{"gene":"PLXNA4","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2014,"finding":"Full-length PLXNA4 isoform (TS1) increases tau phosphorylation in SH-SY5Y cells and primary rat neurons when stimulated by SEMA3A, while shorter isoforms (TS2 and TS3) have the opposite effect. Transfection of any isoform into HEK293 cells stably expressing APP did not result in differential effects on APP processing or Aβ production (negative result for Aβ pathway).","method":"Cell transfection of isoforms into SH-SY5Y cells and primary rat neurons with SEMA3A stimulation; tau phosphorylation assay; HEK293 APP-stable cell line","journal":"Annals of neurology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cell-based overexpression with defined phosphorylation readout and multiple isoforms tested in two cell types, single lab","pmids":["25043464"],"is_preprint":false},{"year":2016,"finding":"FoxO6 transcription factor binds to DAF-16-binding elements in the Plxna4 promoter and regulates its expression; ectopic Plxna4 expression rescues the radial migration defect caused by FoxO6 loss or siRNA knockdown in the developing neocortex, placing Plxna4 downstream of FoxO6 in a pathway controlling cortical neuronal migration.","method":"FoxO6 promoter binding assay (DAF-16-binding element), siRNA knockdown of FoxO6, in utero electroporation, ectopic Plxna4 rescue experiment, genome-wide transcriptome analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — epistasis established by rescue experiment, promoter binding demonstrated, multiple orthogonal methods (ChIP-like binding, siRNA, rescue), peer-reviewed","pmids":["27791111"],"is_preprint":false},{"year":2022,"finding":"In hUC-MSCs undergoing neural differentiation induced by low-intensity sub-sonic vibration, PLXNA4 is required downstream of SEMA3A for neuronal differentiation: SEMA3A expression increases, PLXNA4 knockdown blocks LISSV-induced upregulation of neuron-related genes, and PLXNA4 signaling activates FYN kinase as a downstream effector.","method":"siRNA knockdown of PLXNA4, PLXNA4 recombinant protein addition, RNA sequencing, gene expression analysis of neuron-related genes, FYN activation assay","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function (siRNA) and gain-of-function (recombinant protein) with defined pathway (SEMA3A→PLXNA4→FYN) in a single lab using multiple approaches","pmids":["35163445"],"is_preprint":false},{"year":2026,"finding":"Med13 regulates cortical neuronal radial migration and callosal (contralateral) projection at least in part through PlxnA4: Med13 knockdown in cortical neurons impairs radial migration and callosal projection, and overexpression of PlxnA4 largely restores radial migration and callosal projection (but not dendritic complexity) in Med13 knockdown neurons, placing PlxnA4 downstream of Med13.","method":"In utero electroporation-mediated Med13 knockdown, mass spectrometry proteomics identifying PLXNA4 as dysregulated, PlxnA4 overexpression rescue in Med13 KD neurons","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis by rescue experiment with orthogonal proteomic identification, single lab","pmids":["41663567"],"is_preprint":false},{"year":2025,"finding":"PlxnA4 is locally translated in midbrain dopaminergic (mDA) axons and modulates axonal arborization in response to Sema3a; Plxna4-mediated signaling regulates topographical axon targeting and innervation in the nigrostriatal pathway in vivo.","method":"RiboTag ribosome tagging to isolate axon-specific ribosome-bound mRNAs in mDA neurons (DATIRES-Cre mice), in vitro functional arborization assays, in vivo axon targeting assays","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RiboTag demonstrates local translation, in vitro and in vivo functional assays, preprint not yet peer-reviewed","pmids":["bio_10.1101_2025.11.25.690389"],"is_preprint":true},{"year":2024,"finding":"PlxnA4 controls mossy fiber partitioning into suprapyramidal (SPT) and infrapyramidal (IPT) tracts, SPT axon bundling, laminar targeting to stratum lucidum, and IPT length in the hippocampus. Many of these defects are replicated in mice deficient for PlxnA4 GAP catalytic activity, establishing that the GAP domain is required for these guidance