{"gene":"UNC5D","run_date":"2026-04-28T21:43:01","timeline":{"discoveries":[{"year":2008,"finding":"UNC5D (UNC5H4) is a direct transcriptional target of p53: p53 binds to two tandem responsive elements within intron 1 of UNC5D, as demonstrated by luciferase reporter assay and ChIP analysis, and drives UNC5D expression during DNA damage-induced apoptosis.","method":"Luciferase reporter assay, ChIP analysis, siRNA knockdown, p53 overexpression in p53-deficient cells","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods (ChIP, luciferase, siRNA, overexpression) in a single study","pmids":["18402767"],"is_preprint":false},{"year":2013,"finding":"Upon NGF withdrawal, UNC5D is cleaved by caspases 2/3, and the released intracellular fragment translocates into the nucleus where it interacts with E2F1 to selectively transactivate proapoptotic target genes, forming a positive feedback loop with p53 and E2F1. Netrin-1 strongly inhibits UNC5D cleavage and apoptosis induction.","method":"Caspase cleavage assays, nuclear fractionation, Co-IP of UNC5D intracellular fragment with E2F1, Unc5d knockout mouse model (dorsal root ganglia neuron counts, NGF-depletion apoptosis assay)","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods including genetic KO, Co-IP, and functional apoptosis assays","pmids":["23778138"],"is_preprint":false},{"year":2013,"finding":"Unc5d knockout mice show a significant increase in dorsal root ganglia neurons and resistance to NGF depletion-induced apoptosis in sympathetic neurons compared to wild-type, establishing UNC5D's role in NGF-dependence-mediated programmed cell death in vivo.","method":"Unc5d-/- mouse model, neuron counting, NGF depletion apoptosis assay","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 — clean genetic KO with specific quantitative phenotypic readout","pmids":["23778138"],"is_preprint":false},{"year":2011,"finding":"Netrin-4 binds to UNC5D-expressing cells (cell surface binding assay) and reduces cell death of unc5d-expressing layer 4 cortical cells in vitro, identifying netrin-4 as a functional ligand for UNC5D in cortical cell survival, with lamina-specific effects.","method":"Cell surface binding assay, in vitro cell death assay with exogenous netrin-4 application","journal":"Cerebral cortex","confidence":"Medium","confidence_rationale":"Tier 2-3 — direct binding assay and functional rescue, single lab","pmids":["21216843"],"is_preprint":false},{"year":2008,"finding":"UNC5D protein is localized in multipolar migrating cells in the subventricular zone throughout cortical development, and the Svet1 RNA (SVZ marker) is part of the primary transcript of Unc5d (located in intron 1), retained in the nucleus but not transported to cytoplasm.","method":"In situ hybridization, immunofluorescence, nuclear/cytoplasmic fractionation of RNA","journal":"Molecular and cellular neurosciences","confidence":"Medium","confidence_rationale":"Tier 2-3 — direct localization with mechanistic implication for Unc5d transcription, single lab","pmids":["18547816"],"is_preprint":false},{"year":2014,"finding":"UNC5D overexpression suppresses bladder cancer cell proliferation and sensitizes cells to cisplatin-induced apoptosis via the UNC5D/DAPK (death-associated protein kinase) pathway; DAPK silencing inhibits UNC5D-mediated apoptosis, and cisplatin induces DAPK dephosphorylation alongside UNC5D upregulation.","method":"MTT assay, TUNEL staining, colony formation assay, Western blot, siRNA knockdown of UNC5D and DAPK","journal":"The Journal of urology","confidence":"Medium","confidence_rationale":"Tier 2-3 — epistasis established by double knockdown, single lab, multiple readouts","pmids":["24518784"],"is_preprint":false},{"year":2019,"finding":"UNC5D recruits and activates death-associated protein kinase 1 (DAPK1), which is essential for UNC5D's metastasis-suppressive function in prostate cancer cells; UNC5D ectopic expression reduces migration and invasion in vitro and in vivo.","method":"Ectopic expression, siRNA knockdown, migration/invasion assays, in vivo tumor models, DAPK1 activation assays","journal":"Cancer science","confidence":"Medium","confidence_rationale":"Tier 2-3 — functional epistasis with DAPK1 and in vivo validation, single lab","pmids":["30632669"],"is_preprint":false},{"year":2014,"finding":"UNC5D induces apoptosis in neuroblastoma cells through a mechanism requiring caspase cleavage and the death domain; netrin-1 completely abolishes UNC5D-induced apoptosis, confirming dependence receptor behavior.","method":"Overexpression, netrin-1 rescue experiment, caspase cleavage assay, death domain deletion construct","journal":"Tumour biology","confidence":"Medium","confidence_rationale":"Tier 2-3 — functional domain dissection and ligand rescue, single lab","pmids":["24519068"],"is_preprint":false},{"year":2014,"finding":"UNC5D expression induces phosphorylation of p53 at serine-15, suggesting UNC5D can act upstream of p53 to