{"gene":"SEMA3F","run_date":"2026-04-28T20:42:07","timeline":{"discoveries":[{"year":2008,"finding":"SEMA3F forms a complex with NRP2 (neuropilin-2) and plexin A1, triggering a signaling cascade in which ABL2/ARG tyrosine kinase directly binds the cytoplasmic domain of plexin A1, phosphorylates and activates p190RhoGAP, which inactivates RhoA (GTP→GDP), resulting in cytoskeletal collapse and inhibition of cell migration in glioma and endothelial cells.","method":"Co-immunoprecipitation, in vitro kinase assay, siRNA knockdown of ABL2 and p190RhoGAP, dominant-negative ABL2 mutant overexpression, RhoA activity assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal methods including direct binding assays, mutagenesis of plexin A1 cytoplasmic domain, kinase assays, and siRNA rescue experiments in a single study","pmids":["18660502"],"is_preprint":false},{"year":2003,"finding":"SEMA3F inhibits cell attachment, spreading, lamellipodia extension, and membrane ruffling in breast cancer cells; these effects are mediated through NRP1 in MCF7 cells and NRP2 in C100 cells, and are antagonized by VEGF, which has opposite pro-adhesive effects. SEMA3F binds NRP2 with ~10-fold greater affinity than NRP1.","method":"Cell adhesion/spreading assays, blocking anti-NRP1/NRP2 antibodies, time-lapse microscopy of Rac1-GFP, receptor expression profiling","journal":"Neoplasia (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (functional assays + receptor blocking + live imaging) replicated across two cell lines","pmids":["12659673"],"is_preprint":false},{"year":2005,"finding":"SEMA3F exerts a chemorepulsive effect on motile breast cancer cells via NRP2, while in less motile MCF7 cells (NRP1-only) it inhibits E-cadherin- and β-catenin-mediated cell contacts at the membrane, reducing spreading and proliferation without inducing motility.","method":"3D culture migration assay, neurobiological stripe assay adapted for tumor cells, anti-NRP1/NRP2 blocking antibodies, immunofluorescence for E-cadherin and β-catenin","journal":"Neoplasia (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal assays with receptor-specific blocking, replicated across two breast cancer cell lines","pmids":["15802023"],"is_preprint":false},{"year":2007,"finding":"SEMA3F expression decreases integrin-linked kinase (ILK) kinase activity, activated αVβ3 integrin levels, adhesion to vitronectin, and downstream phospho-ERK1/2, phospho-AKT, and phospho-STAT3 signaling; it also reduces HIF-1α protein (via inhibition of AKT-driven translation initiation) and VEGF mRNA levels, and suppresses tumor microvessel density in vivo.","method":"Stable retroviral transfection, inducible expression systems, ILK kinase assay, ILK siRNA, phospho-protein immunoblotting, HIF-1α mRNA/protein degradation assays, nude mouse xenograft with microvessel density quantification","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal mechanistic assays (kinase assay, siRNA epistasis, in vivo) across multiple cell lines","pmids":["17875711"],"is_preprint":false},{"year":2005,"finding":"SEMA3F antitumor activity in vivo (NCI-H157 lung cancer orthotopic model) requires NRP2 expression; H460 cells expressing NRP1 but not NRP2 showed no survival benefit, establishing NRP2 as the functional receptor for SEMA3F's antitumor signaling in this context. The effect was associated with loss of activated αVβ3 integrin and reduced MAPK phosphorylation.","method":"Stable retroviral transfection, orthotopic nude rat tumor model, receptor expression profiling, integrin activation assay, phospho-ERK immunoblotting","journal":"Neoplasia (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 — in vivo epistasis with matched cell lines differing only in receptor expression, plus molecular readouts","pmids":["15967098"],"is_preprint":false},{"year":2010,"finding":"In the mouse olfactory system, Sema3F is secreted by early-arriving OSN axons and deposited at the anterodorsal olfactory bulb, where it repels later-arriving Nrp2-positive axons, establishing dorsal-ventral topographic map formation through sequential axon arrival and graded complementary expression of Nrp2 and Sema3F.","method":"Nrp2 and Sema3F knockout mice, in situ hybridization, axon tracing, in vivo olfactory map analysis","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 — genetic loss-of-function in mouse with defined anatomical phenotype, replicated with complementary molecular expression data","pmids":["20550939"],"is_preprint":false},{"year":2017,"finding":"Sema3F signals through the Neuropilin-2/PlexinA3 holoreceptor to mediate homeostatic downscaling of synaptic AMPA receptors (GluA1) in cortical neurons in response to increased neuronal activity; Npn-2 physically associates with AMPA receptors and Sema3F regulates this interaction.","method":"Co-immunoprecipitation of Npn-2 with GluA1, genetic knockout of Npn-2 and PlexA3, surface AMPAR quantification, electrophysiology, homeostatic scaling assays","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 1–2 — reciprocal co-IP, genetic KO, and functional electrophysiology in a single study","pmids":["29154130"],"is_preprint":false},{"year":2020,"finding":"CRMP2 mediates Sema3F signaling in primary neurons to regulate axon pruning in hippocampus and visual cortex and dendritic spine remodeling; crmp2-/- mice display prominent defects consistent with impaired Sema3F signaling, including ASD-related social behavior changes.","method":"crmp2-/- knockout mice, in vitro Sema3F signaling assays in primary neurons, stereotyped axon pruning analysis, dendritic spine morphometry, behavioral testing","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 2 — genetic KO with multiple orthogonal phenotypic readouts (anatomical + behavioral) and in vitro mechanistic confirmation","pmids":["31919978"],"is_preprint":false},{"year":2015,"finding":"SEMA3F acts predominantly through NRP2 to induce lymphatic endothelial cell (LEC) collapse and inhibit lymphangiogenesis; reconstitution of all plexin/neuropilin combinations in LECs showed NRP2 is the primary required coreceptor for SEMA3F signaling in LECs, and re-expression of SEMA3F in orthotopic HNSCC mouse models diminished lymphangiogenesis and lymph node metastasis.","method":"Recombinant SEMA3F protein, LEC collapse assay, reconstitution of plexin/neuropilin combinations, in vivo lymphangiogenesis assay, orthotopic HNSCC metastasis mouse model","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 1–2 — receptor reconstitution combined with in vivo rescue model","pmids":["25952650"],"is_preprint":false},{"year":2015,"finding":"SEMA3F inhibits invasion and metastasis of colorectal cancer cells through PI3K-AKT-dependent downregulation of the ASCL2-CXCR4 axis; CXCR4 antagonist AMD3100 rescued the metastasis-suppressive effect of SEMA3F knockdown both in vitro and in vivo.","method":"SEMA3F knockdown/overexpression, invasion assays, xenograft metastasis model, CXCR4 antagonist (AMD3100) rescue, PI3K-AKT pathway inhibition","journal":"The Journal of pathology","confidence":"High","confidence_rationale":"Tier 2 — epistasis with pharmacological rescue in vitro and in vivo, plus pathway validation","pmids":["25866254"],"is_preprint":false},{"year":2012,"finding":"RORα directly regulates SEMA3F transcription; chromatin immunoprecipitation and luciferase reporter assays showed RORα binds the SEMA3F promoter, and SEMA3F knockdown in RORα-expressing cancer cells rescued aggressive 3D phenotypes and tumor invasion, placing SEMA3F downstream of RORα as a mediator of tumor suppression.","method":"Chromatin immunoprecipitation (ChIP), luciferase reporter assay, siRNA knockdown, 3D culture morphogenesis assay, nude mouse tumor model","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 1–2 — direct promoter binding demonstrated by ChIP and reporter assay, epistatic rescue by SEMA3F knockdown","pmids":["22350413"],"is_preprint":false},{"year":2007,"finding":"SEMA3F