functions.","method":"Plxna4 knockout mice, PlxnA4 GAP catalytic mutant knock-in mice, immunohistochemistry, axon tract analysis","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function and catalytic domain mutant with defined axon guidance phenotypes; preprint not yet peer-reviewed","pmids":["bio_10.1101_2024.12.15.628586"],"is_preprint":true},{"year":2025,"finding":"In a PlexinA3/PlexinA4 double knockout mouse, loss of plexin-dependent cardiac sympathetic innervation leads to structurally normal hearts with spontaneous ventricular arrhythmias driven by adrenergic hypersensitivity and increased cardiac β-adrenergic receptor density, establishing a role for PlexinA4 (with PlexinA3) in developmental guidance of sympathetic nerves onto the heart.","method":"PlexinA3/A4 double knockout mouse, tissue clearing, immunohistochemistry, echocardiography, ECG, optical mapping of action potentials, catecholamine measurements, β-adrenergic receptor density quantification","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — knockout mouse with multiple orthogonal electrophysiological and pharmacological readouts; preprint; confounded by double knockout (PlexinA3+A4)","pmids":["bio_10.1101_2025.05.20.655085"],"is_preprint":true},{"year":2025,"finding":"Loss of Plxna4 function in zebrafish results in increased body fat, hypertrophic subcutaneous adipose tissue, shorter body length, increased food consumption, and food-stimulated hyperactivity (increased swimming speed), establishing a role for Plxna4 in regulating feeding behavior and adiposity.","method":"Zebrafish plxna4 loss-of-function mutants (85–92% protein reduction), body fat quantification, feeding assays, locomotor behavior assays","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function animal model with multiple quantitative phenotypic readouts; preprint not yet peer-reviewed","pmids":["bio_10.1101_2025.03.15.643290"],"is_preprint":true}],"current_model":"PLXNA4 is a semaphorin receptor (binding SEMA3A and Sema6A) that functions in axon guidance, neuronal migration, and circuit development: it acts downstream of FoxO6 and Med13 transcription factors to control cortical neuron radial migration and callosal projection, is locally translated in dopaminergic axons to mediate Sema3a-dependent arborization and nigrostriatal targeting, uses its GAP catalytic domain to direct hippocampal mossy fiber tract formation, and promotes tau phosphorylation in an isoform-specific manner upon SEMA3A stimulation; additionally, PlexinA4 (with PlexinA3) guides cardiac sympathetic innervation, and loss of Plxna4 in zebrafish increases adiposity and food intake."},"narrative":{"mechanistic_narrative":"PLXNA4 is a semaphorin receptor that transduces SEMA3A and Sema6A signals to direct axon guidance, neuronal migration, and circuit assembly during nervous system development [PMID:27791111, PMID:bio_10.1101_2025.11.25.690389]. It operates as a transcriptional effector node: FoxO6 binds DAF-16 elements in the Plxna4 promoter and the transcriptional regulator Med13 acts upstream, with ectopic PlxnA4 expression rescuing the cortical neuron radial migration and callosal projection defects produced by loss of either factor, placing Plxna4 downstream in these migration pathways [PMID:27791111, PMID:41663567]. PLXNA4 signaling engages FYN kinase as a downstream effector during SEMA3A-driven neuronal differentiation [PMID:35163445], and its intrinsic GAP catalytic activity is required for hippocampal mossy fiber partitioning, axon bundling, and laminar targeting [PMID:bio_10.1101_2024.12.15.628586]. In dopaminergic neurons, Plxna4 mRNA is locally translated within axons to modulate Sema3a-dependent arborization and nigrostriatal targeting [PMID:bio_10.1101_2025.11.25.690389]. PLXNA4 acts in an isoform-specific manner: the full-length TS1 isoform increases tau phosphorylation upon SEMA3A stimulation while shorter isoforms have the opposite effect, without affecting APP processing or Aβ production [PMID:25043464]. Beyond neurodevelopment, PlexinA4 (together with PlexinA3) guides cardiac sympathetic innervation, with its loss producing adrenergic hypersensitivity and ventricular arrhythmias [PMID:bio_10.1101_2025.05.20.655085], and