{"gene":"LRRC4B","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":2009,"finding":"NGL-3 (LRRC4B) engages in trans-synaptic adhesion with the presynaptic receptor tyrosine phosphatase LAR. Expression of NGL-3 in non-neuronal cells induced presynaptic differentiation in contacting axons, while LAR expression induced postsynaptic differentiation in contacting dendrites. Neuronal overexpression of NGL-3 increased presynaptic contacts; direct aggregation of NGL-3 on dendrites induced co-clustering of excitatory postsynaptic proteins; knockdown of NGL-3 reduced the number and function of excitatory synapses; and soluble LAR competitively inhibited NGL-3-induced presynaptic differentiation.","method":"Co-culture synaptogenesis assay with heterologous cells, co-immunoprecipitation, neuronal overexpression/knockdown, antibody-mediated clustering, soluble competitor inhibition in rat hippocampal neurons","journal":"Nature neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (co-culture assay, Co-IP, KD, clustering, competitive inhibition) in one study, replicated in subsequent papers","pmids":["19252495"],"is_preprint":false},{"year":2010,"finding":"The leucine-rich repeat (LRR) domain of NGL-3 (specifically nine LRRs) interacts with the first two fibronectin III (FNIII) domains of LAR to drive bidirectional synapse formation. Gln-96 in the first LRR motif of NGL-3 is critical for LAR binding and induction of presynaptic differentiation. PTPδ and PTPσ also interact with NGL-3 via their first two FNIII domains: PTPσ–NGL-3 promotes bidirectional synapse formation, while PTPδ–NGL-3 induces only unidirectional presynaptic differentiation.","method":"Domain-mapping binding assays, site-directed mutagenesis (Q96 substitution), co-culture synaptogenesis assay, co-immunoprecipitation","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — mutagenesis identifying critical residue combined with domain-mapping and functional synaptogenesis assay, replicating and extending prior work","pmids":["20139422"],"is_preprint":false},{"year":2013,"finding":"NGL-3 undergoes sequential proteolytic cleavage (ectodomain shedding then intramembrane cleavage) during LTD-inducing stimuli. NMDA treatment of cultured neurons or low-frequency stimulation of brain slices triggers NGL-3 cleavage requiring NMDA receptor activity, matrix metalloproteinases (MMPs), and presenilin/γ-secretase activity, identifying NGL-3 as a novel substrate for both MMPs and γ-secretase.","method":"Pharmacological inhibition of NMDARs, MMPs, and γ-secretase in cultured neurons and hippocampal slices with biochemical detection of cleavage products; LFS-LTD protocol","journal":"Philosophical transactions of the Royal Society of London. Series B, Biological sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple pharmacological inhibitors used orthogonally in two experimental systems (cultured neurons and brain slices), single lab","pmids":["24298159"],"is_preprint":false},{"year":2019,"finding":"NGL-3 knockout mice show near-complete abolition of hippocampal LTD and abnormal hyperactivation of the Akt/GSK3β signaling pathway. Pharmacological inhibition of Akt (but not NMDAR activation) rescued suppressed LTD in Ngl3−/− mice, indicating that NGL-3 normally suppresses Akt activity to permit LTD induction. NGL-3 loss modestly suppressed NMDAR-mediated synaptic transmission without affecting synapse number, AMPAR-mediated basal transmission, or presynaptic release.","method":"Constitutive knockout mouse (Ngl3−/−), electrophysiology (LTD, NMDAR/AMPAR EPSCs), pharmacological rescue with Akt inhibitor and NMDAR activator, Western blot for Akt/GSK3β phosphorylation","journal":"PLoS biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KO with defined electrophysiological and biochemical phenotypes, pharmacological epistasis rescue, multiple orthogonal readouts","pmids":["31166939"],"is_preprint":false},{"year":2017,"finding":"NGL-3-induced presynaptic differentiation in hippocampal neurons is dependent on afadin but independent of nectin-1. β-catenin and γ-catenin (known LAR-binding proteins) co-immunoprecipitate with afadin from mouse brain lysate, suggesting afadin cooperates with the NGL-3/LAR system and catenins to drive presynaptic differentiation.","method":"Co-culture