785607\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Full-length CRMP3 inhibits tubulin polymerization and neurite outgrowth in mature cerebellar granule neurons; calpain-cleaved N-terminal truncated CRMP3 undergoes nuclear translocation through nuclear pores and associates with nuclear vimentin, causing nuclear condensation.\",\n      \"method\": \"Overexpression of full-length vs. truncated CRMP3 in cultured cerebellar granule neurons; in vitro tubulin polymerization assay; nuclear protein pull-down with mass spectrometry; co-localization immunofluorescence; vimentin-null neuron experiments\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro polymerization assay and pulldown/MS, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"19559021\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"The C-terminus of CRMP3 is necessary for its dendritogenic capacity and supports active transport in hippocampal neurons; C-terminally truncated CRMP3 phenocopies CRMP3 gene deletion and acts as a dominant-negative inhibitor. CRMP3-mediated dendritic growth requires L-type voltage-gated calcium channel activity, as L-type channel inhibitors block CRMP3-induced dendritic growth and augmented somatic Ca2+ influx.\",\n      \"method\": \"Deletional domain mapping by overexpression in hippocampal neurons; siRNA knockdown; voltage-gated calcium channel pharmacological inhibition; Ca2+ imaging\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — deletional mutagenesis combined with pharmacological and imaging approaches, single lab\",\n      \"pmids\": [\"23868973\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CRMP3 interacts with semaphorin 4C (SEMA4C) and functions as a deacetylase for α-tubulin; SEMA4C stabilizes CRMP3 to increase α-tubulin deacetylation and promote colon cancer cell motility, an effect attenuated by HDAC inhibitors.\",\n      \"method\": \"Co-immunoprecipitation (SEMA4C–CRMP3 interaction); Western blotting for tubulin acetylation; ectopic overexpression and neutralizing antibody treatment; HDAC inhibitor treatment\",\n      \"journal\": \"American journal of cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — co-IP interaction plus functional Western blot and pharmacological rescue, single lab, multiple methods but no in vitro deacetylase reconstitution\",\n      \"pmids\": [\"35261797\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Dpysl4 (CRMP3/DPYSL4) regulates dental epithelial cell proliferation, polarization, and differentiation during tooth germ morphogenesis; knockdown promotes proliferation and inhibits differentiation of inner enamel epithelial cells into pre-ameloblasts, while overexpression inhibits growth and increases Msx2 expression.\",\n      \"method\": \"Knockdown and overexpression of Dpysl4 in tooth germ; analysis of cell polarization, columnar structure formation, and ameloblast marker gene expression\",\n      \"journal\": \"International journal of biological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss- and gain-of-function with multiple cellular phenotype readouts, single lab\",\n      \"pmids\": [\"23630450\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CRMP3 directly binds KATNA1 (katanin p60) via CRMP3's D region (residues 64–413) and KATNA1's MIT domain (residues 1–77); this interaction enhances KATNA1's microtubule-severing efficiency and promotes hippocampal neurite length and branching, with genetic knockout of either or both proteins inhibiting neurite outgrowth.\",\n      \"method\": \"GST pulldown, co-immunoprecipitation, domain-mapping mutants, microtubule-severing assays, overexpression and CRISPR knockout in cultured hippocampal neurons\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — reciprocal pulldown/co-IP with domain mapping, in vitro severing assay, and genetic KO, multiple orthogonal methods in one study\",\n      \"pmids\": [\"39938451\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DPYSL4/CRMP3 is a multifunctional scaffold protein that (1) is transcriptionally induced by p53 and associates with mitochondrial supercomplexes via its dihydropyrimidinase-like domain to stimulate oxidative phosphorylation and suppress cancer invasion; (2) promotes hippocampal dendrite arborization and LTP through a C-terminal domain linked to L-type calcium channel-dependent Ca2+ influx; (3) modulates microtubule dynamics by inhibiting tubulin polymerization in its full-length form and, upon calpain cleavage, translocates to the nucleus to associate with vimentin; (4) enhances katanin p60 (KATNA1) microtubule-severing activity by direct physical interaction; (5) associates with CRAM and protein-tyrosine kinases in developing brain; and (6) acts as an α-tubulin deacetylase stabilized by SEMA4C to drive cancer cell motility.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DPYSL4 (CRMP3) is a multifunctional cytoskeletal regulator that links microtubule dynamics to neuronal morphogenesis and, independently, to mitochondrial energetics and cancer suppression [#0, #2, #7]. In its neuronal role, DPYSL4 is required for hippocampal CA1 dendrite arborization, spine formation, and long-term potentiation [#2], a dendritogenic activity that depends on its C-terminus and on L-type voltage-gated calcium channel-dependent Ca2+ influx [#4]. At the molecular level it shapes the microtubule cytoskeleton through two opposing modes: full-length DPYSL4 inhibits tubulin polymerization and neurite outgrowth, whereas calpain cleavage generates an N-terminally truncated form that translocates to the nucleus and associates with vimentin to drive nuclear condensation [#3]; it also directly binds katanin p60 (KATNA1) via its D region engaging the KATNA1 MIT domain, enhancing microtubule-severing efficiency to promote neurite length and branching [#7]. In a distinct pathway, DPYSL4 is a p53 transcriptional target whose dihydropyrimidinase-like domain mediates association with mitochondrial supercomplexes, stimulating ATP production and oxygen consumption and suppressing cancer cell invasion and metastasis [#0]. In a cancer-promoting context it interacts with SEMA4C, which stabilizes DPYSL4 to drive \\u03b1-tubulin deacetylation and colon cancer cell motility [#5]. DPYSL4 also regulates dental epithelial proliferation and differentiation during tooth germ morphogenesis [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established that CRMP3/DPYSL4 functions within protein complexes in brain, providing the first physical-partner context by linking it to a CRAM family protein and to tyrosine kinase activity.