loss of Plxna4 in zebrafish increases adiposity and food intake [PMID:bio_10.1101_2025.03.15.643290].","teleology":[{"year":2014,"claim":"Established that PLXNA4 isoforms differentially couple SEMA3A signaling to tau phosphorylation, linking a semaphorin receptor to a neurodegeneration-relevant readout and ruling out an amyloid route.","evidence":"Isoform transfection into SH-SY5Y cells and primary rat neurons with SEMA3A stimulation and tau phosphorylation assay; APP-stable HEK293 negative control","pmids":["25043464"],"confidence":"Medium","gaps":["Mechanism connecting receptor signaling to tau kinases not defined","Overexpression-based, no endogenous isoform validation","In vivo relevance not tested"]},{"year":2016,"claim":"Placed Plxna4 downstream of FoxO6 in cortical radial migration, defining a transcription-factor-to-receptor pathway controlling neuronal positioning.","evidence":"FoxO6 promoter-binding assay, siRNA knockdown, in utero electroporation with ectopic Plxna4 rescue, and transcriptome analysis","pmids":["27791111"],"confidence":"High","gaps":["Ligand and downstream effectors for migration not identified","Whether FoxO6 binding is direct in vivo not fully resolved"]},{"year":2022,"claim":"Identified FYN kinase as a downstream effector of SEMA3A→PLXNA4 signaling during neuronal differentiation, extending the receptor's signaling output.","evidence":"siRNA knockdown and recombinant protein addition in hUC-MSCs undergoing neural differentiation, RNA sequencing, and FYN activation assay","pmids":["35163445"],"confidence":"Medium","gaps":["Mechanism of FYN activation by PLXNA4 not defined","Non-neuronal differentiation model","Single lab"]},{"year":2024,"claim":"Demonstrated that the PlxnA4 GAP catalytic domain is required for hippocampal mossy fiber tract partitioning and laminar targeting, distinguishing enzymatic from structural receptor roles.","evidence":"Plxna4 knockout and GAP catalytic mutant knock-in mice with axon tract analysis (preprint)","pmids":["bio_10.1101_2024.12.15.628586"],"confidence":"Medium","gaps":["GAP substrate (target GTPase) not identified in this system","Preprint not peer-reviewed"]},{"year":2025,"claim":"Showed Plxna4 is locally translated in dopaminergic axons to control Sema3a-dependent arborization and nigrostriatal targeting, adding spatial regulation of receptor expression.","evidence":"RiboTag axon-specific ribosome profiling in DAT-Cre mice with in vitro and in vivo arborization/targeting assays (preprint)","pmids":["bio_10.1101_2025.11.25.690389"],"confidence":"Medium","gaps":["Mechanism targeting mRNA to axons unknown","Downstream signaling in mDA axons not mapped","Preprint"]},{"year":2025,"claim":"Extended PlexinA4 function beyond CNS, showing it (with PlexinA3) guides cardiac sympathetic innervation, with loss causing arrhythmia via adrenergic hypersensitivity.","evidence":"PlexinA3/A4 double knockout mouse with tissue clearing, echocardiography, ECG, optical mapping, catecholamine and β-adrenergic receptor density measurements (preprint)","pmids":["bio_10.1101_2025.05.20.655085"],"confidence":"Medium","gaps":["PlexinA4-specific contribution confounded by double knockout","Ligand driving cardiac innervation not defined","Preprint"]},{"year":2025,"claim":"Revealed a non-neuronal-circuit phenotype, with Plxna4 loss increasing adiposity and food intake in zebrafish, implicating it in feeding regulation.","evidence":"Zebrafish plxna4 loss-of-function mutants with body fat quantification, feeding and locomotor assays (preprint)","pmids":["bio_10.1101_2025.03.15.643290"],"confidence":"Medium","gaps":["Neural circuit or cell type mediating feeding effect unknown","Whether mammalian PLXNA4 has the same role untested","Preprint"]},{"year":null,"claim":"The molecular link between PLXNA4 GAP activity, its GTPase substrate, and the diverse downstream effectors (FYN, tau kinases) remains unresolved across its developmental and metabolic roles.