synaptogenesis assay with COS-7 cells expressing NGL-3, afadin-deficient mouse neurons, co-immunoprecipitation from brain lysate, immunofluorescence and immunoelectron microscopy","journal":"Genes to cells : devoted to molecular & cellular mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-culture functional assay with genetic loss-of-function (afadin KO neurons) plus Co-IP, single lab","pmids":["28695613"],"is_preprint":false},{"year":2024,"finding":"The extracellular domain of NGL-3 binds the presynaptic protein L1cam, and this NGL-3/L1cam interaction promotes formation of VGluT1-positive excitatory presynaptic puncta on neuronal dendrites. Cortical neuron-specific knockout of NGL-3 abolished the pro-synaptogenic and antidepressant-like effects of three-needle electroacupuncture in a post-stroke depression mouse model.","method":"Binding assay for NGL-3 ectodomain with L1cam, VGluT1 puncta formation assay, cortical neuron-specific NGL-3 conditional knockout, behavioral tests in PSD mouse model","journal":"Brain research","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — binding experiment plus conditional KO with functional readout, single lab, limited methodological detail in abstract","pmids":["38871241"],"is_preprint":false},{"year":2009,"finding":"NGL-3 (LRRC4B) localizes to the postsynaptic density and directly interacts with the scaffolding protein PSD-95 via its PDZ-binding motif, positioning it as a postsynaptic adhesion molecule at excitatory synapses.","method":"Co-immunoprecipitation, immunofluorescence colocalization in hippocampal neurons","journal":"Nature neuroscience","confidence":"Medium","confidence_rationale":"Tier 2-3 / Strong — Co-IP and localization replicated across multiple papers in the corpus","pmids":["19252495","24298159"],"is_preprint":false}],"current_model":"LRRC4B (NGL-3) is a postsynaptic LRR-domain adhesion molecule that drives bidirectional excitatory synapse formation by engaging presynaptic LAR-family receptor tyrosine phosphatases (LAR, PTPσ, PTPδ) through its LRR domain (with Gln-96 critical for LAR binding) and the first two FNIII domains of the phosphatases, while intracellularly anchoring to PSD-95; during LTD, NGL-3 is sequentially cleaved by MMPs and γ-secretase downstream of NMDAR activation, and NGL-3 loss abolishes hippocampal LTD by aberrantly hyperactivating Akt/GSK3β signaling; additionally, NGL-3 can bind L1cam to promote excitatory presynaptic differentiation, and its synaptogenic activity via LAR requires the scaffolding protein afadin."},"narrative":{"mechanistic_narrative":"LRRC4B (NGL-3) is a postsynaptic leucine-rich-repeat adhesion molecule that drives bidirectional excitatory synapse formation by trans-synaptically engaging presynaptic LAR-family receptor tyrosine phosphatases [PMID:19252495, PMID:20139422]. Its LRR domain binds the first two FNIII domains of LAR, PTPσ, and PTPδ, with Gln-96 in the first LRR critical for LAR binding and presynaptic induction; LAR and PTPσ promote bidirectional synapse formation whereas PTPδ drives only presynaptic differentiation [PMID:20139422]. Intracellularly, NGL-3 localizes to the postsynaptic density and anchors to PSD-95 through its PDZ-binding motif [PMID:19252495, PMID:24298159]. The synaptogenic output of the NGL-3/LAR system requires the scaffolding protein afadin, which associates with the LAR-binding catenins, while a separate interaction with presynaptic L1cam promotes formation of excitatory presynaptic puncta [PMID:28695613, PMID:38871241]. During long-term depression, NGL-3 is sequentially cleaved by MMPs and γ-secretase downstream of NMDAR activation [PMID:24298159], and loss of NGL-3 abolishes hippocampal LTD by aberrantly hyperactivating Akt/GSK3β signaling, indicating that NGL-3 normally suppresses Akt to permit LTD [PMID:31166939].","teleology":[{"year":2009,"claim":"Established NGL-3 as a postsynaptic adhesion molecule capable of organizing excitatory synapses bidirectionally through a presynaptic phosphatase partner, answering whether NGL-3 has synaptogenic activity and a trans-synaptic ligand.","evidence":"Co-culture synaptogenesis assay, Co-IP, neuronal knockdown/overexpression, antibody clustering, and soluble LAR competition in rat hippocampal