directly binds to the cytoplasmic loop domain of connexin 43 (Cx43), controlling Cx43 localization at the plasma membrane and gap junctional intercellular communication (GJIC); siRNA knockdown of SEMA3F in IAR20 cells reduced membrane-associated Cx43 and GJIC activity.","method":"Yeast two-hybrid complementation and screening, immunofluorescence co-localization, siRNA knockdown of SEMA3F, GJIC functional assay","journal":"The Journal of membrane biology","confidence":"Medium","confidence_rationale":"Tier 2 — direct protein interaction demonstrated by yeast two-hybrid and supported by siRNA functional consequence, but single lab, not replicated","pmids":["17665084"],"is_preprint":false},{"year":2003,"finding":"Sema3F expressed by COS1 cell clusters placed on neocortical slices repels Nrp2-positive GABAergic neurons migrating from the ganglionic eminence; in vivo ectopic Sema3F expression diverts Dlx2-positive cells to the upper intermediate zone, demonstrating a role for Sema3F-Nrp2 interaction in sorting GABAergic interneurons during neocortical development.","method":"COS1 cell cluster placement on embryonic neocortical slices, in vivo ectopic expression, in situ hybridization for receptor expression, anti-NRP2 blocking","journal":"The Journal of comparative neurology","confidence":"High","confidence_rationale":"Tier 2 — functional in vitro slice assay with in vivo ectopic expression confirmation and receptor-specific blocking","pmids":["12454988"],"is_preprint":false},{"year":2005,"finding":"SEMA3F promoter is regulated epigenetically; methylation of a specific region (position −3850 to −3644) correlates with loss of expression in lung cancer cell lines, and histone deacetylase inhibition with Trichostatin A is more effective than demethylation (5-aza-2'-deoxycytidine) in restoring SEMA3F expression, indicating chromatin remodeling is the primary epigenetic mechanism of repression.","method":"Southern blot, methylation-specific PCR, transcriptional initiation site mapping, Trichostatin A and 5-aza-2'-deoxycytidine treatment, RT-PCR expression analysis","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 — direct methylation mapping with pharmacological perturbation, but single lab","pmids":["16005989"],"is_preprint":false},{"year":2017,"finding":"In visceral yolk sac epithelial cells, Sema3F signals to inhibit phosphorylation-dependent degradation of Myc, stabilizing Myc and driving expression of the pro-angiogenic miR-17/92 cluster while suppressing Thbs1 (thrombospondin 1), thereby promoting extraembryonic (but not intraembryonic) angiogenesis.","method":"Sema3f-null mouse characterization, AAV-mediated in vivo overexpression, F9 cell differentiation in vitro, exogenous recombinant Sema3F treatment, Myc phosphorylation/degradation assays, miRNA expression profiling, Thbs1 and Vegf pathway analysis","journal":"Arteriosclerosis, thrombosis, and vascular biology","confidence":"High","confidence_rationale":"Tier 2 — genetic null mouse combined with in vitro reconstitution with recombinant protein and molecular pathway dissection","pmids":["28729362"],"is_preprint":false},{"year":2021,"finding":"SEMA3F signaling through PLXNA1-A3 receptors guides GnRH neurons and olfactory/vomeronasal nerve fibers; loss-of-function variants in SEMA3F and PLXNA3 identified in IHH patients were functionally validated in HEK293T cells as deleterious, and SEMA3F/PLXNA3 were shown to be expressed along the olfactory nerve and GnRH neuron migratory pathway in early human fetal development.","method":"Exome sequencing of IHH patients, transient transfection functional assays in HEK293T, fluorescent immunohistochemistry on human fetal tissue","journal":"Genetics in medicine","confidence":"Medium","confidence_rationale":"Tier 2–3 — human genetic evidence combined with in vitro functional validation and human tissue expression, but mechanistic detail limited to variant loss-of-function","pmids":["33495532"],"is_preprint":false},{"year":2017,"finding":"Sema3f protects against subretinal neovascularization in vivo; AAV-mediated overexpression of Sema3f reduced pathological neovascularization by 56% in the Vldlr-/- model and intravitreal Sema3f injection reduced choroidal neovascularization by 30% in the laser-induced CNV model.","method":"AAV overexpression in Vldlr-/- mice, intravitreal recombinant protein injection in laser-induced CNV mouse model, neovascularization quantification","journal":"EBioMedicine","confidence":"Medium","confidence_rationale":"Tier 2 — two independent in vivo mouse models with gain-of-function intervention, but mechanism downstream of receptor not defined in this study","pmids":["28373097"],"is_preprint":false},{"year":2025,"finding":"Furin-mediated proteolytic processing is required for SEMA3F function; missense variants identified in a hearing-loss patient reduced furin-mediated processing of SEMA3F and abolished its ability to collapse the filamentous actin cytoskeleton in HUVECs. Inner ear-specific Sema3f knockout mice showed hearing loss with abnormal spiral ganglion neuron projections.","method":"In vitro furin cleavage assay with variant SEMA3F proteins, F-actin collapse assay in HUVECs, inner ear-specific Sema3f knockout mice, auditory brainstem response and DPOAE testing, spiral ganglion neuron projection analysis","journal":"Molecules and cells","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro biochemical processing assay with mutagenesis, functional collapse assay, and in vivo genetic model with defined phenotype","pmids":["39909336"],"is_preprint":false},{"year":2012,"finding":"Sema3F downregulates p53 expression in primary hippocampal neurons, contributing to axonal growth cone collapse; overexpression of p53 partially reversed Sema3F-induced growth cone collapse, and p53 inhibition/siRNA knockdown alone induced collapse, establishing p53 as a downstream mediator of Sema3F's collapsing activity.","method":"Primary hippocampal neuron culture, Sema3F treatment, p53 siRNA knockdown, p53 inhibitor, p53 overexpression, growth cone morphometry","journal":"International journal of clinical and experimental pathology","confidence":"Low","confidence_rationale":"Tier 3 — single lab, single set of methods, no direct biochemical link between Sema3F receptor signaling and p53 regulation established","pmids":["22977659"],"is_preprint":false},{"year":2020,"finding":"lncRNA FAM83C-AS1 epigenetically silences SEMA3F by stabilizing EZH2 protein through recruitment of ZRANB1, leading to increased H3K27me3 methylation at the SEMA3F promoter; SEMA3F is required for the tumor-suppressive effects of FAM83C-AS1 knockdown in colorectal cancer.","method":"EZH2 stabilization assay, H3K27me3 ChIP at SEMA3F promoter, ZRANB1 co-IP, FAM83C-AS1 knockdown with SEMA3F rescue in vitro and in vivo","journal":"Aging","confidence":"Medium","confidence_rationale":"Tier 2–3 — ChIP for histone mark at SEMA3F promoter, epistatic rescue, and co-IP, but single lab","pmids":["33109776"],"is_preprint":false},{"year":2025,"finding":"A bispecific antibody that dimerizes PLXNA1 and NRP2 (the SEMA3F receptor complex) mimics NRP2-mediated SEMA3F signaling, suppressing phospho-AKT, oncogene expression, and cell proliferation; structural studies showed the bsAb binds PLXNA1/NRP2 at sites distinct from the SEMA3F-binding site but allows proper receptor complex formation for signaling.","method":"Bispecific antibody engineering, receptor dimerization assay, phospho-AKT assay, cell proliferation assay, structural analysis of antibody-receptor binding","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 1–2 — structural and functional validation of receptor complex mechanism, but focused on agonist antibody rather than direct SEMA3F mechanism","pmids":["41391772"],"is_preprint":false}],"current_model":"SEMA3F is a secreted class 3 semaphorin that signals through heteromeric receptor complexes containing neuropilins (primarily NRP2, but also NRP1) and plexins (PlexinA1, PlexinA3), activating a cascade in which ABL2/ARG tyrosine kinase phosphorylates p190RhoGAP to inactivate RhoA, collapsing the actin cytoskeleton and inhibiting cell migration; it additionally suppresses ILK-ERK1/2, AKT-STAT3, and HIF-1α signaling to reduce tumor growth and angiogenesis, guides axons and GABAergic neurons via Nrp2 during neural development, mediates synaptic homeostatic scaling through Npn-2/PlexA3-AMPAR interactions, and promotes extraembryonic angiogenesis by stabilizing Myc to suppress Thbs1, with its activity requiring furin-mediated proteolytic processing and its transcription directly regulated by RORα and epigenetically repressed by EZH2-mediated H3K27 methylation."