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No identified GTPase substrate for the GAP domain in any system","Unified signaling model connecting ligand binding to cytoskeletal/transcriptional outputs absent","Direct structural data on ligand-receptor engagement not in corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0001618","term_label":"virus receptor activity","supporting_discovery_ids":[1,4]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[1,2,4]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[5]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[1,3,4,5,6]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,5]}],"complexes":[],"partners":["SEMA3A","FYN"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9HCM2","full_name":"Plexin-A4","aliases":[],"length_aa":1894,"mass_kda":212.5,"function":"Coreceptor for SEMA3A. Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance in the developing nervous system. Class 3 semaphorins bind to a complex composed of a neuropilin and a plexin. The plexin modulates the affinity of the complex for specific semaphorins, and its cytoplasmic domain is required for the activation of down-stream signaling events in the cytoplasm (By similarity)","subcellular_location":"Cell membrane","url":"https://www.uniprot.org/uniprotkb/Q9HCM2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PLXNA4","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PLXNA4","total_profiled":1310},"omim":[{"mim_id":"620997","title":"SEMAPHORIN 3G; SEMA3G","url":"https://www.omim.org/entry/620997"},{"mim_id":"618867","title":"RAS HOMOLOG GENE FAMILY, MEMBER F, FILOPODIA-ASSOCIATED; RHOF","url":"https://www.omim.org/entry/618867"},{"mim_id":"608873","title":"SEMAPHORIN 6B; SEMA6B","url":"https://www.omim.org/entry/608873"},{"mim_id":"605885","title":"SEMAPHORIN 6A; SEMA6A","url":"https://www.omim.org/entry/605885"},{"mim_id":"604280","title":"PLEXIN A4; PLXNA4","url":"https://www.omim.org/entry/604280"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Plasma membrane","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"adipose tissue","ntpm":13.0}],"url":"https://www.proteinatlas.org/search/PLXNA4"},"hgnc":{"alias_symbol":["KIAA1550","DKFZp434G0625PRO34003","FAYV2820"],"prev_symbol":["PLXNA4A","PLXNA4B"]},"alphafold":{"accession":"Q9HCM2","domains":[{"cath_id":"2.60.40.10","chopping":"528-655","consensus_level":"high","plddt":86.9334,"start":528,"end":655},{"cath_id":"2.60.40,2.60.40","chopping":"704-804","consensus_level":"high","plddt":88.6083,"start":704,"end":804},{"cath_id":"-","chopping":"811-854","consensus_level":"medium","plddt":78.1655,"start":811,"end":854},{"cath_id":"2.60.40.10","chopping":"860-1036","consensus_level":"medium","plddt":89.3558,"start":860,"end":1036},{"cath_id":"2.60.40.10","chopping":"1040-1140","consensus_level":"medium","plddt":84.5835,"start":1040,"end":1140},{"cath_id":"2.60.40.10","chopping":"1144-1229","consensus_level":"high","plddt":79.558,"start":1144,"end":1229},{"cath_id":"1.10.506.10","chopping":"1434-1476_1676-1841","consensus_level":"medium","plddt":87.8052,"start":1434,"end":1841},{"cath_id":"3.10.20.90","chopping":"1489-1601_1649-1653","consensus_level":"medium","plddt":84.146,"start":1489,"end":1653}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9HCM2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9HCM2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9HCM2-F1-predicted_aligned_error_v6.png","plddt_mean":83.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PLXNA4","jax_strain_url":"https://www.jax.org/strain/search?query=PLXNA4"},"sequence":{"accession":"Q9HCM2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9HCM2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9HCM2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9HCM2"}},"corpus_meta":[{"pmid":"25043464","id":"PMC_25043464","title":"PLXNA4 is associated with Alzheimer disease and modulates tau phosphorylation.","date":"2014","source":"Annals of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/25043464","citation_count":57,"is_preprint":false},{"pmid":"27791111","id":"PMC_27791111","title":"FoxO6 affects Plxna4-mediated neuronal migration during mouse cortical development.","date":"2016","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/27791111","citation_count":17,"is_preprint":false},{"pmid":"34234248","id":"PMC_34234248","title":"An artificial neural network approach integrating plasma proteomics and genetic data identifies PLXNA4 as a new susceptibility locus for pulmonary embolism.