amplify p53-dependent apoptosis, in addition to being a p53 transcriptional target.","method":"Western blot of p53 phosphorylation in UNC5D stable clones co-expressing p53, luciferase reporter assay","journal":"Molecular medicine reports","confidence":"Low","confidence_rationale":"Tier 3 — single lab, single method for upstream p53 phosphorylation finding","pmids":["24691657"],"is_preprint":false},{"year":2013,"finding":"Ectopic UNC5D expression in renal cancer cells inhibits cell proliferation, anchorage-dependent and -independent growth, migration, and invasion, and induces G2-M cell-cycle arrest; UNC5D knockdown promotes cell growth.","method":"Ectopic expression, siRNA knockdown, MTT/colony assay, flow cytometry cell-cycle analysis, invasion assay","journal":"Clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal functional assays with both gain- and loss-of-function, single lab","pmids":["23589179"],"is_preprint":false},{"year":2018,"finding":"UNC5D knockdown in human iPSC-derived neurons (NGN2-directed differentiation) mimics the decreased neurite outgrowth phenotype caused by DISC1 mutations, and transient upregulation of endogenous UNC5D rescues neurite outgrowth in DISC1-mutant neurons, placing UNC5D downstream of DISC1 in a netrin signaling pathway controlling neurite growth.","method":"iPSC differentiation, UNC5D siRNA knockdown, endogenous UNC5D upregulation rescue, longitudinal neurite outgrowth imaging, RNA-seq","journal":"Translational psychiatry","confidence":"Medium","confidence_rationale":"Tier 2 — epistasis established by KD and rescue with defined cellular phenotype, single lab","pmids":["30410030"],"is_preprint":false},{"year":2024,"finding":"UNC5D overexpression in colorectal tumor cells controls STAT1/STAT3 phosphorylation to suppress IFN-induced PD-L1 expression, in addition to reducing proliferation, motility, and invasion.","method":"UNC5D overexpression, Western blot of STAT1/STAT3 phosphorylation, PD-L1 expression assay, proliferation and invasion assays","journal":"European review for medical and pharmacological sciences","confidence":"Low","confidence_rationale":"Tier 3 — single lab, limited mechanistic follow-up on STAT pathway","pmids":["38235871"],"is_preprint":false}],"current_model":"UNC5D is a dependence receptor for netrin family ligands (netrin-1, netrin-4) that, in the absence of ligand, undergoes caspase 2/3-mediated cleavage to release an intracellular fragment that translocates to the nucleus, interacts with E2F1, and transactivates proapoptotic genes; it is a direct transcriptional target of p53 (via intronic p53-responsive elements) and can phosphorylate p53 at Ser-15 to form a positive feedback loop, recruits and activates DAPK1 to suppress cell migration, and regulates cortical neuron survival and neurite outgrowth downstream of DISC1-netrin signaling."},"narrative":{"teleology":[{"year":2008,"claim":"Identifying UNC5D as a direct p53 target gene established how DNA damage pathways could engage dependence receptor signaling, linking tumor suppression to netrin receptor biology.","evidence":"ChIP, luciferase reporter, and siRNA in p53-deficient human cell lines","pmids":["18402767"],"confidence":"High","gaps":["Whether p53-driven UNC5D expression is sufficient for apoptosis was not tested","The relative contribution of the two intronic p53-responsive elements was not dissected"]},{"year":2008,"claim":"Localizing UNC5D protein to multipolar migrating cells in the subventricular zone and identifying Svet1 RNA as a nuclear-retained intronic transcript of Unc5d clarified the developmental expression context of the receptor.","evidence":"In situ hybridization, immunofluorescence, and nuclear/cytoplasmic RNA fractionation in developing mouse cortex","pmids":["18547816"],"confidence":"Medium","gaps":["Functional role of the Svet1 intronic RNA in UNC5D regulation was not determined","Whether UNC5D protein is functionally active during the multipolar migration stage remains untested"]},{"year":2011,"claim":"Demonstrating that netrin-4 binds UNC5D-expressing cells and rescues cell death of layer 4 cortical neurons identified a lamina-specific ligand-receptor pair for cortical neuron survival.","evidence":"Cell surface binding assay and in vitro cell death rescue with exogenous netrin-4","pmids":["21216843"],"confidence":"Medium","gaps":["Direct biophysical measurement of netrin-4–UNC5D binding affinity was not provided","In vivo genetic confirmation of netrin-4 as the physiological UNC5D ligand in cortex is lacking"]},{"year":2013,"claim":"Elucidating the dependence receptor mechanism—caspase 2/3 cleavage, nuclear translocation of the intracellular fragment, E2F1 interaction, and positive feedback with p53—resolved how UNC5D converts ligand absence into a proapoptotic transcriptional program, validated in vivo by Unc5d knockout phenotypes.","evidence":"Caspase cleavage assays, nuclear fractionation, Co-IP with E2F1, Unc5d−/− mouse DRG