},"narrative":{"teleology":[{"year":2003,"claim":"Establishing that SEMA3F is a functional anti-adhesive/chemorepulsive ligand acting through neuropilins answered whether secreted semaphorins directly regulate tumor cell behavior and identified NRP2 as the preferred receptor.","evidence":"Cell adhesion/spreading assays with anti-NRP1/NRP2 blocking antibodies in breast cancer cells; GABAergic neuron repulsion assays on neocortical slices with in vivo ectopic expression","pmids":["12659673","12454988"],"confidence":"High","gaps":["Downstream intracellular signaling cascade not yet identified","Plexin co-receptor requirement not addressed","In vivo tumor-suppressive function not tested"]},{"year":2005,"claim":"In vivo epistasis experiments established that NRP2, not NRP1, is the required receptor for SEMA3F's antitumor activity and linked downstream effects to integrin inactivation and MAPK suppression.","evidence":"Orthotopic lung cancer models comparing NRP1-only vs NRP2-expressing cells; chemorepulsion vs adhesion-disruption phenotypes in matched breast cancer lines","pmids":["15967098","15802023"],"confidence":"High","gaps":["Direct plexin requirement not dissected","How NRP2 engagement leads to integrin inactivation was unknown"]},{"year":2005,"claim":"Demonstrating that SEMA3F is epigenetically silenced in lung cancer through promoter-associated histone modifications revealed a non-genetic mechanism for its loss in tumors.","evidence":"Methylation-specific PCR and TSA/5-aza treatment in lung cancer cell lines","pmids":["16005989"],"confidence":"Medium","gaps":["Specific histone modifier responsible not identified","Causal link between methylation mark and in vivo tumor progression not established"]},{"year":2007,"claim":"Identification of the ILK–ERK1/2, AKT–STAT3, and HIF-1α axes as SEMA3F-suppressed pathways explained how SEMA3F reduces VEGF and tumor angiogenesis in vivo.","evidence":"ILK kinase assay, ILK siRNA epistasis, phospho-protein immunoblotting, HIF-1α degradation assays, nude mouse xenograft with microvessel density quantification","pmids":["17875711"],"confidence":"High","gaps":["Molecular link between NRP2 engagement and ILK inhibition not defined","Relative contribution of each pathway to in vivo tumor suppression unclear"]},{"year":2008,"claim":"Discovery that ABL2/ARG kinase binds PlexinA1 cytoplasm and phosphorylates p190RhoGAP to inactivate RhoA provided the first complete intracellular signaling cascade from SEMA3F receptor to cytoskeletal collapse.","evidence":"Co-immunoprecipitation, in vitro kinase assay, dominant-negative ABL2, RhoA activity assay in glioma and endothelial cells","pmids":["18660502"],"confidence":"High","gaps":["Whether this pathway operates in all SEMA3F-responsive cell types was not tested","Relationship between RhoA inactivation and the integrin/ILK pathway not resolved"]},{"year":2010,"claim":"Demonstration that Sema3F deposited by early-arriving axons repels Nrp2-positive later-arriving axons established a temporal mechanism for olfactory bulb topographic map formation.","evidence":"Nrp2 and Sema3F knockout mice with axon tracing and olfactory map analysis","pmids":["20550939"],"confidence":"High","gaps":["Whether the same mechanism applies to other sensory maps not addressed","Intracellular signaling downstream of Nrp2 in OSN axons not dissected"]},{"year":2012,"claim":"Identification of RORα as a direct transcriptional activator of SEMA3F connected a nuclear receptor to semaphorin-mediated tumor suppression.","evidence":"ChIP showing RORα at SEMA3F promoter, luciferase reporter assay, siRNA epistasis in 3D culture and nude mouse models","pmids":["22350413"],"confidence":"High","gaps":["Whether RORα regulation is tissue-specific not established","Other transcription factors regulating SEMA3F not characterized"]},{"year":2015,"claim":"Receptor reconstitution in lymphatic endothelial cells confirmed NRP2 as the essential coreceptor for SEMA3F and demonstrated anti-lymphangiogenic and anti-metastatic activity in head and neck cancer.","evidence":"Plexin/neuropilin combination reconstitution in LECs, LEC collapse assay, orthotopic HNSCC metastasis mouse model","pmids":["25952650"],"confidence":"High","gaps":["Specific plexin partner required in LECs not fully resolved","Whether anti-lymphangiogenic effect is independent of anti-angiogenic effect unclear"]},{"year":2015,"claim":"Demonstrating that SEMA3F suppresses colorectal cancer metastasis through PI3K–AKT-dependent downregulation of the ASCL2–CXCR4 axis revealed a chemokine-receptor pathway as a distal effector.","evidence":"SEMA3F knockdown/overexpression with CXCR4 antagonist AMD3100 rescue in vitro and in xenograft metastasis model","pmids":["25866254"],"confidence":"High","gaps":["Whether ASCL2–CXCR4 axis suppression is generalizable beyond colorectal cancer not tested","Direct link from NRP2 to PI3K inhibition not mechanistically detailed"]},{"year":2017,"claim":"Discovery that Sema3F mediates homeostatic synaptic downscaling by regulating surface AMPA receptors through NRP2/PlexinA3 extended its function beyond guidance into activity-dependent synaptic plasticity.","evidence":"Co-immunoprecipitation of NRP2 with GluA1, genetic KO of Npn-2 and PlexA3, surface AMPAR quantification, electrophysiology","pmids":["29154130"],"confidence":"High","gaps":["Signaling cascade between PlexA3 and AMPAR internalization not defined","Source of activity-dependent Sema3F release not identified"]},{"year":2017,"claim":"Finding that Sema3F promotes extraembryonic angiogenesis by stabilizing Myc and suppressing Thbs1 revealed a pro-angiogenic role in development, contrasting with its anti-angiogenic tumor function.","evidence":"Sema3f-null mouse, AAV overexpression, F9 cell differentiation, Myc phosphorylation/degradation assays","pmids":["28729362"],"confidence":"High","gaps":["Receptor complex mediating this effect in yolk sac not identified","How Sema3F inhibits Myc phosphorylation mechanistically not resolved"]},{"year":2020,"claim":"Identification of CRMP2 as a downstream effector of Sema3F in axon pruning and dendritic spine remodeling, with behavioral consequences resembling ASD, connected guidance signaling to neurodevelopmental disorders.","evidence":"crmp2-/- mice with axon pruning and spine morphometry analysis, in vitro Sema3F signaling in primary neurons, behavioral testing","pmids":["31919978"],"confidence":"High","gaps":["Direct phosphorylation of CRMP2 by Sema3F pathway components not demonstrated","Whether SEMA3F variants contribute to ASD in humans not established"]},{"year":2020,"claim":"Demonstrating that EZH2-mediated H3K27me3 at the SEMA3F promoter, stabilized by lncRNA FAM83C-AS1/ZRANB1, silences SEMA3F identified the specific epigenetic repressor complex responsible for its loss in colorectal cancer.","evidence":"H3K27me3 ChIP at SEMA3F promoter, EZH2 stabilization assay, ZRANB1 co-IP, epistatic rescue in vitro and in vivo","pmids":["33109776"],"confidence":"Medium","gaps":["Whether this EZH2 mechanism operates across cancer types not tested","Single-lab finding not independently confirmed"]},{"year":2025,"claim":"Establishing that