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/34234248","citation_count":14,"is_preprint":false},{"pmid":"30618575","id":"PMC_30618575","title":"Common Variants in PLXNA4 and Correlation to CSF-related Phenotypes in Alzheimer's Disease.","date":"2018","source":"Frontiers in neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/30618575","citation_count":13,"is_preprint":false},{"pmid":"27127761","id":"PMC_27127761","title":"Association study of the PLXNA4 gene with the risk of Alzheimer's disease.","date":"2016","source":"Annals of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/27127761","citation_count":6,"is_preprint":false},{"pmid":"35163445","id":"PMC_35163445","title":"Induction of PLXNA4 Gene during Neural Differentiation in Human Umbilical-Cord-Derived Mesenchymal Stem Cells by Low-Intensity Sub-Sonic Vibration.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35163445","citation_count":5,"is_preprint":false},{"pmid":"11306810","id":"PMC_11306810","title":"Chromosome assignment of four plexin A genes (Plxna1, Plxna2, Plxna3, Plxna4) in mouse, rat, Syrian hamster and Chinese hamster.","date":"2001","source":"Cytogenetics and cell genetics","url":"https://pubmed.ncbi.nlm.nih.gov/11306810","citation_count":5,"is_preprint":false},{"pmid":"39806094","id":"PMC_39806094","title":"Common Variants in PLXNA4 and Correlation to Neuroimaging Phenotypes in Healthy, Mild Cognitive Impairment, and Alzheimer's Disease Cohorts.","date":"2025","source":"Molecular neurobiology","url":"https://pubmed.ncbi.nlm.nih.gov/39806094","citation_count":0,"is_preprint":false},{"pmid":"37990741","id":"PMC_37990741","title":"Case report of PLXNA4 variant associated with hyper-response to phentermine/topiramate pharmacotherapy: Potential genetic basis for superior weight loss response?","date":"2023","source":"Obesity pillars","url":"https://pubmed.ncbi.nlm.nih.gov/37990741","citation_count":0,"is_preprint":false},{"pmid":"41663567","id":"PMC_41663567","title":"Med13 is involved in the radial migration and contralateral projection of cortical neurons via PlxnA4.","date":"2026","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/41663567","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.11.25.690389","title":"Axon-specific mRNA translation shapes dopaminergic circuit development","date":"2025-11-29","source":"bioRxiv","url":"https://doi.org/10.1101/2025.11.25.690389","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.12.15.628586","title":"Diverse and Location-Specific Roles of PlexinA2, PlexinA4, and NCAM in Developing Hippocampal Mossy Fibers","date":"2024-12-16","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.15.628586","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.03.15.643290","title":"Human genetic studies and zebrafish models identify Plxna4 as a regulator of adiposity, somatic growth, and feeding 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Populations","date":"2024-08-28","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.27.24312631","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11455,"output_tokens":2344,"usd":0.034763,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9415,"output_tokens":2787,"usd":0.058375,"stage2_stop_reason":"end_turn"},"total_usd":0.093138,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"Full-length PLXNA4 isoform (TS1) increases tau phosphorylation in SH-SY5Y cells and primary rat neurons when stimulated by SEMA3A, while shorter isoforms (TS2 and TS3) have the opposite effect. Transfection of any isoform into HEK293 cells stably expressing APP did not result in differential effects on APP processing or Aβ production (negative result for Aβ pathway).\",\n      \"method\": \"Cell transfection of isoforms into SH-SY5Y cells and primary rat neurons with SEMA3A stimulation; tau phosphorylation assay; HEK293 APP-stable cell line\",\n      \"journal\": \"Annals of neurology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cell-based overexpression with defined phosphorylation readout and multiple isoforms tested in two cell types, single lab\",\n      \"pmids\": [\"25043464\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"FoxO6 transcription factor binds to DAF-16-binding elements in the Plxna4 promoter and regulates its expression; ectopic Plxna4 expression rescues the radial migration defect caused by FoxO6 loss or siRNA knockdown in the developing neocortex, placing Plxna4 downstream of FoxO6 in a pathway controlling cortical neuronal migration.