{"gene":"SEMA3E","run_date":"2026-06-10T07:46:30","timeline":{"discoveries":[{"year":2007,"finding":"Sema3E acts as a repellent on neurons expressing PlexinD1 alone, but the extracellular domain of Neuropilin-1 (co-expressed with PlexinD1) is sufficient to convert Sema3E/PlexinD1 repulsive signaling to attraction, defining a 'gating' function of neuropilins in semaphorin-plexin signaling during forebrain axon tract development.","method":"In vivo genetic analysis of Sema3E null mutant mice; neuron-specific expression profiling; axonal projection assays distinguishing PlexinD1-only vs PlexinD1+Neuropilin-1 neurons; behavioral testing","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KO mice with defined axonal phenotype, two cell-type contexts tested, receptor domain-swap experiment establishing mechanistic switch; replicated across multiple neuronal populations","pmids":["18054858"],"is_preprint":false},{"year":2005,"finding":"Full-length Sema3E is proteolytically processed by furin-dependent cleavage to generate a p61-Sema3E isoform; this truncated form is required and sufficient for pro-metastatic, pro-migratory, invasive-growth, and ERK1/2-activating activities in endothelial and pheochromocytoma cells, whereas full-length Sema3E acts as a repelling cue.","method":"In vitro migration and invasion assays; processing-deficient and truncated Sema3E constructs; ERK1/2 phosphorylation assays; in vivo lung metastasis model in mice; furin inhibitor experiments","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — mutant forms (processing-deficient, truncated) dissect the two activities; multiple orthogonal readouts (migration, invasion, ERK activation, metastasis in vivo); replicated in follow-up studies","pmids":["16024618"],"is_preprint":false},{"year":2009,"finding":"Sema3E expressed by specific motor neuron pools signals through its high-affinity receptor Plexin D1 on proprioceptive sensory neurons as a repellent cue to establish monosynaptic sensory-motor circuit specificity; altering Sema3E-Plxnd1 expression in either sensory or motor neurons causes functional and anatomical rewiring of monosynaptic connections.","method":"Molecular genetic manipulation in mice (conditional KO and ectopic expression of Sema3e and Plxnd1); retrograde tracing; electrophysiological recording of monosynaptic connections","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 / Strong — bidirectional genetic manipulation (KO and gain-of-function) in both pre- and post-synaptic neurons; functional (electrophysiology) and anatomical readouts; published in Nature with rigorous controls","pmids":["19421194"],"is_preprint":false},{"year":2010,"finding":"Sema3E signals through Plexin D1 in cancer cells to promote invasion and metastasis via transactivation of the Plexin D1-associated ErbB2/Neu oncogenic kinase; knockdown of either Sema3E or Plexin D1 impairs metastatic potential, while overexpression increases invasiveness, transendothelial migration, and metastatic spreading in mice.","method":"RNAi knockdown and overexpression in human metastatic carcinoma cells; transendothelial migration and invasion assays; mouse metastasis models; ErbB2 transactivation assay","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal gain- and loss-of-function; multiple in vitro and in vivo readouts; ErbB2 transactivation mechanism identified; replicated by subsequent studies on furin-cleaved p61-Sema3E","pmids":["20664171"],"is_preprint":false},{"year":2011,"finding":"Sema3E binding to PlexinD1 in endothelial cells activates the small GTPase RhoJ, which counteracts VEGF-induced filopodia projections and defines retinal vascular pathfinding; intravitreal Sema3E protein selectively suppresses extraretinal vascular outgrowth in ischemic retinopathy.","method":"Mouse retinal vascular development assays; PlexinD1 and RhoJ expression analysis; VEGF signaling inhibition experiments; oxygen-induced retinopathy (OIR) model; intravitreal Sema3E protein administration","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 / Strong — mechanistic pathway (PlexinD1→RhoJ→filopodia suppression) identified with in vivo validation in two models (developmental and ischemic retinopathy); protein rescue experiment","pmids":["21505259"],"is_preprint":false},{"year":2011,"finding":"Sema3E signals through Plexin-D1 to activate PI3K and ERK/MAPK, leading to nuclear localization of Snail1 and epithelial-to-mesenchymal transition (EMT) in ovarian endometrioid cancer cells; RNAi knockdown of Sema3E, Plexin-D1, or Snail1 reverses EMT and reduces cell motility.","method":"RNAi knockdown in cancer cells; Western blotting for EMT markers; nuclear/cytoplasmic fractionation for Snail1; PI3K and ERK inhibitor experiments; wound-healing and invasion assays","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined pathway (PI3K/ERK→Snail1 nuclear localization→EMT); single lab, multiple orthogonal methods","pmids":["21559368"],"is_preprint":false},{"year":2013,"finding":"PlexinD1 controls nanometer-scale β1 integrin adhesion domain clustering in cis on developing thymocytes, while Sema3E ligation in trans shortens individual β1 integrin catch bond lifetimes under force; decreased PlexinD1 expression during developmental progression and thymic medulla Sema3E gradient together enhance thymocyte movement toward the medulla.","method":"Single-molecule force spectroscopy (catch bond measurements); super-resolution imaging of integrin nanoclusters; plexinD1 knockdown on thymocytes; flow chamber adhesion assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Moderate — single-molecule biophysical methods (force spectroscopy, super-resolution imaging) combined with genetic knockdown; mechanistic dissection of cis vs trans regulation at molecular level","pmids":["24344262"],"is_preprint":false},{"year":2015,"finding":"Recombinant wild-type SEMA3E protects maturing GnRH neurons from apoptosis by triggering PLXND1-dependent activation of PI3K-mediated survival signaling; a Kallmann syndrome-associated point mutation in SEMA3E abrogates this neuroprotective activity; loss of either SEMA3E or PLXND1 in mice increases GnRH neuron apoptosis and reduces median eminence innervation.","method":"Exome sequencing; recombinant wild-type and mutant SEMA3E protein treatment of GnRH neurons; PI3K inhibitor experiments; Sema3E and Plxnd1 knockout mouse models; immunofluorescence counting of GnRH neuron apoptosis; median eminence innervation analysis","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 / Strong — recombinant protein rescue, disease mutant abrogation, KO mouse phenotype, PI3K pathway identified; multiple orthogonal methods in one study","pmids":["25985275"],"is_preprint":false},{"year":2016,"finding":"Sema3E directly inhibits Rap1 activation and LFA-1-dependent adhesion in thymocytes through the GTPase-activating protein (GAP) activity of Plexin D1; this suppresses immunological synapse (IS) formation and Ag-scanning migration of thymocytes, promoting their positioning in the thymic medulla.","method":"Rap1 activation assays in thymocytes with sema3e treatment; T cell lineage-specific Plexin D1 conditional KO; supported lipid bilayer IS formation assay; two-photon live imaging of thymic explants/slices","journal":"Journal of immunology","confidence":"High","confidence_rationale":"Tier 2 / Strong — GAP activity mechanism identified; conditional KO with