furin-mediated proteolytic processing is essential for SEMA3F activity, and that inner ear-specific Sema3f loss causes hearing impairment with aberrant spiral ganglion neuron projections, defined a new sensory phenotype and a required activation step.","evidence":"In vitro furin cleavage assay with patient-derived variants, F-actin collapse assay in HUVECs, inner ear-specific Sema3f KO mice with ABR testing","pmids":["39909336"],"confidence":"High","gaps":["Furin cleavage site(s) not mapped at residue resolution","Whether hearing loss is purely neuronal guidance-based or involves vascular dysfunction not resolved"]},{"year":null,"claim":"The molecular link between NRP2 engagement and suppression of ILK activity, the receptor complex mediating Sema3F's pro-angiogenic function in yolk sac, the mechanism by which SEMA3F stabilizes Myc, and structural details of the active processed SEMA3F–NRP2–PlexinA complex remain undefined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of processed SEMA3F bound to its holoreceptor","Mechanism linking receptor to ILK inhibition unknown","How context determines pro- vs anti-angiogenic outcome not resolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0048018","term_label":"receptor ligand activity","supporting_discovery_ids":[0,1,2,6,8]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,9,14]}],"localization":[{"term_id":"GO:0005576","term_label":"extracellular region","supporting_discovery_ids":[0,1,5,8,14]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,3,6,9,14]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[5,7,12,17]},{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[6,7]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[3,4,8,9]}],"complexes":[],"partners":["NRP2","NRP1","PLXNA1","PLXNA3","ABL2","CRMP2","GJA1"],"other_free_text":[]},"mechanistic_narrative":"SEMA3F is a secreted class 3 semaphorin that functions as a repulsive guidance cue and tumor suppressor by signaling through heteromeric receptor complexes containing neuropilin-2 (NRP2) and plexins (PlexinA1, PlexinA3) to reorganize the actin cytoskeleton, inhibit cell adhesion and migration, and regulate synaptic plasticity. Receptor engagement activates ABL2/ARG kinase, which phosphorylates p190RhoGAP to inactivate RhoA, causing cytoskeletal collapse, while simultaneously suppressing ILK–ERK1/2, PI3K–AKT–STAT3, and HIF-1α signaling to reduce integrin activation, VEGF expression, and tumor angiogenesis [PMID:18660502, PMID:17875711, PMID:25866254]. In the nervous system, SEMA3F–NRP2 signaling repels GABAergic interneurons during cortical migration, establishes olfactory bulb topography, mediates axon pruning through CRMP2, and drives homeostatic downscaling of synaptic AMPA receptors via NRP2/PlexinA3 [PMID:12454988, PMID:20550939, PMID:31919978, PMID:29154130]. SEMA3F requires furin-mediated proteolytic processing for activity, and loss-of-function variants in SEMA3F cause hearing loss with aberrant spiral ganglion neuron projections and are associated with idiopathic hypogonadotropic hypogonadism [PMID:39909336, PMID:33495532]."},"prefetch_data":{"uniprot":{"accession":"Q13275","full_name":"Semaphorin-3F","aliases":["Sema III/F","Semaphorin IV","Sema IV"],"length_aa":785,"mass_kda":88.4,"function":"May play a role in cell motility and cell adhesion","subcellular_location":"Secreted","url":"https://www.uniprot.org/uniprotkb/Q13275/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SEMA3F","classification":"Not Classified","n_dependent_lines":31,"n_total_lines":1208,"dependency_fraction":0.02566225165562914},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SEMA3F","total_profiled":1310},"omim":[{"mim_id":"620997","title":"SEMAPHORIN 3G; SEMA3G","url":"https://www.omim.org/entry/620997"},{"mim_id":"616165","title":"NEMALINE MYOPATHY 10; NEM10","url":"https://www.omim.org/entry/616165"},{"mim_id":"616112","title":"LEIOMODIN 3; LMOD3","url":"https://www.omim.org/entry/616112"},{"mim_id":"609907","title":"SEMAPHORIN 3D; SEMA3D","url":"https://www.omim.org/entry/609907"},{"mim_id":"604280","title":"PLEXIN A4; PLXNA4","url":"https://www.omim.org/entry/604280"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"esophagus","ntpm":96.2}],"url":"https://www.proteinatlas.org/search/SEMA3F"},"hgnc":{"alias_symbol":["SEMAK","Sema4"],"prev_symbol":[]},"alphafold":{"accession":"Q13275","domains":[{"cath_id":"-","chopping":"58-151_185-205","consensus_level":"medium","plddt":92.6952,"start":58,"end":205},{"cath_id":"2.130.10.10","chopping":"209-460","consensus_level":"medium","plddt":94.5111,"start":209,"end":460},{"cath_id":"3.30.1680.10","chopping":"547-605","consensus_level":"high","plddt":85.2702,"start":547,"end":605},{"cath_id":"2.60.40.10","chopping":"611-707","consensus_level":"high","plddt":90.9802,"start":611,"end":707},{"cath_id":"2.60.40","chopping":"27-49_466-545","consensus_level":"medium","plddt":94.025,"start":27,"end":545}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13275","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q13275-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q13275-F1-predicted_aligned_error_v6.png","plddt_mean":83.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SEMA3F","jax_strain_url":"https://www.jax.org/strain/search?query=SEMA3F"},"sequence":{"accession":"Q13275","fasta_url":"https://rest.uniprot.org/uniprotkb/Q13275.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q13275/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13275"}},"corpus_meta":[{"pmid":"8786119","id":"PMC_8786119","title":"Isolation of the human semaphorin III/F gene (SEMA3F) at chromosome 3p21, a region deleted in lung cancer.","date":"1996","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/8786119","citation_count":131,"is_preprint":false},{"pmid":"12845630","id":"PMC_12845630","title":"Expression of VEGF, semaphorin SEMA3F, and their common receptors neuropilins NP1 and NP2 in preinvasive bronchial lesions, lung tumours, and cell lines.","date":"2003","source":"The Journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/12845630","citation_count":122,"is_preprint":false},{"pmid":"20550939","id":"PMC_20550939","title":"Sequential arrival and graded secretion of Sema3F by olfactory neuron axons specify map topography at the bulb.","date":"2010","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/20550939","citation_count":111,"is_preprint":false},{"pmid":"22350413","id":"PMC_22350413","title":"RORα suppresses breast tumor invasion by inducing SEMA3F expression.","date":"2012","source":"Cancer 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cancer development by epigenetically inhibits SEMA3F via stabilizing EZH2.","date":"2020","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/33109776","citation_count":16,"is_preprint":false},{"pmid":"31968181","id":"PMC_31968181","title":"SEMA3F Promotes Liver Hepatocellular Carcinoma Metastasis by Activating Focal Adhesion Pathway.","date":"2020","source":"DNA and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/31968181","citation_count":15,"is_preprint":false},{"pmid":"16261621","id":"PMC_16261621","title":"Sema3D, Sema3F, and Sema5A are expressed in overlapping and distinct patterns in chick embryonic heart.","date":"2006","source":"Developmental dynamics : an official publication of the American Association of Anatomists","url":"https://pubmed.ncbi.nlm.nih.gov/16261621","citation_count":15,"is_preprint":false},{"pmid":"28729362","id":"PMC_28729362","title":"Sema3F (Semaphorin 3F) Selectively Drives an Extraembryonic Proangiogenic Program.","date":"2017","source":"Arteriosclerosis, thrombosis, and vascular biology","url":"https://pubmed.ncbi.nlm.nih.gov/28729362","citation_count":14,"is_preprint":false},{"pmid":"21815834","id":"PMC_21815834","title":"Expression patterns of Sema3F, PlexinA4, -A3, Neuropilin1 and -2 in the postnatal mouse molar suggest roles in tooth innervation and