\",\n      \"method\": \"FoxO6 promoter binding assay (DAF-16-binding element), siRNA knockdown of FoxO6, in utero electroporation, ectopic Plxna4 rescue experiment, genome-wide transcriptome analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — epistasis established by rescue experiment, promoter binding demonstrated, multiple orthogonal methods (ChIP-like binding, siRNA, rescue), peer-reviewed\",\n      \"pmids\": [\"27791111\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In hUC-MSCs undergoing neural differentiation induced by low-intensity sub-sonic vibration, PLXNA4 is required downstream of SEMA3A for neuronal differentiation: SEMA3A expression increases, PLXNA4 knockdown blocks LISSV-induced upregulation of neuron-related genes, and PLXNA4 signaling activates FYN kinase as a downstream effector.\",\n      \"method\": \"siRNA knockdown of PLXNA4, PLXNA4 recombinant protein addition, RNA sequencing, gene expression analysis of neuron-related genes, FYN activation assay\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function (siRNA) and gain-of-function (recombinant protein) with defined pathway (SEMA3A→PLXNA4→FYN) in a single lab using multiple approaches\",\n      \"pmids\": [\"35163445\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Med13 regulates cortical neuronal radial migration and callosal (contralateral) projection at least in part through PlxnA4: Med13 knockdown in cortical neurons impairs radial migration and callosal projection, and overexpression of PlxnA4 largely restores radial migration and callosal projection (but not dendritic complexity) in Med13 knockdown neurons, placing PlxnA4 downstream of Med13.\",\n      \"method\": \"In utero electroporation-mediated Med13 knockdown, mass spectrometry proteomics identifying PLXNA4 as dysregulated, PlxnA4 overexpression rescue in Med13 KD neurons\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis by rescue experiment with orthogonal proteomic identification, single lab\",\n      \"pmids\": [\"41663567\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PlxnA4 is locally translated in midbrain dopaminergic (mDA) axons and modulates axonal arborization in response to Sema3a; Plxna4-mediated signaling regulates topographical axon targeting and innervation in the nigrostriatal pathway in vivo.\",\n      \"method\": \"RiboTag ribosome tagging to isolate axon-specific ribosome-bound mRNAs in mDA neurons (DATIRES-Cre mice), in vitro functional arborization assays, in vivo axon targeting assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RiboTag demonstrates local translation, in vitro and in vivo functional assays, preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.11.25.690389\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PlxnA4 controls mossy fiber partitioning into suprapyramidal (SPT) and infrapyramidal (IPT) tracts, SPT axon bundling, laminar targeting to stratum lucidum, and IPT length in the hippocampus. Many of these defects are replicated in mice deficient for PlxnA4 GAP catalytic activity, establishing that the GAP domain is required for these guidance functions.\",\n      \"method\": \"Plxna4 knockout mice, PlxnA4 GAP catalytic mutant knock-in mice, immunohistochemistry, axon tract analysis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function and catalytic domain mutant with defined axon guidance phenotypes; preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2024.12.15.628586\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In a PlexinA3/PlexinA4 double knockout mouse, loss of plexin-dependent cardiac sympathetic innervation leads to structurally normal hearts with spontaneous ventricular arrhythmias driven by adrenergic hypersensitivity and increased cardiac β-adrenergic receptor density, establishing a role for PlexinA4 (with PlexinA3) in developmental guidance of sympathetic nerves onto the heart.