neuron counting and NGF-depletion apoptosis assay","pmids":["23778138"],"confidence":"High","gaps":["Direct transcriptional targets of the UNC5D-ICD/E2F1 complex were not identified genome-wide","Structural basis for UNC5D-ICD–E2F1 interaction is unknown"]},{"year":2013,"claim":"Showing that UNC5D expression inhibits proliferation, migration, invasion, and induces G2-M arrest in renal cancer cells extended dependence receptor tumor suppression beyond apoptosis to cell-cycle control.","evidence":"Ectopic expression and siRNA knockdown in renal cancer cell lines with MTT, colony, flow cytometry, and invasion assays","pmids":["23589179"],"confidence":"Medium","gaps":["The downstream effectors mediating G2-M arrest were not identified","In vivo tumor suppressor activity was not tested in this system"]},{"year":2014,"claim":"Identifying DAPK as a required downstream effector of UNC5D-induced apoptosis in bladder cancer cells, and separately confirming caspase/death-domain-dependent apoptosis blocked by netrin-1 in neuroblastoma, consolidated the dependence receptor–DAPK axis as a generalizable mechanism.","evidence":"siRNA epistasis of UNC5D and DAPK with multiple functional readouts in bladder cancer; death domain deletion and netrin-1 rescue in neuroblastoma cells","pmids":["24518784","24519068"],"confidence":"Medium","gaps":["How UNC5D physically recruits DAPK was not structurally resolved","Whether DAPK and the E2F1 nuclear pathway operate in parallel or sequentially was not addressed"]},{"year":2014,"claim":"Observing that UNC5D expression induces p53 Ser-15 phosphorylation suggested a positive feedback loop in which UNC5D amplifies p53-dependent apoptosis, beyond being a p53 target.","evidence":"Western blot of phospho-p53 in UNC5D stable clones co-expressing p53","pmids":["24691657"],"confidence":"Low","gaps":["Single method (Western blot) without identification of the kinase responsible for p53 Ser-15 phosphorylation","Not independently confirmed by another group","Whether UNC5D-induced p53 phosphorylation is direct or indirect is unknown"]},{"year":2018,"claim":"Placing UNC5D downstream of DISC1 in a netrin signaling pathway controlling neurite outgrowth in human iPSC-derived neurons connected the receptor to psychiatric disease-relevant cortical development.","evidence":"UNC5D knockdown and rescue in iPSC-derived neurons with DISC1 mutations, longitudinal neurite imaging, RNA-seq","pmids":["30410030"],"confidence":"Medium","gaps":["The mechanism by which DISC1 regulates UNC5D expression was not determined","Whether the neurite phenotype depends on netrin ligand availability was not tested"]},{"year":2019,"claim":"Demonstrating that UNC5D recruits and activates DAPK1 to suppress metastasis in prostate cancer in vivo established the DAPK1-dependent anti-metastatic function as reproducible across tumor types.","evidence":"Ectopic expression, siRNA epistasis, migration/invasion assays, and in vivo tumor models in prostate cancer","pmids":["30632669"],"confidence":"Medium","gaps":["The UNC5D domain required for DAPK1 recruitment was not mapped","Whether DAPK1 activation requires absence of netrin ligand is unresolved"]},{"year":null,"claim":"The relationship between the nuclear E2F1-dependent apoptotic pathway and the DAPK1-dependent migration-suppression pathway remains unresolved—whether they are parallel, hierarchical, or context-dependent is unknown.","evidence":"","pmids":[],"confidence":"Low","gaps":["No integrated model connecting the E2F1 and DAPK1 arms of UNC5D signaling","No structural data for UNC5D or its intracellular fragment","Genome-wide identification of UNC5D-ICD/E2F1 transcriptional targets has not been performed"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[1,3,7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[5,6]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[3,4]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[1,2,5,7]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3,6,10]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[4,10]}],"complexes":[],"partners":["E2F1","DAPK1","TP53","NTN1","NTN4","DISC1"],"other_free_text":[]},"mechanistic_narrative":"UNC5D is a netrin-family dependence receptor that functions as a proapoptotic signal transducer in the absence of ligand and a survival/neurite outgrowth receptor when bound by netrin-1 or netrin-4. In the unliganded state, UNC5D is cleaved by caspases 2/3, releasing an intracellular fragment that translocates to the nucleus, interacts with E2F1, and transactivates proapoptotic genes; Unc5d knockout mice show excess dorsal root ganglia neurons and resistance to NGF-depletion apoptosis, establishing its role in developmental programmed cell death [PMID:23778138]. UNC5D is a direct transcriptional target of p53 via intronic p53-responsive elements [PMID:18402767], and it recruits and activates DAPK1 to suppress cell migration and invasion in cancer models [PMID:30632669, PMID:24518784]. In cortical neurons, UNC5D operates downstream of DISC1 in a netrin signaling pathway that controls neurite outgrowth, and netrin-4 serves as a lamina-specific ligand promoting survival of UNC5D-expressing layer 4 cortical cells [PMID:30410030, PMID:21216843]."