neurons","pmids":["19252495"],"confidence":"High","gaps":["Did not map the binding interface or critical residues","In vivo requirement not tested"]},{"year":2009,"claim":"Defined the intracellular coupling of NGL-3 to the postsynaptic scaffold, showing it binds PSD-95 via its PDZ-binding motif and resides at the postsynaptic density.","evidence":"Co-IP and immunofluorescence colocalization in hippocampal neurons","pmids":["19252495","24298159"],"confidence":"Medium","gaps":["Functional consequence of disrupting the PSD-95 interaction not isolated","Other intracellular partners not characterized"]},{"year":2010,"claim":"Resolved the molecular interface and broadened the receptor repertoire, identifying the LRR/FNIII contacts, the critical Gln-96 residue, and distinguishing bidirectional (LAR, PTPσ) from unidirectional (PTPδ) signaling.","evidence":"Domain-mapping binding assays, Q96 site-directed mutagenesis, co-culture synaptogenesis, and Co-IP","pmids":["20139422"],"confidence":"High","gaps":["Structural basis of bidirectional vs unidirectional outcome unresolved","No co-crystal structure"]},{"year":2013,"claim":"Showed that NGL-3 is a regulated proteolytic substrate, undergoing NMDAR-driven ectodomain shedding by MMPs followed by γ-secretase intramembrane cleavage during LTD-inducing activity.","evidence":"Pharmacological inhibition of NMDARs, MMPs, and γ-secretase with biochemical detection of cleavage products in cultured neurons and hippocampal slices","pmids":["24298159"],"confidence":"Medium","gaps":["Specific MMP not identified","Fate and signaling role of cleavage fragments unknown","Single lab"]},{"year":2017,"claim":"Identified afadin as a required scaffolding cofactor for NGL-3-induced presynaptic differentiation, linking the system to LAR-binding catenins.","evidence":"Co-culture assay with afadin-deficient neurons, Co-IP from brain lysate, immunofluorescence and immunoelectron microscopy","pmids":["28695613"],"confidence":"Medium","gaps":["Direct vs indirect afadin interaction not resolved","Catenin contribution shown only by co-IP","Single lab"]},{"year":2019,"claim":"Defined the in vivo physiological role, showing NGL-3 is required for hippocampal LTD by restraining Akt/GSK3β signaling rather than by maintaining synapse number.","evidence":"Constitutive knockout mice, electrophysiology, Akt-inhibitor pharmacological rescue, and Western blot for Akt/GSK3β phosphorylation","pmids":["31166939"],"confidence":"High","gaps":["Mechanistic link between NGL-3 and Akt suppression not defined","How adhesion signaling couples to Akt unknown"]},{"year":2024,"claim":"Extended the presynaptic ligand repertoire to L1cam and connected NGL-3 to a circuit-level therapeutic response, showing its requirement for electroacupuncture-induced synaptogenesis in post-stroke depression.","evidence":"Ectodomain binding assay with L1cam, VGluT1 puncta formation assay, cortical neuron-specific conditional knockout, and behavioral tests in a PSD mouse model","pmids":["38871241"],"confidence":"Medium","gaps":["L1cam binding interface not mapped","Relationship between L1cam and LAR signaling unclear","Limited methodological detail"]},{"year":null,"claim":"How NGL-3 adhesion signaling is biochemically transduced to suppress Akt/GSK3β, and how its proteolytic processing integrates with this signaling during LTD, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No defined molecular pathway from NGL-3 to Akt","Role of cleavage fragments in intracellular signaling unknown","No structural model of receptor complexes"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098631","term_label":"cell adhesion mediator activity","supporting_discovery_ids":[0,1,5]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[6]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,6]}],"pathway":[{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[0,3]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[0,1]}],"complexes":[],"partners":["PTPRF","PTPRS","PTPRD","DLG4","AFDN","L1CAM"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NT99","full_name":"Leucine-rich repeat-containing protein 4B","aliases":["Netrin-G3 ligand","NGL-3"],"length_aa":713,"mass_kda":76.4,"function":"Synaptic adhesion protein. Regulates the formation of excitatory synapses. The trans-synaptic