organogenesis.","date":"2011","source":"Acta odontologica Scandinavica","url":"https://pubmed.ncbi.nlm.nih.gov/21815834","citation_count":12,"is_preprint":false},{"pmid":"39909336","id":"PMC_39909336","title":"Biallelic variants of SEMA3F are associated with nonsyndromic hearing loss.","date":"2025","source":"Molecules and cells","url":"https://pubmed.ncbi.nlm.nih.gov/39909336","citation_count":6,"is_preprint":false},{"pmid":"22977659","id":"PMC_22977659","title":"Sema3F downregulates p53 expression leading to axonal growth cone collapse in primary hippocampal neurons.","date":"2012","source":"International journal of clinical and 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BCR","url":"https://pubmed.ncbi.nlm.nih.gov/39138514","citation_count":1,"is_preprint":false},{"pmid":"12561429","id":"PMC_12561429","title":"[Mutation and expression of SEMA3B and SEMA3F gene in nasopharyngeal carcinoma].","date":"2003","source":"Ai zheng = Aizheng = Chinese journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/12561429","citation_count":1,"is_preprint":false},{"pmid":"41029010","id":"PMC_41029010","title":"Effect of Sema3F on VEGF in Primary Rat Hippocampal Neurons In vitro.","date":"2025","source":"Current molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41029010","citation_count":0,"is_preprint":false},{"pmid":"41391772","id":"PMC_41391772","title":"A bispecific antibody designed to act as a NRP2/PLXNA1 agonist mimics anticancer activity of SEMA3F.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/41391772","citation_count":0,"is_preprint":false},{"pmid":"40319865","id":"PMC_40319865","title":"Effect of SEMA3F on Proliferation, Migration, and Ferroptosis of Endometrial Stromal Cells in Patients with Endometriosis.","date":"2025","source":"Gynecologic and obstetric investigation","url":"https://pubmed.ncbi.nlm.nih.gov/40319865","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.07.18.665640","title":"Semaphorin 3A and 3F overexpression in TIE2 hyperactive endothelial cells contribute to the pathological lumen expansion in venous malformation","date":"2025-07-20","source":"bioRxiv","url":"https://doi.org/10.1101/2025.07.18.665640","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.09.12.612713","title":"Gene identification for ocular congenital cranial motor neuron disorders using human sequencing, zebrafish screening, and protein binding microarrays","date":"2024-09-15","source":"bioRxiv","url":"https://doi.org/10.1101/2024.09.12.612713","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.10.16.618445","title":"Microglia attenuate regenerative neurogenesis via  <i>sema4ab</i>  after spinal cord injury in zebrafish","date":"2024-10-18","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.16.618445","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":23521,"output_tokens":5634,"usd":0.077536},"stage2":{"model":"claude-opus-4-6","input_tokens":9222,"output_tokens":3489,"usd":0.200002},"total_usd":0.277538,"stage1_batch_id":"msgbatch_011rkcQdVV1RaFq9XhcG6df6","stage2_batch_id":"msgbatch_01RzgrJafdF4EWHhj5mNi6dh","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2008,\n      \"finding\": \"SEMA3F forms a complex with NRP2 (neuropilin-2) and plexin A1, triggering a signaling cascade in which ABL2/ARG tyrosine kinase directly binds the cytoplasmic domain of plexin A1, phosphorylates and activates p190RhoGAP, which inactivates RhoA (GTP→GDP), resulting in cytoskeletal collapse and inhibition of cell migration in glioma and endothelial cells.\",\n      \"method\": \"Co-immunoprecipitation, in vitro kinase assay, siRNA knockdown of ABL2 and p190RhoGAP, dominant-negative ABL2 mutant overexpression, RhoA activity assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal methods including direct binding assays, mutagenesis of plexin A1 cytoplasmic domain, kinase assays, and siRNA rescue experiments in a single study\",\n      \"pmids\": [\"18660502\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"SEMA3F inhibits cell attachment, spreading, lamellipodia extension, and membrane ruffling in breast cancer cells; these effects are mediated through NRP1 in MCF7 cells and NRP2 in C100 cells, and are antagonized by VEGF, which has opposite pro-adhesive effects. SEMA3F binds NRP2 with ~10-fold greater affinity than NRP1.\",\n      \"method\": \"Cell adhesion/spreading assays, blocking anti-NRP1/NRP2 antibodies, time-lapse microscopy of Rac1-GFP, receptor expression profiling\",\n      \"journal\": \"Neoplasia (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (functional assays + receptor blocking + live imaging) replicated across two cell lines\",\n      \"pmids\": [\"12659673\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"SEMA3F exerts a chemorepulsive effect on motile breast cancer cells via NRP2, while in less motile MCF7 cells (NRP1-only) it inhibits E-cadherin- and β-catenin-mediated cell contacts at the membrane, reducing spreading and proliferation without inducing motility.\",\n      \"method\": \"3D culture migration assay, neurobiological stripe assay adapted for tumor cells, anti-NRP1/NRP2 blocking antibodies, immunofluorescence for E-cadherin and β-catenin\",\n      \"journal\": \"Neoplasia (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal assays with receptor-specific blocking, replicated across two breast cancer cell lines\",\n      \"pmids\": [\"15802023\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"SEMA3F expression decreases integrin-linked kinase (ILK) kinase activity, activated αVβ3 integrin levels, adhesion to vitronectin, and downstream phospho-ERK1/2, phospho-AKT, and phospho-STAT3 signaling; it also reduces HIF-1α protein (via inhibition of AKT-driven translation initiation) and VEGF mRNA levels, and suppresses tumor microvessel density in vivo.\",\n      \"method\": \"Stable retroviral transfection, inducible expression systems, ILK kinase assay, ILK siRNA, phospho-protein immunoblotting, HIF-1α mRNA/protein degradation assays, nude mouse xenograft with microvessel density quantification\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal mechanistic assays (kinase assay, siRNA epistasis, in vivo) across multiple cell lines\",\n      \"pmids\": [\"17875711\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"SEMA3F antitumor activity in vivo (NCI-H157 lung cancer orthotopic model) requires NRP2 expression; H460 cells expressing NRP1 but not NRP2 showed no survival benefit, establishing NRP2 as the functional receptor for SEMA3F's antitumor signaling in this context. The effect was associated with loss of activated αVβ3 integrin and reduced MAPK phosphorylation.\",\n      \"method\": \"Stable retroviral transfection, orthotopic nude rat tumor model, receptor expression profiling, integrin activation assay, phospho-ERK immunoblotting\",\n      \"journal\": \"Neoplasia (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo epistasis with matched cell lines differing only in receptor expression, plus molecular readouts\",\n      \"pmids\": [\"15967098\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"In the mouse olfactory system, Sema3F is secreted by early-arriving OSN axons and deposited at the anterodorsal olfactory bulb, where it repels later-arriving Nrp2-positive axons, establishing dorsal-ventral topographic map formation through sequential axon arrival and graded complementary expression of Nrp2 and Sema3F.\",\n      \"method\": \"Nrp2 and Sema3F knockout mice, in situ hybridization, axon tracing, in vivo olfactory map analysis\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic loss-of-function in mouse with defined anatomical phenotype, replicated with complementary molecular expression data\",\n      \"pmids\": [\"20550939\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Sema3F signals through the Neuropilin-2/PlexinA3 holoreceptor to mediate homeostatic downscaling of synaptic AMPA receptors (GluA1) in cortical neurons in response to increased neuronal activity; Npn-2 physically associates with AMPA receptors and Sema3F regulates this interaction.