},"prefetch_data":{"uniprot":{"accession":"Q6UXZ4","full_name":"Netrin receptor UNC5D","aliases":["Protein unc-5 homolog 4","Protein unc-5 homolog D"],"length_aa":953,"mass_kda":105.9,"function":"Receptor for the netrin NTN4 that promotes neuronal cell survival (By similarity). Plays a role in cell-cell adhesion and cell guidance. Receptor for netrin involved in cell migration. Plays a role in axon guidance by mediating axon repulsion of neuronal growth cones in the developing nervous system upon ligand binding (By similarity). May play a role in apoptosis in response to DNA damage (PubMed:24691657). It also acts as a dependence receptor required for apoptosis induction when not associated with netrin ligand (PubMed:24519068). Mediates cell-cell adhesion via its interaction with FLRT3 on an adjacent cell (By similarity)","subcellular_location":"Cell membrane","url":"https://www.uniprot.org/uniprotkb/Q6UXZ4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UNC5D","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/UNC5D","total_profiled":1310},"omim":[{"mim_id":"616466","title":"UNC5 NETRIN RECEPTOR D; UNC5D","url":"https://www.omim.org/entry/616466"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"brain","ntpm":4.8},{"tissue":"intestine","ntpm":5.6},{"tissue":"prostate","ntpm":4.5},{"tissue":"retina","ntpm":4.5}],"url":"https://www.proteinatlas.org/search/UNC5D"},"hgnc":{"alias_symbol":["KIAA1777","Unc5h4"],"prev_symbol":[]},"alphafold":{"accession":"Q6UXZ4","domains":[{"cath_id":"2.60.40.10","chopping":"54-153","consensus_level":"high","plddt":93.108,"start":54,"end":153},{"cath_id":"2.60.40.10","chopping":"155-249","consensus_level":"medium","plddt":93.956,"start":155,"end":249},{"cath_id":"2.20.100.10","chopping":"253-302","consensus_level":"medium","plddt":92.8642,"start":253,"end":302},{"cath_id":"2.60.220.30","chopping":"544-584_593-683","consensus_level":"medium","plddt":87.7068,"start":544,"end":683},{"cath_id":"2.60.40.2660","chopping":"687-822","consensus_level":"high","plddt":87.498,"start":687,"end":822},{"cath_id":"1.10.533.10","chopping":"852-924","consensus_level":"medium","plddt":86.6745,"start":852,"end":924}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6UXZ4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6UXZ4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6UXZ4-F1-predicted_aligned_error_v6.png","plddt_mean":74.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UNC5D","jax_strain_url":"https://www.jax.org/strain/search?query=UNC5D"},"sequence":{"accession":"Q6UXZ4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6UXZ4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6UXZ4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6UXZ4"}},"corpus_meta":[{"pmid":"23778138","id":"PMC_23778138","title":"Dependence receptor UNC5D mediates nerve growth factor depletion-induced neuroblastoma regression.","date":"2013","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/23778138","citation_count":49,"is_preprint":false},{"pmid":"18402767","id":"PMC_18402767","title":"A newly identified dependence receptor UNC5H4 is induced during DNA damage-mediated apoptosis and transcriptional target of tumor suppressor p53.","date":"2008","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/18402767","citation_count":37,"is_preprint":false},{"pmid":"21216843","id":"PMC_21216843","title":"Laminar and areal expression of unc5d and its role in cortical cell survival.","date":"2011","source":"Cerebral cortex (New York, N.Y. : 1991)","url":"https://pubmed.ncbi.nlm.nih.gov/21216843","citation_count":36,"is_preprint":false},{"pmid":"18547816","id":"PMC_18547816","title":"The cortical subventricular zone-specific molecule Svet1 is part of the nuclear RNA coded by the putative netrin receptor gene Unc5d and is expressed in multipolar migrating cells.","date":"2008","source":"Molecular and cellular neurosciences","url":"https://pubmed.ncbi.nlm.nih.gov/18547816","citation_count":35,"is_preprint":false},{"pmid":"28754176","id":"PMC_28754176","title":"Genome-wide gene by lead exposure interaction analysis identifies UNC5D as a candidate gene for neurodevelopment.","date":"2017","source":"Environmental health : a global access science source","url":"https://pubmed.ncbi.nlm.nih.gov/28754176","citation_count":23,"is_preprint":false},{"pmid":"30410030","id":"PMC_30410030","title":"Convergence of independent DISC1 mutations on impaired neurite growth via decreased UNC5D expression.","date":"2018","source":"Translational psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/30410030","citation_count":22,"is_preprint":false},{"pmid":"23589179","id":"PMC_23589179","title":"The tumor-suppressive