live imaging; multiple readouts (Rap1 activation, IS formation, migration) in one study","pmids":["26921307"],"is_preprint":false},{"year":2019,"finding":"Sema3E/PlexinD1 signaling inhibits postischemic angiogenesis by: (1) suppressing DLL4 expression via inhibiting Rac1-induced JNK phosphorylation in brain microvascular endothelial cells; and (2) promoting F-actin disassembly and focal adhesion reduction by activating RhoJ through release of RhoGEF Tuba from direct binding to PlexinD1, causing endothelial filopodia retraction.","method":"In vivo stroke model (transient middle cerebral artery occlusion) with PlexinD1-shRNA; micro-optical sectioning tomography; cultured brain microvascular endothelial cells; JNK phosphorylation assays; RhoJ activation; co-immunoprecipitation of Tuba-PlexinD1; F-actin/focal adhesion imaging","journal":"FASEB journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — two distinct downstream mechanisms defined (Rac1/JNK/DLL4 and Tuba release/RhoJ/actin); co-IP identifying Tuba-PlexinD1 interaction; in vitro and in vivo validation","pmids":["30653356"],"is_preprint":false},{"year":2021,"finding":"Sema3E-Plexin-D1 signaling promotes post-stroke vascular remodeling and functional recovery by downregulating VEGF signaling; Plxnd1 knockout causes aberrantly increased VEGF signaling, abnormal vascular morphogenesis, and blood-brain barrier (BBB) impairment (junctional protein mislocalization), which are restored by VEGF signaling inhibition.","method":"Plxnd1 conditional KO mice; transient brain infarction model; neurological deficit scoring; infarct volume measurement; intravascular tracer extravasation; junctional protein immunofluorescence; VEGF pathway inhibitor rescue experiment","journal":"Translational stroke research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO phenotype with VEGF inhibitor rescue establishing pathway epistasis; single lab; multiple readouts","pmids":["33978913"],"is_preprint":false},{"year":2024,"finding":"Repulsive Sema3E-Plexin-D1 signaling induces expression of Mtss1 (metastasis suppressor 1) in striatonigral neurons as an autoregulatory feedback; Mtss1 localizes to the axonal side of neurites, promotes neurite outgrowth, and aids Plexin-D1 trafficking to the growth cone where it mediates collapse in response to Sema3E; Mtss1 KO mice exhibit fewer striatonigral projections and irregular axonal routes, phenocopying Plxnd1 and Sema3e KO mice.","method":"In vitro neurite outgrowth and growth cone collapse assays; Mtss1 KO mice; Plxnd1 and Sema3e KO mice; subcellular localization of Mtss1 by live imaging; Plexin-D1 trafficking assay; genetic epistasis (Mtss1 KO phenotype compared to Plxnd1/Sema3e KO)","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple KO models with phenotypic convergence establishing genetic epistasis; subcellular trafficking mechanism; in vitro reconstitution of collapse assay; single lab with multiple orthogonal methods","pmids":["38526535"],"is_preprint":false},{"year":2019,"finding":"Knockdown of sema3E in zebrafish causes severe craniofacial malformations and impairs cranial neural crest cell migration (cells are misrouted/scattered in the hindbrain region); overexpression of sema3E rescues scattered cranial neural crest cells in chd7 homozygous mutants, placing sema3E downstream of chd7 in neural crest migration.","method":"Morpholino knockdown of sema3E in zebrafish; time-lapse imaging of sox10:EGFP neural crest cells; sema3E overexpression rescue in chd7 mutants; immunostaining of postmigratory neural crest cells","journal":"International journal of experimental pathology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — live imaging with genetic rescue establishing epistasis (Chd7→Sema3E); morpholino approach has inherent limitations; single lab","pmids":["31464029"],"is_preprint":false},{"year":2019,"finding":"PlexinD1 and Sema3E signaling controls the laminar positioning of heterotopically projecting callosal neurons; Plxnd1 and Sema3e mutant mice exhibit ectopic neurons aberrantly located in layers 2/3 instead of their normal layer 5A position.","method":"Retrograde tracing of callosal projection neurons; immunofluorescence for PlexinD1 expression; Plxnd1 and Sema3e mutant mouse cortex analysis; laminar distribution quantification","journal":"Molecular and cellular neurosciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two independent KO lines (Plxnd1 and Sema3e) showing same phenotype; direct anatomical readout; single lab","pmids":["31454665"],"is_preprint":false},{"year":2012,"finding":"Recombinant Sema3e inhibits osteoblast migration (wound-healing assay) and decreases osteoclast formation by 81% in mouse bone marrow macrophage cultures, with concomitant downregulation of osteoclast differentiation markers (Itgb3, Acp5, Cd51, Nfatc1, CalcR, Ctsk); Sema3e receptor PlexinD1 is expressed on osteoblasts, macrophages, and osteoclasts.","method":"Recombinant Sema3e protein treatment; wound-healing migration assay; TRAP-positive osteoclast counting; qPCR for osteoclast markers; PlexinD1 expression analysis","journal":"Calcified tissue international","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — recombinant protein functional assays with defined cellular phenotypes; receptor expression confirmed; single lab","pmids":["22227882"],"is_preprint":false},{"year":2022,"finding":"A novel loss-of-function SEMA3E variant impairs protein secretion and hampers binding to embryonic mouse neuronal cells and tissues, establishing that secretion and neuronal cell binding are required for SEMA3E function in brain development.","method":"In vitro secretion assay of mutant vs wild-type SEMA3E; binding assay to embryonic mouse neuronal cells and brain tissue sections; exome sequencing","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional characterization of disease variant (secretion + binding assays); mechanistic insight into required properties; single lab, limited to in vitro readouts","pmids":["35628442"],"is_preprint":false},{"year":2025,"finding":"SETD2-mediated H3K36me3 at the Sema3e locus is required for Sema3e transcription in odontoblasts; SEMA3E (together with COL11A2) acts upstream of AKT1 signaling to promote odontoblastic differentiation, and AKT1 activator SC79 partially rescues impaired odontoblast differentiation caused by Setd2 deficiency.","method":"Conditional Setd2 knockout mouse models; spike-in CUT&Tag sequencing for H3K36me3 occupancy; RNA-seq; in vitro knockdown; AKT1 activator (SC79) rescue experiments","journal":"Development","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epigenetic mechanism (SETD2/H3K36me3) identified for Sema3e transcription; pathway placement (SEMA3E→AKT1) via activator rescue; single lab with multiple orthogonal methods","pmids":["40554768"],"is_preprint":false},{"year":2026,"finding":"SEMA3E promotes beige adipocyte differentiation and thermogenesis via the Wnt/β-catenin pathway; SEMA3E knockdown delays β-catenin degradation and suppresses thermogenic gene expression, while inhibiting the Wnt/β-catenin pathway with IWR-1 rescues the suppressed differentiation caused by SEMA3E knockdown; SEMA3E knockdown also reduces mitochondrial respiration by downregulating respiratory chain component expression.","method":"AAV-mediated SEMA3E knockdown in inguinal white adipose tissue in vivo; loss- and gain-of-function in vitro; RNA-seq; mitochondrial