\",\n      \"method\": \"Co-immunoprecipitation of Npn-2 with GluA1, genetic knockout of Npn-2 and PlexA3, surface AMPAR quantification, electrophysiology, homeostatic scaling assays\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — reciprocal co-IP, genetic KO, and functional electrophysiology in a single study\",\n      \"pmids\": [\"29154130\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CRMP2 mediates Sema3F signaling in primary neurons to regulate axon pruning in hippocampus and visual cortex and dendritic spine remodeling; crmp2-/- mice display prominent defects consistent with impaired Sema3F signaling, including ASD-related social behavior changes.\",\n      \"method\": \"crmp2-/- knockout mice, in vitro Sema3F signaling assays in primary neurons, stereotyped axon pruning analysis, dendritic spine morphometry, behavioral testing\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic KO with multiple orthogonal phenotypic readouts (anatomical + behavioral) and in vitro mechanistic confirmation\",\n      \"pmids\": [\"31919978\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"SEMA3F acts predominantly through NRP2 to induce lymphatic endothelial cell (LEC) collapse and inhibit lymphangiogenesis; reconstitution of all plexin/neuropilin combinations in LECs showed NRP2 is the primary required coreceptor for SEMA3F signaling in LECs, and re-expression of SEMA3F in orthotopic HNSCC mouse models diminished lymphangiogenesis and lymph node metastasis.\",\n      \"method\": \"Recombinant SEMA3F protein, LEC collapse assay, reconstitution of plexin/neuropilin combinations, in vivo lymphangiogenesis assay, orthotopic HNSCC metastasis mouse model\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — receptor reconstitution combined with in vivo rescue model\",\n      \"pmids\": [\"25952650\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"SEMA3F inhibits invasion and metastasis of colorectal cancer cells through PI3K-AKT-dependent downregulation of the ASCL2-CXCR4 axis; CXCR4 antagonist AMD3100 rescued the metastasis-suppressive effect of SEMA3F knockdown both in vitro and in vivo.\",\n      \"method\": \"SEMA3F knockdown/overexpression, invasion assays, xenograft metastasis model, CXCR4 antagonist (AMD3100) rescue, PI3K-AKT pathway inhibition\",\n      \"journal\": \"The Journal of pathology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — epistasis with pharmacological rescue in vitro and in vivo, plus pathway validation\",\n      \"pmids\": [\"25866254\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"RORα directly regulates SEMA3F transcription; chromatin immunoprecipitation and luciferase reporter assays showed RORα binds the SEMA3F promoter, and SEMA3F knockdown in RORα-expressing cancer cells rescued aggressive 3D phenotypes and tumor invasion, placing SEMA3F downstream of RORα as a mediator of tumor suppression.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), luciferase reporter assay, siRNA knockdown, 3D culture morphogenesis assay, nude mouse tumor model\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — direct promoter binding demonstrated by ChIP and reporter assay, epistatic rescue by SEMA3F knockdown\",\n      \"pmids\": [\"22350413\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"SEMA3F directly binds to the cytoplasmic loop domain of connexin 43 (Cx43), controlling Cx43 localization at the plasma membrane and gap junctional intercellular communication (GJIC); siRNA knockdown of SEMA3F in IAR20 cells reduced membrane-associated Cx43 and GJIC activity.\",\n      \"method\": \"Yeast two-hybrid complementation and screening, immunofluorescence co-localization, siRNA knockdown of SEMA3F, GJIC functional assay\",\n      \"journal\": \"The Journal of membrane biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct protein interaction demonstrated by yeast two-hybrid and supported by siRNA functional consequence, but single lab, not replicated\",\n      \"pmids\": [\"17665084\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Sema3F expressed by COS1 cell clusters placed on neocortical slices repels Nrp2-positive GABAergic neurons migrating from the ganglionic eminence; in vivo ectopic Sema3F expression diverts Dlx2-positive cells to the upper intermediate zone, demonstrating a role for Sema3F-Nrp2 interaction in sorting GABAergic interneurons during neocortical development.\",\n      \"method\": \"COS1 cell cluster placement on embryonic neocortical slices, in vivo ectopic expression, in situ hybridization for receptor expression, anti-NRP2 blocking\",\n      \"journal\": \"The Journal of comparative neurology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — functional in vitro slice assay with in vivo ectopic expression confirmation and receptor-specific blocking\",\n      \"pmids\": [\"12454988\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"SEMA3F promoter is regulated epigenetically; methylation of a specific region (position −3850 to −3644) correlates with loss of expression in lung cancer cell lines, and histone deacetylase inhibition with Trichostatin A is more effective than demethylation (5-aza-2'-deoxycytidine) in restoring SEMA3F expression, indicating chromatin remodeling is the primary epigenetic mechanism of repression.\",\n      \"method\": \"Southern blot, methylation-specific PCR, transcriptional initiation site mapping, Trichostatin A and 5-aza-2'-deoxycytidine treatment, RT-PCR expression analysis\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct methylation mapping with pharmacological perturbation, but single lab\",\n      \"pmids\": [\"16005989\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"In visceral yolk sac epithelial cells, Sema3F signals to inhibit phosphorylation-dependent degradation of Myc, stabilizing Myc and driving expression of the pro-angiogenic miR-17/92 cluster while suppressing Thbs1 (thrombospondin 1), thereby promoting extraembryonic (but not intraembryonic) angiogenesis.\",\n      \"method\": \"Sema3f-null mouse characterization, AAV-mediated in vivo overexpression, F9 cell differentiation in vitro, exogenous recombinant Sema3F treatment, Myc phosphorylation/degradation assays, miRNA expression profiling, Thbs1 and Vegf pathway analysis\",\n      \"journal\": \"Arteriosclerosis, thrombosis, and vascular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic null mouse combined with in vitro reconstitution with recombinant protein and molecular pathway dissection\",\n      \"pmids\": [\"28729362\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SEMA3F signaling through PLXNA1-A3 receptors guides GnRH neurons and olfactory/vomeronasal nerve fibers; loss-of-function variants in SEMA3F and PLXNA3 identified in IHH patients were functionally validated in HEK293T cells as deleterious, and SEMA3F/PLXNA3 were shown to be expressed along the olfactory nerve and GnRH neuron migratory pathway in early human fetal development.\",\n      \"method\": \"Exome sequencing of IHH patients, transient transfection functional assays in HEK293T, fluorescent immunohistochemistry on human fetal tissue\",\n      \"journal\": \"Genetics in medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — human genetic evidence combined with in vitro functional validation and human tissue expression, but mechanistic detail limited to variant loss-of-function\",\n      \"pmids\": [\"33495532\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Sema3f protects against subretinal neovascularization in vivo; AAV-mediated overexpression of Sema3f reduced pathological neovascularization by 56% in the Vldlr-/- model and intravitreal Sema3f injection reduced choroidal neovascularization by 30% in the laser-induced CNV model.