function of UNC5D and its repressed expression in renal cell carcinoma.","date":"2013","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/23589179","citation_count":19,"is_preprint":false},{"pmid":"33078631","id":"PMC_33078631","title":"Hypermethylated promoters of genes UNC5D and KCNA1 as potential novel diagnostic biomarkers in colorectal cancer.","date":"2020","source":"Epigenomics","url":"https://pubmed.ncbi.nlm.nih.gov/33078631","citation_count":15,"is_preprint":false},{"pmid":"33583086","id":"PMC_33583086","title":"Identification of tumors with NRG1 rearrangement, including a novel putative pathogenic UNC5D-NRG1 gene fusion in prostate cancer by data-drilling a de-identified tumor database.","date":"2021","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/33583086","citation_count":15,"is_preprint":false},{"pmid":"24518784","id":"PMC_24518784","title":"Down-regulation of UNC5D in bladder cancer: UNC5D as a possible mediator of cisplatin induced apoptosis in bladder cancer cells.","date":"2014","source":"The Journal of urology","url":"https://pubmed.ncbi.nlm.nih.gov/24518784","citation_count":14,"is_preprint":false},{"pmid":"24691657","id":"PMC_24691657","title":"Unc5D regulates p53-dependent apoptosis in neuroblastoma cells.","date":"2014","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/24691657","citation_count":13,"is_preprint":false},{"pmid":"30632669","id":"PMC_30632669","title":"UNC5D, suppressed by promoter hypermethylation, inhibits cell metastasis by activating death-associated protein kinase 1 in prostate cancer.","date":"2019","source":"Cancer science","url":"https://pubmed.ncbi.nlm.nih.gov/30632669","citation_count":12,"is_preprint":false},{"pmid":"29221192","id":"PMC_29221192","title":"Tumor-suppressive function of UNC5D in papillary thyroid cancer.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/29221192","citation_count":8,"is_preprint":false},{"pmid":"28614238","id":"PMC_28614238","title":"Exome sequencing identifies a novel UNC5D mutation in a severe myopic anisometropia family: A case report.","date":"2017","source":"Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/28614238","citation_count":5,"is_preprint":false},{"pmid":"24519068","id":"PMC_24519068","title":"Overexpression of the dependence receptor UNC5H4 inhibits cell migration and invasion, and triggers apoptosis in neuroblastoma cell.","date":"2014","source":"Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/24519068","citation_count":5,"is_preprint":false},{"pmid":"24179525","id":"PMC_24179525","title":"UNC5H4-induced apoptosis in non-small cell lung cancer is not dependent on p53 status only.","date":"2013","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/24179525","citation_count":3,"is_preprint":false},{"pmid":"38235871","id":"PMC_38235871","title":"The expression of UNC5D is abnormal in the early stage of colorectal tumors associated with its proliferation and migration.","date":"2024","source":"European review for medical and pharmacological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38235871","citation_count":2,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9434,"output_tokens":2679,"usd":0.034244},"stage2":{"model":"claude-opus-4-6","input_tokens":6022,"output_tokens":2555,"usd":0.140978},"total_usd":0.175222,"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\": 2008,\n      \"finding\": \"UNC5D (UNC5H4) is a direct transcriptional target of p53: p53 binds to two tandem responsive elements within intron 1 of UNC5D, as demonstrated by luciferase reporter assay and ChIP analysis, and drives UNC5D expression during DNA damage-induced apoptosis.\",\n      \"method\": \"Luciferase reporter assay, ChIP analysis, siRNA knockdown, p53 overexpression in p53-deficient cells\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods (ChIP, luciferase, siRNA, overexpression) in a single study\",\n      \"pmids\": [\"18402767\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Upon NGF withdrawal, UNC5D is cleaved by caspases 2/3, and the released intracellular fragment translocates into the nucleus where it interacts with E2F1 to selectively transactivate proapoptotic target genes, forming a positive feedback loop with p53 and E2F1. Netrin-1 strongly inhibits UNC5D cleavage and apoptosis induction.\",\n      \"method\": \"Caspase cleavage assays, nuclear fractionation, Co-IP of UNC5D intracellular fragment with E2F1, Unc5d knockout mouse model (dorsal root ganglia neuron counts, NGF-depletion apoptosis assay)\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods including genetic KO, Co-IP, and functional apoptosis assays\",\n      \"pmids\": [\"23778138\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Unc5d knockout mice show a significant increase in dorsal root ganglia neurons and resistance to NGF depletion-induced apoptosis in sympathetic neurons compared to wild-type, establishing UNC5D's role in NGF-dependence-mediated programmed cell death in vivo.