oxygen consumption rate measurement; IWR-1 (β-catenin inhibitor) rescue; cold exposure and β-agonist models","journal":"Apoptosis","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo AAV knockdown plus in vitro rescue with pathway inhibitor; multiple readouts; single lab; novel context","pmids":["41627586"],"is_preprint":false},{"year":2026,"finding":"A PLEXIND1-SEMA3E/F signaling axis between fetal endothelial cells and chorionic trophoblast precursors is required for fetoplacental vascularization; this axis is impaired in retinoic acid (RA)-deficient embryos and rescued by all-trans-RA administration, placing SEMA3E/PLEXIND1 downstream of RA signaling in placental vascular development.","method":"Raldh2-/- mouse embryos; single-cell RNA sequencing; ATRA rescue via maternal diet; functional vascular assays","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — single-cell RNA-seq plus genetic KO with dietary rescue; pathway epistasis established; single lab, novel context","pmids":["41884003"],"is_preprint":false}],"current_model":"SEMA3E is a secreted class 3 semaphorin that directly binds its high-affinity receptor PlexinD1 (without requiring neuropilins) and, depending on cellular context and proteolytic processing, acts as a repulsive guidance cue or pro-invasive signal: full-length Sema3E repels axons, inhibits angiogenesis via RhoJ/Rac1/F-actin/DLL4 pathways, and promotes GnRH neuron survival via PLXND1/PI3K; furin-cleaved p61-Sema3E acts pro-invasively through ErbB2 transactivation and EMT via PI3K/ERK/Snail1; co-expression of Neuropilin-1 with PlexinD1 switches Sema3E signaling from repulsion to attraction; and in immune cells Sema3E/PlexinD1 inhibits Rap1 activation through PlexinD1's GAP activity to regulate integrin adhesion and thymocyte trafficking."},"narrative":{"mechanistic_narrative":"SEMA3E is a secreted class 3 semaphorin guidance cue that signals through its high-affinity receptor PlexinD1 to control cell positioning, axon guidance, and vascular patterning across neural, immune, vascular, and skeletal tissues [PMID:19421194, PMID:21505259]. In neurons, full-length Sema3E acts as a repellent through PlexinD1 to establish circuit specificity—dictating monosynaptic sensory-motor connectivity, laminar positioning of callosal neurons, and striatonigral projection routing—while co-expression of Neuropilin-1 with PlexinD1 gates this signaling, converting repulsion to attraction [PMID:18054858, PMID:19421194, PMID:31454665]. The repulsive growth-cone collapse response is reinforced by an autoregulatory feedback loop in which Sema3E-PlexinD1 induces Mtss1 to aid PlexinD1 trafficking to the growth cone [PMID:38526535]. SEMA3E also promotes maturing GnRH neuron survival via PLXND1-dependent PI3K signaling, and a Kallmann syndrome-associated point mutation, as well as a loss-of-function variant impairing secretion and neuronal binding, abrogates SEMA3E function in brain development [PMID:25985275, PMID:35628442]. In the vasculature, Sema3E-PlexinD1 inhibits angiogenesis by activating RhoJ to suppress VEGF-induced endothelial filopodia—via release of the RhoGEF Tuba from PlexinD1—and by suppressing DLL4 through inhibition of Rac1/JNK signaling [PMID:21505259, PMID:30653356]. In immune cells, Sema3E engages PlexinD1's intrinsic GAP activity to inhibit Rap1 activation, dampening LFA-1/integrin adhesion and immunological synapse formation to direct thymocyte positioning in the thymic medulla [PMID:24344262, PMID:26921307]. A distinct pro-invasive output arises from furin-dependent cleavage of full-length Sema3E to a p61 isoform, which drives migration, invasion, and metastasis through PlexinD1-associated ErbB2 transactivation and a PI3K/ERK/Snail1 EMT program [PMID:16024618, PMID:20664171, PMID:21559368].","teleology":[{"year":2005,"claim":"Established that proteolytic processing functionally splits SEMA3E into opposing activities, explaining how a single repellent cue can also drive invasion.","evidence":"Furin-cleavage-deficient and truncated constructs with migration, invasion, ERK, and in vivo metastasis readouts in endothelial and pheochromocytoma cells","pmids":["16024618"],"confidence":"High","gaps":["Receptor used by p61 not resolved in this study","Structural basis of the cleavage-dependent activity switch unknown"]},{"year":2007,"claim":"Defined PlexinD1 as the signaling receptor and showed Neuropilin-1 gates the sign of the response, converting repulsion to attraction.","evidence":"Sema3E-null mice, cell-type-specific expression profiling, and receptor domain-swap axon guidance assays in forebrain","pmids":["18054858"],"confidence":"High","gaps":["Molecular mechanism by which Neuropilin-1 ectodomain switches signaling output not defined","Downstream effectors distinguishing attraction vs repulsion not identified"]},{"year":2009,"claim":"Demonstrated that Sema3E-PlexinD1 repulsion wires specific neural circuits, giving the cue a defined developmental purpose.","evidence":"Bidirectional conditional KO and ectopic expression in mice with retrograde tracing and electrophysiology of monosynaptic sensory-motor connections","pmids":["19421194"],"confidence":"High","gaps":["Intracellular signaling effectors in sensory neurons not dissected"]},{"year":2010,"claim":"Identified the pro-invasive signaling mechanism as PlexinD1-associated ErbB2 transactivation in cancer cells.","evidence":"Reciprocal RNAi/overexpression in human carcinoma cells, transendothelial migration/invasion assays, mouse metastasis models, ErbB2 transactivation assay","pmids":["20664171"],"confidence":"High","gaps":["Direct biochemical coupling of PlexinD1 to ErbB2 not structurally resolved"]},{"year":2011,"claim":"Resolved how Sema3E-PlexinD1 inhibits angiogenesis, linking the receptor to RhoJ-mediated suppression of VEGF-induced filopodia.","evidence":"Mouse retinal vascular development and oxygen-induced retinopathy models with RhoJ analysis and intravitreal Sema3E protein rescue","pmids":["21505259"],"confidence":"High","gaps":["Link between PlexinD1 and RhoJ activation not biochemically defined at this stage"]},{"year":2011,"claim":"Connected Sema3E-PlexinD1 to an EMT program via PI3K/ERK-driven nuclear Snail1.","evidence":"RNAi knockdown of Sema3E/Plexin-D1/Snail1 with EMT marker blotting, Snail1 fractionation, and PI3K/ERK inhibitor experiments in ovarian cancer cells","pmids":["21559368"],"confidence":"Medium","gaps":["Single lab","Relationship to furin-cleaved p61 isoform not addressed"]},{"year":2013,"claim":"Showed Sema3E/PlexinD1 controls integrin adhesion at the single-molecule level, regulating thymocyte movement.","evidence":"Single-molecule force spectroscopy of β1 integrin catch bonds, super-resolution imaging of nanoclusters, and PlexinD1 knockdown on thymocytes","pmids":["24344262"],"confidence":"High","gaps":["Signaling intermediary between PlexinD1 and integrin bond lifetime not identified here"]},{"year":2015,"claim":"Established a pro-survival role via PLXND1/PI3K and linked SEMA3E to a human reproductive disorder through a function-abrogating mutation.","evidence":"Recombinant WT/mutant SEMA3E protein on GnRH neurons, PI3K inhibition, Sema3E/Plxnd1 KO mice, and exome sequencing of a Kallmann syndrome variant","pmids":["25985275"],"confidence":"High","gaps":["How the same ligand-receptor pair triggers survival versus repulsion in different neurons not