\",\n      \"method\": \"PlexinA3/A4 double knockout mouse, tissue clearing, immunohistochemistry, echocardiography, ECG, optical mapping of action potentials, catecholamine measurements, β-adrenergic receptor density quantification\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — knockout mouse with multiple orthogonal electrophysiological and pharmacological readouts; preprint; confounded by double knockout (PlexinA3+A4)\",\n      \"pmids\": [\"bio_10.1101_2025.05.20.655085\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Loss of Plxna4 function in zebrafish results in increased body fat, hypertrophic subcutaneous adipose tissue, shorter body length, increased food consumption, and food-stimulated hyperactivity (increased swimming speed), establishing a role for Plxna4 in regulating feeding behavior and adiposity.\",\n      \"method\": \"Zebrafish plxna4 loss-of-function mutants (85–92% protein reduction), body fat quantification, feeding assays, locomotor behavior assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function animal model with multiple quantitative phenotypic readouts; preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.03.15.643290\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"PLXNA4 is a semaphorin receptor (binding SEMA3A and Sema6A) that functions in axon guidance, neuronal migration, and circuit development: it acts downstream of FoxO6 and Med13 transcription factors to control cortical neuron radial migration and callosal projection, is locally translated in dopaminergic axons to mediate Sema3a-dependent arborization and nigrostriatal targeting, uses its GAP catalytic domain to direct hippocampal mossy fiber tract formation, and promotes tau phosphorylation in an isoform-specific manner upon SEMA3A stimulation; additionally, PlexinA4 (with PlexinA3) guides cardiac sympathetic innervation, and loss of Plxna4 in zebrafish increases adiposity and food intake.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PLXNA4 is a semaphorin receptor that transduces SEMA3A and Sema6A signals to direct axon guidance, neuronal migration, and circuit assembly during nervous system development [#1, #4]. It operates as a transcriptional effector node: FoxO6 binds DAF-16 elements in the Plxna4 promoter and the transcriptional regulator Med13 acts upstream, with ectopic PlxnA4 expression rescuing the cortical neuron radial migration and callosal projection defects produced by loss of either factor, placing Plxna4 downstream in these migration pathways [#1, #3]. PLXNA4 signaling engages FYN kinase as a downstream effector during SEMA3A-driven neuronal differentiation [#2], and its intrinsic GAP catalytic activity is required for hippocampal mossy fiber partitioning, axon bundling, and laminar targeting [#5]. In dopaminergic neurons, Plxna4 mRNA is locally translated within axons to modulate Sema3a-dependent arborization and nigrostriatal targeting [#4]. PLXNA4 acts in an isoform-specific manner: the full-length TS1 isoform increases tau phosphorylation upon SEMA3A stimulation while shorter isoforms have the opposite effect, without affecting APP processing or Aβ production [#0]. Beyond neurodevelopment, PlexinA4 (together with PlexinA3) guides cardiac sympathetic innervation, with its loss producing adrenergic hypersensitivity and ventricular arrhythmias [#6], and loss of Plxna4 in zebrafish increases adiposity and food intake [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Established that PLXNA4 isoforms differentially couple SEMA3A signaling to tau phosphorylation, linking a semaphorin receptor to a neurodegeneration-relevant readout and ruling out an amyloid route.\",\n      \"evidence\": \"Isoform transfection into SH-SY5Y cells and primary rat neurons with SEMA3A stimulation and tau phosphorylation assay; APP-stable HEK293 negative control\",\n      \"pmids\": [\"25043464\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting receptor signaling to tau kinases not defined\", \"Overexpression-based, no endogenous isoform validation\", \"In vivo relevance not tested\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Placed Plxna4 downstream of FoxO6 in cortical radial migration, defining a transcription-factor-to-receptor pathway controlling neuronal positioning.