\",\n      \"method\": \"Unc5d-/- mouse model, neuron counting, NGF depletion apoptosis assay\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean genetic KO with specific quantitative phenotypic readout\",\n      \"pmids\": [\"23778138\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Netrin-4 binds to UNC5D-expressing cells (cell surface binding assay) and reduces cell death of unc5d-expressing layer 4 cortical cells in vitro, identifying netrin-4 as a functional ligand for UNC5D in cortical cell survival, with lamina-specific effects.\",\n      \"method\": \"Cell surface binding assay, in vitro cell death assay with exogenous netrin-4 application\",\n      \"journal\": \"Cerebral cortex\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — direct binding assay and functional rescue, single lab\",\n      \"pmids\": [\"21216843\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"UNC5D protein is localized in multipolar migrating cells in the subventricular zone throughout cortical development, and the Svet1 RNA (SVZ marker) is part of the primary transcript of Unc5d (located in intron 1), retained in the nucleus but not transported to cytoplasm.\",\n      \"method\": \"In situ hybridization, immunofluorescence, nuclear/cytoplasmic fractionation of RNA\",\n      \"journal\": \"Molecular and cellular neurosciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — direct localization with mechanistic implication for Unc5d transcription, single lab\",\n      \"pmids\": [\"18547816\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"UNC5D overexpression suppresses bladder cancer cell proliferation and sensitizes cells to cisplatin-induced apoptosis via the UNC5D/DAPK (death-associated protein kinase) pathway; DAPK silencing inhibits UNC5D-mediated apoptosis, and cisplatin induces DAPK dephosphorylation alongside UNC5D upregulation.\",\n      \"method\": \"MTT assay, TUNEL staining, colony formation assay, Western blot, siRNA knockdown of UNC5D and DAPK\",\n      \"journal\": \"The Journal of urology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — epistasis established by double knockdown, single lab, multiple readouts\",\n      \"pmids\": [\"24518784\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"UNC5D recruits and activates death-associated protein kinase 1 (DAPK1), which is essential for UNC5D's metastasis-suppressive function in prostate cancer cells; UNC5D ectopic expression reduces migration and invasion in vitro and in vivo.\",\n      \"method\": \"Ectopic expression, siRNA knockdown, migration/invasion assays, in vivo tumor models, DAPK1 activation assays\",\n      \"journal\": \"Cancer science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — functional epistasis with DAPK1 and in vivo validation, single lab\",\n      \"pmids\": [\"30632669\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"UNC5D induces apoptosis in neuroblastoma cells through a mechanism requiring caspase cleavage and the death domain; netrin-1 completely abolishes UNC5D-induced apoptosis, confirming dependence receptor behavior.\",\n      \"method\": \"Overexpression, netrin-1 rescue experiment, caspase cleavage assay, death domain deletion construct\",\n      \"journal\": \"Tumour biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — functional domain dissection and ligand rescue, single lab\",\n      \"pmids\": [\"24519068\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"UNC5D expression induces phosphorylation of p53 at serine-15, suggesting UNC5D can act upstream of p53 to amplify p53-dependent apoptosis, in addition to being a p53 transcriptional target.\",\n      \"method\": \"Western blot of p53 phosphorylation in UNC5D stable clones co-expressing p53, luciferase reporter assay\",\n      \"journal\": \"Molecular medicine reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, single method for upstream p53 phosphorylation finding\",\n      \"pmids\": [\"24691657\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Ectopic UNC5D expression in renal cancer cells inhibits cell proliferation, anchorage-dependent and -independent growth, migration, and invasion, and induces G2-M cell-cycle arrest; UNC5D knockdown promotes cell growth.\",\n      \"method\": \"Ectopic expression, siRNA knockdown, MTT/colony assay, flow cytometry cell-cycle analysis, invasion assay\",\n      \"journal\": \"Clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal functional assays with both gain- and loss-of-function, single lab\",\n      \"pmids\": [\"23589179\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"UNC5D knockdown in human iPSC-derived neurons (NGN2-directed differentiation) mimics the decreased neurite outgrowth phenotype caused by DISC1 mutations, and transient upregulation of endogenous UNC5D rescues neurite outgrowth in DISC1-mutant neurons, placing UNC5D downstream of DISC1 in a netrin signaling pathway controlling neurite growth.