resolved"]},{"year":2016,"claim":"Defined the immune signaling mechanism as PlexinD1 GAP-mediated inhibition of Rap1, controlling adhesion and synapse formation.","evidence":"Rap1 activation assays, T-cell-specific Plexin D1 conditional KO, lipid bilayer immunological synapse assays, and two-photon imaging of thymic explants","pmids":["26921307"],"confidence":"High","gaps":["Direct GAP substrate specificity within the Rap1 cascade not fully mapped"]},{"year":2019,"claim":"Resolved dual endothelial mechanisms of anti-angiogenic signaling—Rac1/JNK/DLL4 suppression and Tuba-release/RhoJ actin remodeling.","evidence":"Stroke model with PlexinD1-shRNA, brain microvascular endothelial cell assays, JNK/RhoJ readouts, and Tuba-PlexinD1 co-immunoprecipitation","pmids":["30653356"],"confidence":"High","gaps":["Single co-IP for the Tuba-PlexinD1 interaction without reciprocal structural validation"]},{"year":2019,"claim":"Extended the guidance role to cranial neural crest migration and placed sema3E downstream of chd7.","evidence":"Morpholino knockdown and overexpression rescue in chd7 mutant zebrafish with time-lapse imaging of neural crest cells","pmids":["31464029"],"confidence":"Medium","gaps":["Morpholino approach has off-target limitations","Receptor in neural crest not confirmed"]},{"year":2019,"claim":"Showed Sema3E/PlexinD1 controls laminar positioning of callosal projection neurons.","evidence":"Retrograde tracing and laminar quantification in Plxnd1 and Sema3e mutant mouse cortex","pmids":["31454665"],"confidence":"Medium","gaps":["Single lab","Mechanism of positioning control not dissected"]},{"year":2021,"claim":"Established that post-stroke vascular remodeling depends on Sema3E-PlexinD1 restraining VEGF signaling to maintain BBB integrity.","evidence":"Plxnd1 conditional KO mice in brain infarction model with tracer extravasation, junctional protein imaging, and VEGF inhibitor rescue","pmids":["33978913"],"confidence":"Medium","gaps":["Single lab","Direct molecular crosstalk between PlexinD1 and VEGF receptor not defined"]},{"year":2022,"claim":"Defined secretion and neuronal binding as functional requirements via a loss-of-function disease variant.","evidence":"In vitro secretion and embryonic neuronal/tissue binding assays of mutant vs WT SEMA3E with exome sequencing","pmids":["35628442"],"confidence":"Medium","gaps":["In vitro readouts only","In vivo developmental consequence of the variant not tested"]},{"year":2024,"claim":"Revealed an autoregulatory feedback loop in which repulsive signaling induces Mtss1 to aid PlexinD1 trafficking and growth-cone collapse.","evidence":"Neurite outgrowth/collapse assays, Mtss1/Plxnd1/Sema3e KO mice with phenotypic convergence, and live-imaging trafficking assays in striatonigral neurons","pmids":["38526535"],"confidence":"High","gaps":["Molecular basis of Mtss1-mediated PlexinD1 trafficking not fully defined"]},{"year":2025,"claim":"Placed Sema3e transcription under SETD2/H3K36me3 epigenetic control and SEMA3E upstream of AKT1 in odontoblast differentiation.","evidence":"Conditional Setd2 KO mice, H3K36me3 CUT&Tag, RNA-seq, and AKT1 activator (SC79) rescue","pmids":["40554768"],"confidence":"Medium","gaps":["Receptor mediating SEMA3E-AKT1 coupling in odontoblasts not identified","Single lab"]},{"year":2026,"claim":"Extended SEMA3E function to metabolic tissue, driving beige adipocyte thermogenesis via Wnt/β-catenin.","evidence":"AAV knockdown in white adipose tissue in vivo, in vitro loss/gain-of-function, RNA-seq, mitochondrial respiration, and IWR-1 β-catenin inhibitor rescue","pmids":["41627586"],"confidence":"Medium","gaps":["Receptor mediating adipocyte effect not defined","Single lab, novel context"]},{"year":2026,"claim":"Defined a PLEXIND1-SEMA3E/F axis in fetoplacental vascularization downstream of retinoic acid signaling.","evidence":"Raldh2-/- mouse embryos, single-cell RNA-seq, and all-trans-RA dietary rescue with vascular assays","pmids":["41884003"],"confidence":"Medium","gaps":["SEMA3E vs SEMA3F contributions not disentangled","Single lab"]},{"year":null,"claim":"How a single Sema3E-PlexinD1 axis selects among opposing outputs (repulsion vs attraction vs survival vs invasion) across cell types remains unresolved at the level of shared molecular switches.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying structural model linking receptor context (Neuropilin-1, furin cleavage, GAP activity) to output selection","Cross-tissue comparison of effector usage lacking"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0048018","term_label":"receptor ligand activity","supporting_discovery_ids":[0,2,4,7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[6,8]}],"localization":[{"term_id":"GO:0005576","term_label":"extracellular region","supporting_discovery_ids":[1,15]}],"pathway":[{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[0,2,13]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[4,7,8]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[6,8]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[1,3,7]}],"complexes":[],"partners":["PLXND1","NRP1","ERBB2","TUBA","MTSS1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O15041","full_name":"Semaphorin-3E","aliases":[],"length_aa":775,"mass_kda":89.2,"function":"Plays an important role in signaling via the cell surface receptor PLXND1. Mediates reorganization of the actin cytoskeleton, leading to the retraction of cell projections. Promotes focal adhesion disassembly and inhibits adhesion of endothelial cells to the extracellular matrix. Regulates angiogenesis, both during embryogenesis and after birth. Can down-regulate sprouting angiogenesis. Required for normal vascular patterning during embryogenesis. Plays an important role in ensuring the specificity of synapse formation (By similarity)","subcellular_location":"Secreted","url":"https://www.uniprot.org/uniprotkb/O15041/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SEMA3E","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SEMA3E","total_profiled":1310},"omim":[{"mim_id":"620997","title":"SEMAPHORIN 3G; SEMA3G","url":"https://www.omim.org/entry/620997"},{"mim_id":"612370","title":"HYPOGONADOTROPIC HYPOGONADISM 5 WITH OR WITHOUT ANOSMIA; HH5","url":"https://www.omim.org/entry/612370"},{"mim_id":"608166","title":"SEMAPHORIN 3E; SEMA3E","url":"https://www.omim.org/entry/608166"},{"mim_id":"604282","title":"PLEXIN D1; PLXND1","url":"https://www.omim.org/entry/604282"},{"mim_id":"214800","title":"CHARGE SYNDROME","url":"https://www.omim.org/entry/214800"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Vesicles","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SEMA3E"},"hgnc":{"alias_symbol":["M-SemaK","KIAA0331","coll-5"],"prev_symbol":["SEMAH"]},"alphafold":{"accession":"O15041","domains":[{"cath_id":"-","chopping":"26-55_434-517","consensus_level":"medium","plddt":94.2913,"start":26,"end":517},{"cath_id":"-","chopping":"59-178","consensus_level":"medium","plddt":92.7319,"start":59,"end":178},{"cath_id":"3.30.1680.10","chopping":"525-573","consensus_level":"high","plddt":85.9873,"start":525,"end":573},{"cath_id":"2.60.40.10","chopping":"587-677","consensus_level":"high","plddt":89.208,"start":587,"end":677}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O15041","model_url":"https://alphafold.ebi.ac.uk/files/AF-O15041-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O15041-F1-predicted_aligned_error_v6.png","plddt_mean":84.