\",\n      \"method\": \"AAV overexpression in Vldlr-/- mice, intravitreal recombinant protein injection in laser-induced CNV mouse model, neovascularization quantification\",\n      \"journal\": \"EBioMedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — two independent in vivo mouse models with gain-of-function intervention, but mechanism downstream of receptor not defined in this study\",\n      \"pmids\": [\"28373097\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Furin-mediated proteolytic processing is required for SEMA3F function; missense variants identified in a hearing-loss patient reduced furin-mediated processing of SEMA3F and abolished its ability to collapse the filamentous actin cytoskeleton in HUVECs. Inner ear-specific Sema3f knockout mice showed hearing loss with abnormal spiral ganglion neuron projections.\",\n      \"method\": \"In vitro furin cleavage assay with variant SEMA3F proteins, F-actin collapse assay in HUVECs, inner ear-specific Sema3f knockout mice, auditory brainstem response and DPOAE testing, spiral ganglion neuron projection analysis\",\n      \"journal\": \"Molecules and cells\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro biochemical processing assay with mutagenesis, functional collapse assay, and in vivo genetic model with defined phenotype\",\n      \"pmids\": [\"39909336\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Sema3F downregulates p53 expression in primary hippocampal neurons, contributing to axonal growth cone collapse; overexpression of p53 partially reversed Sema3F-induced growth cone collapse, and p53 inhibition/siRNA knockdown alone induced collapse, establishing p53 as a downstream mediator of Sema3F's collapsing activity.\",\n      \"method\": \"Primary hippocampal neuron culture, Sema3F treatment, p53 siRNA knockdown, p53 inhibitor, p53 overexpression, growth cone morphometry\",\n      \"journal\": \"International journal of clinical and experimental pathology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, single set of methods, no direct biochemical link between Sema3F receptor signaling and p53 regulation established\",\n      \"pmids\": [\"22977659\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"lncRNA FAM83C-AS1 epigenetically silences SEMA3F by stabilizing EZH2 protein through recruitment of ZRANB1, leading to increased H3K27me3 methylation at the SEMA3F promoter; SEMA3F is required for the tumor-suppressive effects of FAM83C-AS1 knockdown in colorectal cancer.\",\n      \"method\": \"EZH2 stabilization assay, H3K27me3 ChIP at SEMA3F promoter, ZRANB1 co-IP, FAM83C-AS1 knockdown with SEMA3F rescue in vitro and in vivo\",\n      \"journal\": \"Aging\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — ChIP for histone mark at SEMA3F promoter, epistatic rescue, and co-IP, but single lab\",\n      \"pmids\": [\"33109776\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A bispecific antibody that dimerizes PLXNA1 and NRP2 (the SEMA3F receptor complex) mimics NRP2-mediated SEMA3F signaling, suppressing phospho-AKT, oncogene expression, and cell proliferation; structural studies showed the bsAb binds PLXNA1/NRP2 at sites distinct from the SEMA3F-binding site but allows proper receptor complex formation for signaling.\",\n      \"method\": \"Bispecific antibody engineering, receptor dimerization assay, phospho-AKT assay, cell proliferation assay, structural analysis of antibody-receptor binding\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 — structural and functional validation of receptor complex mechanism, but focused on agonist antibody rather than direct SEMA3F mechanism\",\n      \"pmids\": [\"41391772\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SEMA3F is a secreted class 3 semaphorin that signals through heteromeric receptor complexes containing neuropilins (primarily NRP2, but also NRP1) and plexins (PlexinA1, PlexinA3), activating a cascade in which ABL2/ARG tyrosine kinase phosphorylates p190RhoGAP to inactivate RhoA, collapsing the actin cytoskeleton and inhibiting cell migration; it additionally suppresses ILK-ERK1/2, AKT-STAT3, and HIF-1α signaling to reduce tumor growth and angiogenesis, guides axons and GABAergic neurons via Nrp2 during neural development, mediates synaptic homeostatic scaling through Npn-2/PlexA3-AMPAR interactions, and promotes extraembryonic angiogenesis by stabilizing Myc to suppress Thbs1, with its activity requiring furin-mediated proteolytic processing and its transcription directly regulated by RORα and epigenetically repressed by EZH2-mediated H3K27 methylation.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SEMA3F is a secreted class 3 semaphorin that functions as a repulsive guidance cue and tumor suppressor by signaling through heteromeric receptor complexes containing neuropilin-2 (NRP2) and plexins (PlexinA1, PlexinA3) to reorganize the actin cytoskeleton, inhibit cell adhesion and migration, and regulate synaptic plasticity. Receptor engagement activates ABL2/ARG kinase, which phosphorylates p190RhoGAP to inactivate RhoA, causing cytoskeletal collapse, while simultaneously suppressing ILK–ERK1/2, PI3K–AKT–STAT3, and HIF-1α signaling to reduce integrin activation, VEGF expression, and tumor angiogenesis [PMID:18660502, PMID:17875711, PMID:25866254]. In the nervous system, SEMA3F–NRP2 signaling repels GABAergic interneurons during cortical migration, establishes olfactory bulb topography, mediates axon pruning through CRMP2, and drives homeostatic downscaling of synaptic AMPA receptors via NRP2/PlexinA3 [PMID:12454988, PMID:20550939, PMID:31919978, PMID:29154130]. SEMA3F requires furin-mediated proteolytic processing for activity, and loss-of-function variants in SEMA3F cause hearing loss with aberrant spiral ganglion neuron projections and are associated with idiopathic hypogonadotropic hypogonadism [PMID:39909336, PMID:33495532].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Establishing that SEMA3F is a functional anti-adhesive/chemorepulsive ligand acting through neuropilins answered whether secreted semaphorins directly regulate tumor cell behavior and identified NRP2 as the preferred receptor.\",\n      \"evidence\": \"Cell adhesion/spreading assays with anti-NRP1/NRP2 blocking antibodies in breast cancer cells; GABAergic neuron repulsion assays on neocortical slices with in vivo ectopic expression\",\n      \"pmids\": [\"12659673\", \"12454988\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream intracellular signaling cascade not yet identified\", \"Plexin co-receptor requirement not addressed\", \"In vivo tumor-suppressive function not tested\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"In vivo epistasis experiments established that NRP2, not NRP1, is the required receptor for SEMA3F's antitumor activity and linked downstream effects to integrin inactivation and MAPK suppression.\",\n      \"evidence\": \"Orthotopic lung cancer models comparing NRP1-only vs NRP2-expressing cells; chemorepulsion vs adhesion-disruption phenotypes in matched breast cancer lines\",\n      \"pmids\": [\"15967098\", \"15802023\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct plexin requirement not dissected\", \"How NRP2 engagement leads to integrin inactivation was unknown\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Demonstrating that SEMA3F is epigenetically silenced in lung cancer through promoter-associated histone modifications revealed a non-genetic mechanism for its loss in tumors.\",\n      \"evidence\": \"Methylation-specific PCR and TSA/5-aza treatment in lung cancer cell lines\",\n      \"pmids\": [\"16005989\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific histone modifier responsible not identified\", \"Causal link between methylation mark and in vivo tumor progression not established\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Identification of the ILK–ERK1/2, AKT–STAT3, and HIF-1α axes as SEMA3F-suppressed pathways explained how SEMA3F reduces VEGF and tumor angiogenesis in vivo.