adhesion between LRRC4B and PTPRF regulates the formation of excitatory synapses in a bidirectional manner (By similarity)","subcellular_location":"Membrane; Presynaptic cell membrane","url":"https://www.uniprot.org/uniprotkb/Q9NT99/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/LRRC4B","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/LRRC4B","total_profiled":1310},"omim":[],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":99.9},{"tissue":"cervix","ntpm":35.5}],"url":"https://www.proteinatlas.org/search/LRRC4B"},"hgnc":{"alias_symbol":["DKFZp761A179","HSM","NGL-3"],"prev_symbol":["LRIG4"]},"alphafold":{"accession":"Q9NT99","domains":[{"cath_id":"2.60.40.10","chopping":"365-453","consensus_level":"high","plddt":94.1706,"start":365,"end":453}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NT99","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NT99-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NT99-F1-predicted_aligned_error_v6.png","plddt_mean":71.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LRRC4B","jax_strain_url":"https://www.jax.org/strain/search?query=LRRC4B"},"sequence":{"accession":"Q9NT99","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NT99.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NT99/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NT99"}},"corpus_meta":[{"pmid":"19252495","id":"PMC_19252495","title":"Trans-synaptic adhesion between NGL-3 and LAR regulates the formation of excitatory synapses.","date":"2009","source":"Nature neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/19252495","citation_count":179,"is_preprint":false},{"pmid":"20139422","id":"PMC_20139422","title":"Trans-synaptic adhesions between netrin-G ligand-3 (NGL-3) and receptor tyrosine phosphatases LAR, protein-tyrosine phosphatase delta (PTPdelta), and PTPsigma via specific domains regulate excitatory synapse formation.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20139422","citation_count":126,"is_preprint":false},{"pmid":"24298159","id":"PMC_24298159","title":"Long-term depression-inducing stimuli promote cleavage of the synaptic adhesion molecule NGL-3 through NMDA receptors, matrix metalloproteinases and presenilin/γ-secretase.","date":"2013","source":"Philosophical transactions of the Royal Society of London. Series B, Biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/24298159","citation_count":27,"is_preprint":false},{"pmid":"5884627","id":"PMC_5884627","title":"Studies of native glycogen isolated from synchronized Tetrahymena pyriformis (HSM).","date":"1965","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/5884627","citation_count":21,"is_preprint":false},{"pmid":"31166939","id":"PMC_31166939","title":"NGL-3 in the regulation of brain development, Akt/GSK3b signaling, long-term depression, and locomotive and cognitive behaviors.","date":"2019","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/31166939","citation_count":15,"is_preprint":false},{"pmid":"28695613","id":"PMC_28695613","title":"NGL-3-induced presynaptic differentiation of hippocampal neurons in an afadin-dependent, nectin-1-independent manner.","date":"2017","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/28695613","citation_count":7,"is_preprint":false},{"pmid":"9444946","id":"PMC_9444946","title":"Effects of transfection of p210bcr-abl and bcr-v-abl into the factor-dependent human leukemia cell line HSM-911.","date":"1997","source":"Leukemia research","url":"https://pubmed.ncbi.nlm.nih.gov/9444946","citation_count":6,"is_preprint":false},{"pmid":"38871241","id":"PMC_38871241","title":"Three-needle electroacupuncture ameliorates depressive-like behaviors in a mouse model of post-stroke depression by promoting excitatory synapse formation via the NGL-3/L1cam pathway.","date":"2024","source":"Brain research","url":"https://pubmed.ncbi.nlm.nih.gov/38871241","citation_count":5,"is_preprint":false},{"pmid":"23266641","id":"PMC_23266641","title":"HSM - a hybrid system based approach for modelling intracellular networks.","date":"2012","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/23266641","citation_count":3,"is_preprint":false},{"pmid":"8974913","id":"PMC_8974913","title":"[Mutator genes from Saccharomyces cerevisiae. 