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SEMA3E","jax_strain_url":"https://www.jax.org/strain/search?query=SEMA3E"},"sequence":{"accession":"O15041","fasta_url":"https://rest.uniprot.org/uniprotkb/O15041.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O15041/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O15041"}},"corpus_meta":[{"pmid":"18054858","id":"PMC_18054858","title":"Gating 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Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/30653356","citation_count":18,"is_preprint":false},{"pmid":"35917012","id":"PMC_35917012","title":"PLXND1/SEMA3E Promotes Epithelial-Mesenchymal Transition Partly via the PI3K/AKT-Signaling Pathway and Induces Heterogenity in Colorectal Cancer.","date":"2022","source":"Annals of surgical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/35917012","citation_count":16,"is_preprint":false},{"pmid":"31464029","id":"PMC_31464029","title":"Sema3E is required for migration of cranial neural crest cells in zebrafish: Implications for the pathogenesis of CHARGE syndrome.","date":"2019","source":"International journal of experimental pathology","url":"https://pubmed.ncbi.nlm.nih.gov/31464029","citation_count":13,"is_preprint":false},{"pmid":"35628442","id":"PMC_35628442","title":"A Novel Loss-of-Function SEMA3E Mutation in a Patient with Severe Intellectual Disability and Cognitive Regression.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35628442","citation_count":10,"is_preprint":false},{"pmid":"31454665","id":"PMC_31454665","title":"PlexinD1 and Sema3E determine laminar positioning of heterotopically projecting callosal neurons.","date":"2019","source":"Molecular and cellular neurosciences","url":"https://pubmed.ncbi.nlm.nih.gov/31454665","citation_count":10,"is_preprint":false},{"pmid":"28249916","id":"PMC_28249916","title":"Association of Increased Serum Sema3E with TRIB3 Q84R Polymorphism and Carotid Atherosclerosis in Metabolic Syndrome.","date":"2017","source":"Annals of clinical and laboratory science","url":"https://pubmed.ncbi.nlm.nih.gov/28249916","citation_count":10,"is_preprint":false},{"pmid":"24229706","id":"PMC_24229706","title":"To die or not to die: Sema3E rules the game.","date":"2013","source":"Cancer 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neuron-specific expression profiling; axonal projection assays distinguishing PlexinD1-only vs PlexinD1+Neuropilin-1 neurons; behavioral testing\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO mice with defined axonal phenotype, two cell-type contexts tested, receptor domain-swap experiment establishing mechanistic switch; replicated across multiple neuronal populations\",\n      \"pmids\": [\"18054858\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Full-length Sema3E is proteolytically processed by furin-dependent cleavage to generate a p61-Sema3E isoform; this truncated form is required and sufficient for pro-metastatic, pro-migratory, invasive-growth, and ERK1/2-activating activities in endothelial and pheochromocytoma cells, whereas full-length Sema3E acts as a repelling cue.\",\n      \"method\": \"In vitro migration and invasion assays; processing-deficient and truncated Sema3E constructs; ERK1/2 phosphorylation assays; in vivo lung metastasis model in mice; furin inhibitor experiments\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — mutant forms (processing-deficient, truncated) dissect the two activities; multiple orthogonal readouts (migration, invasion, ERK activation, metastasis in vivo); replicated in follow-up studies\",\n      \"pmids\": [\"16024618\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Sema3E expressed by specific motor neuron pools signals through its high-affinity receptor Plexin D1 on proprioceptive sensory neurons as a repellent cue to establish monosynaptic sensory-motor circuit specificity; altering Sema3E-Plxnd1 expression in either sensory or motor neurons causes functional and anatomical rewiring of monosynaptic connections.\",\n      \"method\": \"Molecular genetic manipulation in mice (conditional KO and ectopic expression of Sema3e and Plxnd1); retrograde tracing; electrophysiological recording of monosynaptic connections\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — bidirectional genetic manipulation (KO and gain-of-function) in both pre- and post-synaptic neurons; functional (electrophysiology) and anatomical readouts; published in Nature with rigorous controls\",\n      \"pmids\": [\"19421194\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Sema3E signals through Plexin D1 in cancer cells to promote invasion and metastasis via transactivation of the Plexin D1-associated ErbB2/Neu oncogenic kinase; knockdown of either Sema3E or Plexin D1 impairs metastatic potential, while overexpression increases invasiveness, transendothelial migration, and metastatic spreading in mice.\",\n      \"method\": \"RNAi knockdown and overexpression in human metastatic carcinoma cells; transendothelial migration and invasion assays; mouse metastasis models; ErbB2 transactivation assay\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal gain- and loss-of-function; multiple in vitro and in vivo readouts; ErbB2 transactivation mechanism identified; replicated by subsequent studies on furin-cleaved p61-Sema3E\",\n      \"pmids\": [\"20664171\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Sema3E binding to PlexinD1 in endothelial cells activates the small GTPase RhoJ, which counteracts VEGF-induced filopodia projections and defines retinal vascular pathfinding; intravitreal Sema3E protein selectively suppresses extraretinal vascular outgrowth in ischemic retinopathy.\",\n      \"method\": \"Mouse retinal vascular development assays; PlexinD1 and RhoJ expression analysis; VEGF signaling inhibition experiments; oxygen-induced retinopathy (OIR) model; intravitreal Sema3E protein administration\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — mechanistic pathway (PlexinD1→RhoJ→filopodia suppression) identified with in vivo validation in two models (developmental and ischemic retinopathy); protein rescue experiment\",\n      \"pmids\": [\"21505259\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Sema3E signals through Plexin-D1 to activate PI3K and ERK/MAPK, leading to nuclear localization of Snail1 and epithelial-to-mesenchymal transition (EMT) in ovarian endometrioid cancer cells; RNAi knockdown of Sema3E, Plexin-D1, or Snail1 reverses EMT and reduces cell motility.\",\n      \"method\": \"RNAi knockdown in cancer cells; Western blotting for EMT markers; nuclear/cytoplasmic fractionation for Snail1; PI3K and ERK inhibitor experiments; wound-healing and invasion assays\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined pathway (PI3K/ERK→Snail1 nuclear localization→EMT); single lab, multiple orthogonal methods\",\n      \"pmids\": [\"21559368\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"PlexinD1 controls nanometer-scale β1 integrin adhesion domain clustering in cis on developing thymocytes, while Sema3E ligation in trans shortens individual β1 integrin catch bond lifetimes under force; decreased PlexinD1 expression during developmental progression and thymic medulla Sema3E gradient together enhance thymocyte movement toward the medulla.