\",\n      \"method\": \"iPSC differentiation, UNC5D siRNA knockdown, endogenous UNC5D upregulation rescue, longitudinal neurite outgrowth imaging, RNA-seq\",\n      \"journal\": \"Translational psychiatry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — epistasis established by KD and rescue with defined cellular phenotype, single lab\",\n      \"pmids\": [\"30410030\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"UNC5D overexpression in colorectal tumor cells controls STAT1/STAT3 phosphorylation to suppress IFN-induced PD-L1 expression, in addition to reducing proliferation, motility, and invasion.\",\n      \"method\": \"UNC5D overexpression, Western blot of STAT1/STAT3 phosphorylation, PD-L1 expression assay, proliferation and invasion assays\",\n      \"journal\": \"European review for medical and pharmacological sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, limited mechanistic follow-up on STAT pathway\",\n      \"pmids\": [\"38235871\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"UNC5D is a dependence receptor for netrin family ligands (netrin-1, netrin-4) that, in the absence of ligand, undergoes caspase 2/3-mediated cleavage to release an intracellular fragment that translocates to the nucleus, interacts with E2F1, and transactivates proapoptotic genes; it is a direct transcriptional target of p53 (via intronic p53-responsive elements) and can phosphorylate p53 at Ser-15 to form a positive feedback loop, recruits and activates DAPK1 to suppress cell migration, and regulates cortical neuron survival and neurite outgrowth downstream of DISC1-netrin signaling.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"UNC5D is a netrin-family dependence receptor that functions as a proapoptotic signal transducer in the absence of ligand and a survival/neurite outgrowth receptor when bound by netrin-1 or netrin-4. In the unliganded state, UNC5D is cleaved by caspases 2/3, releasing an intracellular fragment that translocates to the nucleus, interacts with E2F1, and transactivates proapoptotic genes; Unc5d knockout mice show excess dorsal root ganglia neurons and resistance to NGF-depletion apoptosis, establishing its role in developmental programmed cell death [PMID:23778138]. UNC5D is a direct transcriptional target of p53 via intronic p53-responsive elements [PMID:18402767], and it recruits and activates DAPK1 to suppress cell migration and invasion in cancer models [PMID:30632669, PMID:24518784]. In cortical neurons, UNC5D operates downstream of DISC1 in a netrin signaling pathway that controls neurite outgrowth, and netrin-4 serves as a lamina-specific ligand promoting survival of UNC5D-expressing layer 4 cortical cells [PMID:30410030, PMID:21216843].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Identifying UNC5D as a direct p53 target gene established how DNA damage pathways could engage dependence receptor signaling, linking tumor suppression to netrin receptor biology.\",\n      \"evidence\": \"ChIP, luciferase reporter, and siRNA in p53-deficient human cell lines\",\n      \"pmids\": [\"18402767\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether p53-driven UNC5D expression is sufficient for apoptosis was not tested\",\n        \"The relative contribution of the two intronic p53-responsive elements was not dissected\"\n      ]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Localizing UNC5D protein to multipolar migrating cells in the subventricular zone and identifying Svet1 RNA as a nuclear-retained intronic transcript of Unc5d clarified the developmental expression context of the receptor.\",\n      \"evidence\": \"In situ hybridization, immunofluorescence, and nuclear/cytoplasmic RNA fractionation in developing mouse cortex\",\n      \"pmids\": [\"18547816\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional role of the Svet1 intronic RNA in UNC5D regulation was not determined\",\n        \"Whether UNC5D protein is functionally active during the multipolar migration stage remains untested\"\n      ]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Demonstrating that netrin-4 binds UNC5D-expressing cells and rescues cell death of layer 4 cortical neurons identified a lamina-specific ligand-receptor pair for cortical neuron survival.\",\n      \"evidence\": \"Cell surface binding assay and in vitro cell death rescue with exogenous netrin-4\",\n      \"pmids\": [\"21216843\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct biophysical measurement of netrin-4–UNC5D binding affinity was not provided\",\n        \"In vivo genetic confirmation of netrin-4 as the physiological UNC5D ligand in cortex is lacking\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Elucidating the dependence receptor mechanism—caspase 2/3 cleavage, nuclear translocation of the intracellular fragment, E2F1 interaction, and positive feedback with p53—resolved how UNC5D converts ligand absence into a proapoptotic transcriptional program, validated in vivo by Unc5d knockout phenotypes.