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Expression of NGL-3 in non-neuronal cells induced presynaptic differentiation in contacting axons, while LAR expression induced postsynaptic differentiation in contacting dendrites. Neuronal overexpression of NGL-3 increased presynaptic contacts; direct aggregation of NGL-3 on dendrites induced co-clustering of excitatory postsynaptic proteins; knockdown of NGL-3 reduced the number and function of excitatory synapses; and soluble LAR competitively inhibited NGL-3-induced presynaptic differentiation.\",\n      \"method\": \"Co-culture synaptogenesis assay with heterologous cells, co-immunoprecipitation, neuronal overexpression/knockdown, antibody-mediated clustering, soluble competitor inhibition in rat hippocampal neurons\",\n      \"journal\": \"Nature neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (co-culture assay, Co-IP, KD, clustering, competitive inhibition) in one study, replicated in subsequent papers\",\n      \"pmids\": [\"19252495\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The leucine-rich repeat (LRR) domain of NGL-3 (specifically nine LRRs) interacts with the first two fibronectin III (FNIII) domains of LAR to drive bidirectional synapse formation. Gln-96 in the first LRR motif of NGL-3 is critical for LAR binding and induction of presynaptic differentiation. PTPδ and PTPσ also interact with NGL-3 via their first two FNIII domains: PTPσ–NGL-3 promotes bidirectional synapse formation, while PTPδ–NGL-3 induces only unidirectional presynaptic differentiation.\",\n      \"method\": \"Domain-mapping binding assays, site-directed mutagenesis (Q96 substitution), co-culture synaptogenesis assay, co-immunoprecipitation\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — mutagenesis identifying critical residue combined with domain-mapping and functional synaptogenesis assay, replicating and extending prior work\",\n      \"pmids\": [\"20139422\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"NGL-3 undergoes sequential proteolytic cleavage (ectodomain shedding then intramembrane cleavage) during LTD-inducing stimuli. NMDA treatment of cultured neurons or low-frequency stimulation of brain slices triggers NGL-3 cleavage requiring NMDA receptor activity, matrix metalloproteinases (MMPs), and presenilin/γ-secretase activity, identifying NGL-3 as a novel substrate for both MMPs and γ-secretase.\",\n      \"method\": \"Pharmacological inhibition of NMDARs, MMPs, and γ-secretase in cultured neurons and hippocampal slices with biochemical detection of cleavage products; LFS-LTD protocol\",\n      \"journal\": \"Philosophical transactions of the Royal Society of London. Series B, Biological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple pharmacological inhibitors used orthogonally in two experimental systems (cultured neurons and brain slices), single lab\",\n      \"pmids\": [\"24298159\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"NGL-3 knockout mice show near-complete abolition of hippocampal LTD and abnormal hyperactivation of the Akt/GSK3β signaling pathway. Pharmacological inhibition of Akt (but not NMDAR activation) rescued suppressed LTD in Ngl3−/− mice, indicating that NGL-3 normally suppresses Akt activity to permit LTD induction. NGL-3 loss modestly suppressed NMDAR-mediated synaptic transmission without affecting synapse number, AMPAR-mediated basal transmission, or presynaptic release.\",\n      \"method\": \"Constitutive knockout mouse (Ngl3−/−), electrophysiology (LTD, NMDAR/AMPAR EPSCs), pharmacological rescue with Akt inhibitor and NMDAR activator, Western blot for Akt/GSK3β phosphorylation\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO with defined electrophysiological and biochemical phenotypes, pharmacological epistasis rescue, multiple orthogonal readouts\",\n      \"pmids\": [\"31166939\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"NGL-3-induced presynaptic differentiation in hippocampal neurons is dependent on afadin but independent of nectin-1. β-catenin and γ-catenin (known LAR-binding proteins) co-immunoprecipitate with afadin from mouse brain lysate, suggesting afadin cooperates with the NGL-3/LAR system and catenins to drive presynaptic differentiation.