\",\n      \"method\": \"Single-molecule force spectroscopy (catch bond measurements); super-resolution imaging of integrin nanoclusters; plexinD1 knockdown on thymocytes; flow chamber adhesion assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — single-molecule biophysical methods (force spectroscopy, super-resolution imaging) combined with genetic knockdown; mechanistic dissection of cis vs trans regulation at molecular level\",\n      \"pmids\": [\"24344262\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Recombinant wild-type SEMA3E protects maturing GnRH neurons from apoptosis by triggering PLXND1-dependent activation of PI3K-mediated survival signaling; a Kallmann syndrome-associated point mutation in SEMA3E abrogates this neuroprotective activity; loss of either SEMA3E or PLXND1 in mice increases GnRH neuron apoptosis and reduces median eminence innervation.\",\n      \"method\": \"Exome sequencing; recombinant wild-type and mutant SEMA3E protein treatment of GnRH neurons; PI3K inhibitor experiments; Sema3E and Plxnd1 knockout mouse models; immunofluorescence counting of GnRH neuron apoptosis; median eminence innervation analysis\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — recombinant protein rescue, disease mutant abrogation, KO mouse phenotype, PI3K pathway identified; multiple orthogonal methods in one study\",\n      \"pmids\": [\"25985275\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Sema3E directly inhibits Rap1 activation and LFA-1-dependent adhesion in thymocytes through the GTPase-activating protein (GAP) activity of Plexin D1; this suppresses immunological synapse (IS) formation and Ag-scanning migration of thymocytes, promoting their positioning in the thymic medulla.\",\n      \"method\": \"Rap1 activation assays in thymocytes with sema3e treatment; T cell lineage-specific Plexin D1 conditional KO; supported lipid bilayer IS formation assay; two-photon live imaging of thymic explants/slices\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — GAP activity mechanism identified; conditional KO with live imaging; multiple readouts (Rap1 activation, IS formation, migration) in one study\",\n      \"pmids\": [\"26921307\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Sema3E/PlexinD1 signaling inhibits postischemic angiogenesis by: (1) suppressing DLL4 expression via inhibiting Rac1-induced JNK phosphorylation in brain microvascular endothelial cells; and (2) promoting F-actin disassembly and focal adhesion reduction by activating RhoJ through release of RhoGEF Tuba from direct binding to PlexinD1, causing endothelial filopodia retraction.\",\n      \"method\": \"In vivo stroke model (transient middle cerebral artery occlusion) with PlexinD1-shRNA; micro-optical sectioning tomography; cultured brain microvascular endothelial cells; JNK phosphorylation assays; RhoJ activation; co-immunoprecipitation of Tuba-PlexinD1; F-actin/focal adhesion imaging\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — two distinct downstream mechanisms defined (Rac1/JNK/DLL4 and Tuba release/RhoJ/actin); co-IP identifying Tuba-PlexinD1 interaction; in vitro and in vivo validation\",\n      \"pmids\": [\"30653356\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Sema3E-Plexin-D1 signaling promotes post-stroke vascular remodeling and functional recovery by downregulating VEGF signaling; Plxnd1 knockout causes aberrantly increased VEGF signaling, abnormal vascular morphogenesis, and blood-brain barrier (BBB) impairment (junctional protein mislocalization), which are restored by VEGF signaling inhibition.\",\n      \"method\": \"Plxnd1 conditional KO mice; transient brain infarction model; neurological deficit scoring; infarct volume measurement; intravascular tracer extravasation; junctional protein immunofluorescence; VEGF pathway inhibitor rescue experiment\",\n      \"journal\": \"Translational stroke research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO phenotype with VEGF inhibitor rescue establishing pathway epistasis; single lab; multiple readouts\",\n      \"pmids\": [\"33978913\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Repulsive Sema3E-Plexin-D1 signaling induces expression of Mtss1 (metastasis suppressor 1) in striatonigral neurons as an autoregulatory feedback; Mtss1 localizes to the axonal side of neurites, promotes neurite outgrowth, and aids Plexin-D1 trafficking to the growth cone where it mediates collapse in response to Sema3E; Mtss1 KO mice exhibit fewer striatonigral projections and irregular axonal routes, phenocopying Plxnd1 and Sema3e KO mice.\",\n      \"method\": \"In vitro neurite outgrowth and growth cone collapse assays; Mtss1 KO mice; Plxnd1 and Sema3e KO mice; subcellular localization of Mtss1 by live imaging; Plexin-D1 trafficking assay; genetic epistasis (Mtss1 KO phenotype compared to Plxnd1/Sema3e KO)\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple KO models with phenotypic convergence establishing genetic epistasis; subcellular trafficking mechanism; in vitro reconstitution of collapse assay; single lab with multiple orthogonal methods\",\n      \"pmids\": [\"38526535\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Knockdown of sema3E in zebrafish causes severe craniofacial malformations and impairs cranial neural crest cell migration (cells are misrouted/scattered in the hindbrain region); overexpression of sema3E rescues scattered cranial neural crest cells in chd7 homozygous mutants, placing sema3E downstream of chd7 in neural crest migration.\",\n      \"method\": \"Morpholino knockdown of sema3E in zebrafish; time-lapse imaging of sox10:EGFP neural crest cells; sema3E overexpression rescue in chd7 mutants; immunostaining of postmigratory neural crest cells\",\n      \"journal\": \"International journal of experimental pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — live imaging with genetic rescue establishing epistasis (Chd7→Sema3E); morpholino approach has inherent limitations; single lab\",\n      \"pmids\": [\"31464029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PlexinD1 and Sema3E signaling controls the laminar positioning of heterotopically projecting callosal neurons; Plxnd1 and Sema3e mutant mice exhibit ectopic neurons aberrantly located in layers 2/3 instead of their normal layer 5A position.\",\n      \"method\": \"Retrograde tracing of callosal projection neurons; immunofluorescence for PlexinD1 expression; Plxnd1 and Sema3e mutant mouse cortex analysis; laminar distribution quantification\",\n      \"journal\": \"Molecular and cellular neurosciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two independent KO lines (Plxnd1 and Sema3e) showing same phenotype; direct anatomical readout; single lab\",\n      \"pmids\": [\"31454665\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Recombinant Sema3e inhibits osteoblast migration (wound-healing assay) and decreases osteoclast formation by 81% in mouse bone marrow macrophage cultures, with concomitant downregulation of osteoclast differentiation markers (Itgb3, Acp5, Cd51, Nfatc1, CalcR, Ctsk); Sema3e receptor PlexinD1 is expressed on osteoblasts, macrophages, and osteoclasts.