\",\n      \"evidence\": \"Co-expression and reciprocal co-IP in COS-7 cells plus IP of rat brain extracts coupled to tyrosine kinase activity assay\",\n      \"pmids\": [\"10851247\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Identity of the associated tyrosine kinase not resolved\", \"Functional consequence of the CRAM complex unknown\", \"No structural mapping of the interaction\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Defined an in vivo neuronal requirement, showing DPYSL4 is needed for hippocampal dendrite morphogenesis, spine formation, and synaptic plasticity rather than being merely a brain-enriched marker.\",\n      \"evidence\": \"Targeted gene disruption in mice with Golgi staining, immunohistochemistry, and LTP electrophysiology\",\n      \"pmids\": [\"17785607\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Molecular pathway connecting DPYSL4 to dendrite growth not defined in this study\", \"Mechanism of LTP impairment unresolved\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Revealed a dual cytoskeletal mechanism in which full-length DPYSL4 inhibits tubulin polymerization while calpain cleavage redirects it to the nucleus to bind vimentin, connecting proteolytic processing to subcellular relocalization.\",\n      \"evidence\": \"In vitro tubulin polymerization assays, overexpression of full-length vs. truncated forms, nuclear pulldown/MS, and vimentin-null neuron experiments\",\n      \"pmids\": [\"19559021\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Trigger and physiological context for calpain cleavage unclear\", \"Functional consequence of nuclear vimentin association beyond condensation not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Mapped the dendritogenic activity to the C-terminus and tied DPYSL4-driven dendrite growth to L-type calcium channel-dependent Ca2+ influx, linking morphology to signaling.\",\n      \"evidence\": \"Deletional domain mapping, siRNA knockdown, L-type channel pharmacology, and Ca2+ imaging in hippocampal neurons\",\n      \"pmids\": [\"23868973\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"How the C-terminus couples to calcium channels mechanistically unknown\", \"Direct binding partners mediating Ca2+ effect not identified\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Extended DPYSL4 function beyond neurons by showing it controls dental epithelial proliferation, polarization, and differentiation during tooth germ morphogenesis.\",\n      \"evidence\": \"Knockdown and overexpression in tooth germ with cellular phenotype and ameloblast marker analysis\",\n      \"pmids\": [\"23630450\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Molecular effectors in epithelium not defined\", \"Relationship to its cytoskeletal activities untested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identified a non-cytoskeletal role as a p53 target that engages mitochondrial supercomplexes through its dihydropyrimidinase-like domain to boost oxidative phosphorylation and suppress cancer invasion.\",\n      \"evidence\": \"ChIP-seq, CRISPR/siRNA knockdown, domain-deletion mutagenesis, mitochondrial co-fractionation, ATP/O2 assays, and xenograft/metastasis models\",\n      \"pmids\": [\"30061407\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Identity of the supercomplex components contacted not resolved\", \"Mechanism by which OXPHOS stimulation suppresses invasion unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Assigned an \\u03b1-tubulin deacetylase function stabilized by SEMA4C, defining a cancer-promoting axis that opposes the tumor-suppressive mitochondrial role.\",\n      \"evidence\": \"Co-IP of SEMA4C\\u2013CRMP3, tubulin acetylation Westerns, overexpression/neutralizing antibody, and HDAC inhibitor rescue in colon cancer cells\",\n      \"pmids\": [\"35261797\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No in vitro deacetylase reconstitution to confirm direct enzymatic activity\", \"Reconciliation with tumor-suppressive role in other contexts unaddressed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Provided a direct biochemical mechanism for DPYSL4 in neurite growth by showing its D region binds the KATNA1 MIT domain to enhance microtubule-severing.\",\n      \"evidence\": \"GST pulldown, co-IP, domain-mapping mutants, in vitro microtubule-severing assays, and CRISPR knockout in hippocampal neurons\",\n      \"pmids\": [\"39938451\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"How severing enhancement integrates with the tubulin-polymerization-inhibiting activity unresolved\", \"Regulation of the DPYSL4\\u2013KATNA1 interaction unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How DPYSL4's opposing molecular activities\\u2014tubulin polymerization inhibition, katanin-enhanced severing, \\u03b1-tubulin deacetylation, and mitochondrial supercomplex association\\u2014are coordinated and switched between contexts remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No unifying model linking cytoskeletal and mitochondrial roles\", \"Context-dependent tumor-suppressive vs. tumor-promoting behavior unexplained\", \"Upstream regulation of calpain processing and SEMA4C stabilization unmapped\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [3, 7]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [3, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [2, 4]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [0, 5]}\n    ],\n    \"complexes\": [\"mitochondrial respiratory supercomplexes\"],\n    \"partners\": [\"KATNA1\", \"SEMA4C\", \"CRAM\", \"vimentin\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}