\",\n      \"method\": \"Co-culture synaptogenesis assay with COS-7 cells expressing NGL-3, afadin-deficient mouse neurons, co-immunoprecipitation from brain lysate, immunofluorescence and immunoelectron microscopy\",\n      \"journal\": \"Genes to cells : devoted to molecular & cellular mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-culture functional assay with genetic loss-of-function (afadin KO neurons) plus Co-IP, single lab\",\n      \"pmids\": [\"28695613\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"The extracellular domain of NGL-3 binds the presynaptic protein L1cam, and this NGL-3/L1cam interaction promotes formation of VGluT1-positive excitatory presynaptic puncta on neuronal dendrites. Cortical neuron-specific knockout of NGL-3 abolished the pro-synaptogenic and antidepressant-like effects of three-needle electroacupuncture in a post-stroke depression mouse model.\",\n      \"method\": \"Binding assay for NGL-3 ectodomain with L1cam, VGluT1 puncta formation assay, cortical neuron-specific NGL-3 conditional knockout, behavioral tests in PSD mouse model\",\n      \"journal\": \"Brain research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — binding experiment plus conditional KO with functional readout, single lab, limited methodological detail in abstract\",\n      \"pmids\": [\"38871241\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"NGL-3 (LRRC4B) localizes to the postsynaptic density and directly interacts with the scaffolding protein PSD-95 via its PDZ-binding motif, positioning it as a postsynaptic adhesion molecule at excitatory synapses.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence colocalization in hippocampal neurons\",\n      \"journal\": \"Nature neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Strong — Co-IP and localization replicated across multiple papers in the corpus\",\n      \"pmids\": [\"19252495\", \"24298159\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LRRC4B (NGL-3) is a postsynaptic LRR-domain adhesion molecule that drives bidirectional excitatory synapse formation by engaging presynaptic LAR-family receptor tyrosine phosphatases (LAR, PTPσ, PTPδ) through its LRR domain (with Gln-96 critical for LAR binding) and the first two FNIII domains of the phosphatases, while intracellularly anchoring to PSD-95; during LTD, NGL-3 is sequentially cleaved by MMPs and γ-secretase downstream of NMDAR activation, and NGL-3 loss abolishes hippocampal LTD by aberrantly hyperactivating Akt/GSK3β signaling; additionally, NGL-3 can bind L1cam to promote excitatory presynaptic differentiation, and its synaptogenic activity via LAR requires the scaffolding protein afadin.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LRRC4B (NGL-3) is a postsynaptic leucine-rich-repeat adhesion molecule that drives bidirectional excitatory synapse formation by trans-synaptically engaging presynaptic LAR-family receptor tyrosine phosphatases [#0, #1]. Its LRR domain binds the first two FNIII domains of LAR, PTPσ, and PTPδ, with Gln-96 in the first LRR critical for LAR binding and presynaptic induction; LAR and PTPσ promote bidirectional synapse formation whereas PTPδ drives only presynaptic differentiation [#1]. Intracellularly, NGL-3 localizes to the postsynaptic density and anchors to PSD-95 through its PDZ-binding motif [#6]. The synaptogenic output of the NGL-3/LAR system requires the scaffolding protein afadin, which associates with the LAR-binding catenins, while a separate interaction with presynaptic L1cam promotes formation of excitatory presynaptic puncta [#4, #5]. During long-term depression, NGL-3 is sequentially cleaved by MMPs and γ-secretase downstream of NMDAR activation [#2], and loss of NGL-3 abolishes hippocampal LTD by aberrantly hyperactivating Akt/GSK3β signaling, indicating that NGL-3 normally suppresses Akt to permit LTD [#3].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Established NGL-3 as a postsynaptic adhesion molecule capable of organizing excitatory synapses bidirectionally through a presynaptic phosphatase partner, answering whether NGL-3 has synaptogenic activity and a trans-synaptic ligand.