\",\n      \"method\": \"Recombinant Sema3e protein treatment; wound-healing migration assay; TRAP-positive osteoclast counting; qPCR for osteoclast markers; PlexinD1 expression analysis\",\n      \"journal\": \"Calcified tissue international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — recombinant protein functional assays with defined cellular phenotypes; receptor expression confirmed; single lab\",\n      \"pmids\": [\"22227882\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"A novel loss-of-function SEMA3E variant impairs protein secretion and hampers binding to embryonic mouse neuronal cells and tissues, establishing that secretion and neuronal cell binding are required for SEMA3E function in brain development.\",\n      \"method\": \"In vitro secretion assay of mutant vs wild-type SEMA3E; binding assay to embryonic mouse neuronal cells and brain tissue sections; exome sequencing\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional characterization of disease variant (secretion + binding assays); mechanistic insight into required properties; single lab, limited to in vitro readouts\",\n      \"pmids\": [\"35628442\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SETD2-mediated H3K36me3 at the Sema3e locus is required for Sema3e transcription in odontoblasts; SEMA3E (together with COL11A2) acts upstream of AKT1 signaling to promote odontoblastic differentiation, and AKT1 activator SC79 partially rescues impaired odontoblast differentiation caused by Setd2 deficiency.\",\n      \"method\": \"Conditional Setd2 knockout mouse models; spike-in CUT&Tag sequencing for H3K36me3 occupancy; RNA-seq; in vitro knockdown; AKT1 activator (SC79) rescue experiments\",\n      \"journal\": \"Development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epigenetic mechanism (SETD2/H3K36me3) identified for Sema3e transcription; pathway placement (SEMA3E→AKT1) via activator rescue; single lab with multiple orthogonal methods\",\n      \"pmids\": [\"40554768\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"SEMA3E promotes beige adipocyte differentiation and thermogenesis via the Wnt/β-catenin pathway; SEMA3E knockdown delays β-catenin degradation and suppresses thermogenic gene expression, while inhibiting the Wnt/β-catenin pathway with IWR-1 rescues the suppressed differentiation caused by SEMA3E knockdown; SEMA3E knockdown also reduces mitochondrial respiration by downregulating respiratory chain component expression.\",\n      \"method\": \"AAV-mediated SEMA3E knockdown in inguinal white adipose tissue in vivo; loss- and gain-of-function in vitro; RNA-seq; mitochondrial oxygen consumption rate measurement; IWR-1 (β-catenin inhibitor) rescue; cold exposure and β-agonist models\",\n      \"journal\": \"Apoptosis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo AAV knockdown plus in vitro rescue with pathway inhibitor; multiple readouts; single lab; novel context\",\n      \"pmids\": [\"41627586\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"A PLEXIND1-SEMA3E/F signaling axis between fetal endothelial cells and chorionic trophoblast precursors is required for fetoplacental vascularization; this axis is impaired in retinoic acid (RA)-deficient embryos and rescued by all-trans-RA administration, placing SEMA3E/PLEXIND1 downstream of RA signaling in placental vascular development.\",\n      \"method\": \"Raldh2-/- mouse embryos; single-cell RNA sequencing; ATRA rescue via maternal diet; functional vascular assays\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — single-cell RNA-seq plus genetic KO with dietary rescue; pathway epistasis established; single lab, novel context\",\n      \"pmids\": [\"41884003\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SEMA3E is a secreted class 3 semaphorin that directly binds its high-affinity receptor PlexinD1 (without requiring neuropilins) and, depending on cellular context and proteolytic processing, acts as a repulsive guidance cue or pro-invasive signal: full-length Sema3E repels axons, inhibits angiogenesis via RhoJ/Rac1/F-actin/DLL4 pathways, and promotes GnRH neuron survival via PLXND1/PI3K; furin-cleaved p61-Sema3E acts pro-invasively through ErbB2 transactivation and EMT via PI3K/ERK/Snail1; co-expression of Neuropilin-1 with PlexinD1 switches Sema3E signaling from repulsion to attraction; and in immune cells Sema3E/PlexinD1 inhibits Rap1 activation through PlexinD1's GAP activity to regulate integrin adhesion and thymocyte trafficking.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SEMA3E is a secreted class 3 semaphorin guidance cue that signals through its high-affinity receptor PlexinD1 to control cell positioning, axon guidance, and vascular patterning across neural, immune, vascular, and skeletal tissues [#2, #4]. In neurons, full-length Sema3E acts as a repellent through PlexinD1 to establish circuit specificity—dictating monosynaptic sensory-motor connectivity, laminar positioning of callosal neurons, and striatonigral projection routing—while co-expression of Neuropilin-1 with PlexinD1 gates this signaling, converting repulsion to attraction [#0, #2, #13]. The repulsive growth-cone collapse response is reinforced by an autoregulatory feedback loop in which Sema3E-PlexinD1 induces Mtss1 to aid PlexinD1 trafficking to the growth cone [#11]. SEMA3E also promotes maturing GnRH neuron survival via PLXND1-dependent PI3K signaling, and a Kallmann syndrome-associated point mutation, as well as a loss-of-function variant impairing secretion and neuronal binding, abrogates SEMA3E function in brain development [#7, #15]. In the vasculature, Sema3E-PlexinD1 inhibits angiogenesis by activating RhoJ to suppress VEGF-induced endothelial filopodia—via release of the RhoGEF Tuba from PlexinD1—and by suppressing DLL4 through inhibition of Rac1/JNK signaling [#4, #9]. In immune cells, Sema3E engages PlexinD1's intrinsic GAP activity to inhibit Rap1 activation, dampening LFA-1/integrin adhesion and immunological synapse formation to direct thymocyte positioning in the thymic medulla [#6, #8]. A distinct pro-invasive output arises from furin-dependent cleavage of full-length Sema3E to a p61 isoform, which drives migration, invasion, and metastasis through PlexinD1-associated ErbB2 transactivation and a PI3K/ERK/Snail1 EMT program [#1, #3, #5].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Established that proteolytic processing functionally splits SEMA3E into opposing activities, explaining how a single repellent cue can also drive invasion.\",\n      \"evidence\": \"Furin-cleavage-deficient and truncated constructs with migration, invasion, ERK, and in vivo metastasis readouts in endothelial and pheochromocytoma cells\",\n      \"pmids\": [\"16024618\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Receptor used by p61 not resolved in this study\", \"Structural basis of the cleavage-dependent activity switch unknown\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Defined PlexinD1 as the signaling receptor and showed Neuropilin-1 gates the sign of the response, converting repulsion to attraction.\",\n      \"evidence\": \"Sema3E-null mice, cell-type-specific expression profiling, and receptor domain-swap axon guidance assays in forebrain\",\n      \"pmids\": [\"18054858\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism by which Neuropilin-1 ectodomain switches signaling output not defined\", \"Downstream effectors distinguishing attraction vs repulsion not identified\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Demonstrated that Sema3E-PlexinD1 repulsion wires specific neural circuits, giving the cue a defined developmental purpose.