\",\n      \"evidence\": \"ILK kinase assay, ILK siRNA epistasis, phospho-protein immunoblotting, HIF-1α degradation assays, nude mouse xenograft with microvessel density quantification\",\n      \"pmids\": [\"17875711\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular link between NRP2 engagement and ILK inhibition not defined\", \"Relative contribution of each pathway to in vivo tumor suppression unclear\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Discovery that ABL2/ARG kinase binds PlexinA1 cytoplasm and phosphorylates p190RhoGAP to inactivate RhoA provided the first complete intracellular signaling cascade from SEMA3F receptor to cytoskeletal collapse.\",\n      \"evidence\": \"Co-immunoprecipitation, in vitro kinase assay, dominant-negative ABL2, RhoA activity assay in glioma and endothelial cells\",\n      \"pmids\": [\"18660502\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether this pathway operates in all SEMA3F-responsive cell types was not tested\", \"Relationship between RhoA inactivation and the integrin/ILK pathway not resolved\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Demonstration that Sema3F deposited by early-arriving axons repels Nrp2-positive later-arriving axons established a temporal mechanism for olfactory bulb topographic map formation.\",\n      \"evidence\": \"Nrp2 and Sema3F knockout mice with axon tracing and olfactory map analysis\",\n      \"pmids\": [\"20550939\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the same mechanism applies to other sensory maps not addressed\", \"Intracellular signaling downstream of Nrp2 in OSN axons not dissected\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identification of RORα as a direct transcriptional activator of SEMA3F connected a nuclear receptor to semaphorin-mediated tumor suppression.\",\n      \"evidence\": \"ChIP showing RORα at SEMA3F promoter, luciferase reporter assay, siRNA epistasis in 3D culture and nude mouse models\",\n      \"pmids\": [\"22350413\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether RORα regulation is tissue-specific not established\", \"Other transcription factors regulating SEMA3F not characterized\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Receptor reconstitution in lymphatic endothelial cells confirmed NRP2 as the essential coreceptor for SEMA3F and demonstrated anti-lymphangiogenic and anti-metastatic activity in head and neck cancer.\",\n      \"evidence\": \"Plexin/neuropilin combination reconstitution in LECs, LEC collapse assay, orthotopic HNSCC metastasis mouse model\",\n      \"pmids\": [\"25952650\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific plexin partner required in LECs not fully resolved\", \"Whether anti-lymphangiogenic effect is independent of anti-angiogenic effect unclear\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrating that SEMA3F suppresses colorectal cancer metastasis through PI3K–AKT-dependent downregulation of the ASCL2–CXCR4 axis revealed a chemokine-receptor pathway as a distal effector.\",\n      \"evidence\": \"SEMA3F knockdown/overexpression with CXCR4 antagonist AMD3100 rescue in vitro and in xenograft metastasis model\",\n      \"pmids\": [\"25866254\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether ASCL2–CXCR4 axis suppression is generalizable beyond colorectal cancer not tested\", \"Direct link from NRP2 to PI3K inhibition not mechanistically detailed\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Discovery that Sema3F mediates homeostatic synaptic downscaling by regulating surface AMPA receptors through NRP2/PlexinA3 extended its function beyond guidance into activity-dependent synaptic plasticity.\",\n      \"evidence\": \"Co-immunoprecipitation of NRP2 with GluA1, genetic KO of Npn-2 and PlexA3, surface AMPAR quantification, electrophysiology\",\n      \"pmids\": [\"29154130\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signaling cascade between PlexA3 and AMPAR internalization not defined\", \"Source of activity-dependent Sema3F release not identified\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Finding that Sema3F promotes extraembryonic angiogenesis by stabilizing Myc and suppressing Thbs1 revealed a pro-angiogenic role in development, contrasting with its anti-angiogenic tumor function.\",\n      \"evidence\": \"Sema3f-null mouse, AAV overexpression, F9 cell differentiation, Myc phosphorylation/degradation assays\",\n      \"pmids\": [\"28729362\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Receptor complex mediating this effect in yolk sac not identified\", \"How Sema3F inhibits Myc phosphorylation mechanistically not resolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identification of CRMP2 as a downstream effector of Sema3F in axon pruning and dendritic spine remodeling, with behavioral consequences resembling ASD, connected guidance signaling to neurodevelopmental disorders.\",\n      \"evidence\": \"crmp2-/- mice with axon pruning and spine morphometry analysis, in vitro Sema3F signaling in primary neurons, behavioral testing\",\n      \"pmids\": [\"31919978\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct phosphorylation of CRMP2 by Sema3F pathway components not demonstrated\", \"Whether SEMA3F variants contribute to ASD in humans not established\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Demonstrating that EZH2-mediated H3K27me3 at the SEMA3F promoter, stabilized by lncRNA FAM83C-AS1/ZRANB1, silences SEMA3F identified the specific epigenetic repressor complex responsible for its loss in colorectal cancer.\",\n      \"evidence\": \"H3K27me3 ChIP at SEMA3F promoter, EZH2 stabilization assay, ZRANB1 co-IP, epistatic rescue in vitro and in vivo\",\n      \"pmids\": [\"33109776\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether this EZH2 mechanism operates across cancer types not tested\", \"Single-lab finding not independently confirmed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Establishing that furin-mediated proteolytic processing is essential for SEMA3F activity, and that inner ear-specific Sema3f loss causes hearing impairment with aberrant spiral ganglion neuron projections, defined a new sensory phenotype and a required activation step.\",\n      \"evidence\": \"In vitro furin cleavage assay with patient-derived variants, F-actin collapse assay in HUVECs, inner ear-specific Sema3f KO mice with ABR testing\",\n      \"pmids\": [\"39909336\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Furin cleavage site(s) not mapped at residue resolution\", \"Whether hearing loss is purely neuronal guidance-based or involves vascular dysfunction not resolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular link between NRP2 engagement and suppression of ILK activity, the receptor complex mediating Sema3F's pro-angiogenic function in yolk sac, the mechanism by which SEMA3F stabilizes Myc, and structural details of the active processed SEMA3F–NRP2–PlexinA complex remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of processed SEMA3F bound to its holoreceptor\", \"Mechanism linking receptor to ILK inhibition unknown\", \"How context determines pro- vs anti-angiogenic outcome not resolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0048018\", \"supporting_discovery_ids\": [0, 1, 2, 6, 8]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 9, 14]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [0, 1, 5, 8, 14]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 3, 6, 9, 14]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [5, 7, 12, 17]},\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [6, 7]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [3, 4, 8, 9]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"NRP2\", \"NRP1\", \"PLXNA1\", \"PLXNA3\", \"ABL2\", \"CRMP2\", \"GJA1\"],\n    \"other_free_text\": []\n  }\n}\n```"}