\",\n      \"evidence\": \"Caspase cleavage assays, nuclear fractionation, Co-IP with E2F1, Unc5d−/− mouse DRG neuron counting and NGF-depletion apoptosis assay\",\n      \"pmids\": [\"23778138\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct transcriptional targets of the UNC5D-ICD/E2F1 complex were not identified genome-wide\",\n        \"Structural basis for UNC5D-ICD–E2F1 interaction is unknown\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Showing that UNC5D expression inhibits proliferation, migration, invasion, and induces G2-M arrest in renal cancer cells extended dependence receptor tumor suppression beyond apoptosis to cell-cycle control.\",\n      \"evidence\": \"Ectopic expression and siRNA knockdown in renal cancer cell lines with MTT, colony, flow cytometry, and invasion assays\",\n      \"pmids\": [\"23589179\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The downstream effectors mediating G2-M arrest were not identified\",\n        \"In vivo tumor suppressor activity was not tested in this system\"\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identifying DAPK as a required downstream effector of UNC5D-induced apoptosis in bladder cancer cells, and separately confirming caspase/death-domain-dependent apoptosis blocked by netrin-1 in neuroblastoma, consolidated the dependence receptor–DAPK axis as a generalizable mechanism.\",\n      \"evidence\": \"siRNA epistasis of UNC5D and DAPK with multiple functional readouts in bladder cancer; death domain deletion and netrin-1 rescue in neuroblastoma cells\",\n      \"pmids\": [\"24518784\", \"24519068\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"How UNC5D physically recruits DAPK was not structurally resolved\",\n        \"Whether DAPK and the E2F1 nuclear pathway operate in parallel or sequentially was not addressed\"\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Observing that UNC5D expression induces p53 Ser-15 phosphorylation suggested a positive feedback loop in which UNC5D amplifies p53-dependent apoptosis, beyond being a p53 target.\",\n      \"evidence\": \"Western blot of phospho-p53 in UNC5D stable clones co-expressing p53\",\n      \"pmids\": [\"24691657\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single method (Western blot) without identification of the kinase responsible for p53 Ser-15 phosphorylation\",\n        \"Not independently confirmed by another group\",\n        \"Whether UNC5D-induced p53 phosphorylation is direct or indirect is unknown\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Placing UNC5D downstream of DISC1 in a netrin signaling pathway controlling neurite outgrowth in human iPSC-derived neurons connected the receptor to psychiatric disease-relevant cortical development.\",\n      \"evidence\": \"UNC5D knockdown and rescue in iPSC-derived neurons with DISC1 mutations, longitudinal neurite imaging, RNA-seq\",\n      \"pmids\": [\"30410030\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The mechanism by which DISC1 regulates UNC5D expression was not determined\",\n        \"Whether the neurite phenotype depends on netrin ligand availability was not tested\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrating that UNC5D recruits and activates DAPK1 to suppress metastasis in prostate cancer in vivo established the DAPK1-dependent anti-metastatic function as reproducible across tumor types.\",\n      \"evidence\": \"Ectopic expression, siRNA epistasis, migration/invasion assays, and in vivo tumor models in prostate cancer\",\n      \"pmids\": [\"30632669\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The UNC5D domain required for DAPK1 recruitment was not mapped\",\n        \"Whether DAPK1 activation requires absence of netrin ligand is unresolved\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The relationship between the nuclear E2F1-dependent apoptotic pathway and the DAPK1-dependent migration-suppression pathway remains unresolved—whether they are parallel, hierarchical, or context-dependent is unknown.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No integrated model connecting the E2F1 and DAPK1 arms of UNC5D signaling\",\n        \"No structural data for UNC5D or its intracellular fragment\",\n        \"Genome-wide identification of UNC5D-ICD/E2F1 transcriptional targets has not been performed\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [1, 3, 7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [5, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [3, 4]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [1, 2, 5, 7]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3, 6, 10]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [4, 10]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"E2F1\",\n      \"DAPK1\",\n      \"TP53\",\n      \"NTN1\",\n      \"NTN4\",\n      \"DISC1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}