\",\n      \"evidence\": \"Co-culture synaptogenesis assay, Co-IP, neuronal knockdown/overexpression, antibody clustering, and soluble LAR competition in rat hippocampal neurons\",\n      \"pmids\": [\"19252495\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not map the binding interface or critical residues\", \"In vivo requirement not tested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Defined the intracellular coupling of NGL-3 to the postsynaptic scaffold, showing it binds PSD-95 via its PDZ-binding motif and resides at the postsynaptic density.\",\n      \"evidence\": \"Co-IP and immunofluorescence colocalization in hippocampal neurons\",\n      \"pmids\": [\"19252495\", \"24298159\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of disrupting the PSD-95 interaction not isolated\", \"Other intracellular partners not characterized\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Resolved the molecular interface and broadened the receptor repertoire, identifying the LRR/FNIII contacts, the critical Gln-96 residue, and distinguishing bidirectional (LAR, PTPσ) from unidirectional (PTPδ) signaling.\",\n      \"evidence\": \"Domain-mapping binding assays, Q96 site-directed mutagenesis, co-culture synaptogenesis, and Co-IP\",\n      \"pmids\": [\"20139422\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of bidirectional vs unidirectional outcome unresolved\", \"No co-crystal structure\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Showed that NGL-3 is a regulated proteolytic substrate, undergoing NMDAR-driven ectodomain shedding by MMPs followed by γ-secretase intramembrane cleavage during LTD-inducing activity.\",\n      \"evidence\": \"Pharmacological inhibition of NMDARs, MMPs, and γ-secretase with biochemical detection of cleavage products in cultured neurons and hippocampal slices\",\n      \"pmids\": [\"24298159\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific MMP not identified\", \"Fate and signaling role of cleavage fragments unknown\", \"Single lab\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identified afadin as a required scaffolding cofactor for NGL-3-induced presynaptic differentiation, linking the system to LAR-binding catenins.\",\n      \"evidence\": \"Co-culture assay with afadin-deficient neurons, Co-IP from brain lysate, immunofluorescence and immunoelectron microscopy\",\n      \"pmids\": [\"28695613\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect afadin interaction not resolved\", \"Catenin contribution shown only by co-IP\", \"Single lab\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined the in vivo physiological role, showing NGL-3 is required for hippocampal LTD by restraining Akt/GSK3β signaling rather than by maintaining synapse number.\",\n      \"evidence\": \"Constitutive knockout mice, electrophysiology, Akt-inhibitor pharmacological rescue, and Western blot for Akt/GSK3β phosphorylation\",\n      \"pmids\": [\"31166939\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanistic link between NGL-3 and Akt suppression not defined\", \"How adhesion signaling couples to Akt unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended the presynaptic ligand repertoire to L1cam and connected NGL-3 to a circuit-level therapeutic response, showing its requirement for electroacupuncture-induced synaptogenesis in post-stroke depression.\",\n      \"evidence\": \"Ectodomain binding assay with L1cam, VGluT1 puncta formation assay, cortical neuron-specific conditional knockout, and behavioral tests in a PSD mouse model\",\n      \"pmids\": [\"38871241\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"L1cam binding interface not mapped\", \"Relationship between L1cam and LAR signaling unclear\", \"Limited methodological detail\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How NGL-3 adhesion signaling is biochemically transduced to suppress Akt/GSK3β, and how its proteolytic processing integrates with this signaling during LTD, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No defined molecular pathway from NGL-3 to Akt\", \"Role of cleavage fragments in intracellular signaling unknown\", \"No structural model of receptor complexes\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098631\", \"supporting_discovery_ids\": [0, 1, 5]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PTPRF\", \"PTPRS\", \"PTPRD\", \"DLG4\", \"AFDN\", \"L1CAM\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}