\",\n      \"evidence\": \"FoxO6 promoter-binding assay, siRNA knockdown, in utero electroporation with ectopic Plxna4 rescue, and transcriptome analysis\",\n      \"pmids\": [\"27791111\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ligand and downstream effectors for migration not identified\", \"Whether FoxO6 binding is direct in vivo not fully resolved\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identified FYN kinase as a downstream effector of SEMA3A→PLXNA4 signaling during neuronal differentiation, extending the receptor's signaling output.\",\n      \"evidence\": \"siRNA knockdown and recombinant protein addition in hUC-MSCs undergoing neural differentiation, RNA sequencing, and FYN activation assay\",\n      \"pmids\": [\"35163445\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of FYN activation by PLXNA4 not defined\", \"Non-neuronal differentiation model\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated that the PlxnA4 GAP catalytic domain is required for hippocampal mossy fiber tract partitioning and laminar targeting, distinguishing enzymatic from structural receptor roles.\",\n      \"evidence\": \"Plxna4 knockout and GAP catalytic mutant knock-in mice with axon tract analysis (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.12.15.628586\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"GAP substrate (target GTPase) not identified in this system\", \"Preprint not peer-reviewed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed Plxna4 is locally translated in dopaminergic axons to control Sema3a-dependent arborization and nigrostriatal targeting, adding spatial regulation of receptor expression.\",\n      \"evidence\": \"RiboTag axon-specific ribosome profiling in DAT-Cre mice with in vitro and in vivo arborization/targeting assays (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.11.25.690389\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism targeting mRNA to axons unknown\", \"Downstream signaling in mDA axons not mapped\", \"Preprint\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended PlexinA4 function beyond CNS, showing it (with PlexinA3) guides cardiac sympathetic innervation, with loss causing arrhythmia via adrenergic hypersensitivity.\",\n      \"evidence\": \"PlexinA3/A4 double knockout mouse with tissue clearing, echocardiography, ECG, optical mapping, catecholamine and β-adrenergic receptor density measurements (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.05.20.655085\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"PlexinA4-specific contribution confounded by double knockout\", \"Ligand driving cardiac innervation not defined\", \"Preprint\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Revealed a non-neuronal-circuit phenotype, with Plxna4 loss increasing adiposity and food intake in zebrafish, implicating it in feeding regulation.\",\n      \"evidence\": \"Zebrafish plxna4 loss-of-function mutants with body fat quantification, feeding and locomotor assays (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.03.15.643290\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Neural circuit or cell type mediating feeding effect unknown\", \"Whether mammalian PLXNA4 has the same role untested\", \"Preprint\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular link between PLXNA4 GAP activity, its GTPase substrate, and the diverse downstream effectors (FYN, tau kinases) remains unresolved across its developmental and metabolic roles.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No identified GTPase substrate for the GAP domain in any system\", \"Unified signaling model connecting ligand binding to cytoskeletal/transcriptional outputs absent\", \"Direct structural data on ligand-receptor engagement not in corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0001618\", \"supporting_discovery_ids\": [1, 4]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [1, 2, 4]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [1, 3, 4, 5, 6]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 5]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"SEMA3A\", \"FYN\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":2,"faith_total":4,"faith_pct":50.0}}