\",\n      \"evidence\": \"Bidirectional conditional KO and ectopic expression in mice with retrograde tracing and electrophysiology of monosynaptic sensory-motor connections\",\n      \"pmids\": [\"19421194\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Intracellular signaling effectors in sensory neurons not dissected\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identified the pro-invasive signaling mechanism as PlexinD1-associated ErbB2 transactivation in cancer cells.\",\n      \"evidence\": \"Reciprocal RNAi/overexpression in human carcinoma cells, transendothelial migration/invasion assays, mouse metastasis models, ErbB2 transactivation assay\",\n      \"pmids\": [\"20664171\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct biochemical coupling of PlexinD1 to ErbB2 not structurally resolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Resolved how Sema3E-PlexinD1 inhibits angiogenesis, linking the receptor to RhoJ-mediated suppression of VEGF-induced filopodia.\",\n      \"evidence\": \"Mouse retinal vascular development and oxygen-induced retinopathy models with RhoJ analysis and intravitreal Sema3E protein rescue\",\n      \"pmids\": [\"21505259\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Link between PlexinD1 and RhoJ activation not biochemically defined at this stage\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Connected Sema3E-PlexinD1 to an EMT program via PI3K/ERK-driven nuclear Snail1.\",\n      \"evidence\": \"RNAi knockdown of Sema3E/Plexin-D1/Snail1 with EMT marker blotting, Snail1 fractionation, and PI3K/ERK inhibitor experiments in ovarian cancer cells\",\n      \"pmids\": [\"21559368\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Relationship to furin-cleaved p61 isoform not addressed\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Showed Sema3E/PlexinD1 controls integrin adhesion at the single-molecule level, regulating thymocyte movement.\",\n      \"evidence\": \"Single-molecule force spectroscopy of β1 integrin catch bonds, super-resolution imaging of nanoclusters, and PlexinD1 knockdown on thymocytes\",\n      \"pmids\": [\"24344262\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signaling intermediary between PlexinD1 and integrin bond lifetime not identified here\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Established a pro-survival role via PLXND1/PI3K and linked SEMA3E to a human reproductive disorder through a function-abrogating mutation.\",\n      \"evidence\": \"Recombinant WT/mutant SEMA3E protein on GnRH neurons, PI3K inhibition, Sema3E/Plxnd1 KO mice, and exome sequencing of a Kallmann syndrome variant\",\n      \"pmids\": [\"25985275\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How the same ligand-receptor pair triggers survival versus repulsion in different neurons not resolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Defined the immune signaling mechanism as PlexinD1 GAP-mediated inhibition of Rap1, controlling adhesion and synapse formation.\",\n      \"evidence\": \"Rap1 activation assays, T-cell-specific Plexin D1 conditional KO, lipid bilayer immunological synapse assays, and two-photon imaging of thymic explants\",\n      \"pmids\": [\"26921307\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct GAP substrate specificity within the Rap1 cascade not fully mapped\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Resolved dual endothelial mechanisms of anti-angiogenic signaling—Rac1/JNK/DLL4 suppression and Tuba-release/RhoJ actin remodeling.\",\n      \"evidence\": \"Stroke model with PlexinD1-shRNA, brain microvascular endothelial cell assays, JNK/RhoJ readouts, and Tuba-PlexinD1 co-immunoprecipitation\",\n      \"pmids\": [\"30653356\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Single co-IP for the Tuba-PlexinD1 interaction without reciprocal structural validation\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Extended the guidance role to cranial neural crest migration and placed sema3E downstream of chd7.\",\n      \"evidence\": \"Morpholino knockdown and overexpression rescue in chd7 mutant zebrafish with time-lapse imaging of neural crest cells\",\n      \"pmids\": [\"31464029\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Morpholino approach has off-target limitations\", \"Receptor in neural crest not confirmed\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Showed Sema3E/PlexinD1 controls laminar positioning of callosal projection neurons.\",\n      \"evidence\": \"Retrograde tracing and laminar quantification in Plxnd1 and Sema3e mutant mouse cortex\",\n      \"pmids\": [\"31454665\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Mechanism of positioning control not dissected\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Established that post-stroke vascular remodeling depends on Sema3E-PlexinD1 restraining VEGF signaling to maintain BBB integrity.\",\n      \"evidence\": \"Plxnd1 conditional KO mice in brain infarction model with tracer extravasation, junctional protein imaging, and VEGF inhibitor rescue\",\n      \"pmids\": [\"33978913\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Direct molecular crosstalk between PlexinD1 and VEGF receptor not defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined secretion and neuronal binding as functional requirements via a loss-of-function disease variant.\",\n      \"evidence\": \"In vitro secretion and embryonic neuronal/tissue binding assays of mutant vs WT SEMA3E with exome sequencing\",\n      \"pmids\": [\"35628442\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vitro readouts only\", \"In vivo developmental consequence of the variant not tested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Revealed an autoregulatory feedback loop in which repulsive signaling induces Mtss1 to aid PlexinD1 trafficking and growth-cone collapse.\",\n      \"evidence\": \"Neurite outgrowth/collapse assays, Mtss1/Plxnd1/Sema3e KO mice with phenotypic convergence, and live-imaging trafficking assays in striatonigral neurons\",\n      \"pmids\": [\"38526535\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of Mtss1-mediated PlexinD1 trafficking not fully defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placed Sema3e transcription under SETD2/H3K36me3 epigenetic control and SEMA3E upstream of AKT1 in odontoblast differentiation.\",\n      \"evidence\": \"Conditional Setd2 KO mice, H3K36me3 CUT&Tag, RNA-seq, and AKT1 activator (SC79) rescue\",\n      \"pmids\": [\"40554768\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Receptor mediating SEMA3E-AKT1 coupling in odontoblasts not identified\", \"Single lab\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Extended SEMA3E function to metabolic tissue, driving beige adipocyte thermogenesis via Wnt/β-catenin.\",\n      \"evidence\": \"AAV knockdown in white adipose tissue in vivo, in vitro loss/gain-of-function, RNA-seq, mitochondrial respiration, and IWR-1 β-catenin inhibitor rescue\",\n      \"pmids\": [\"41627586\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Receptor mediating adipocyte effect not defined\", \"Single lab, novel context\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined a PLEXIND1-SEMA3E/F axis in fetoplacental vascularization downstream of retinoic acid signaling.\",\n      \"evidence\": \"Raldh2-/- mouse embryos, single-cell RNA-seq, and all-trans-RA dietary rescue with vascular assays\",\n      \"pmids\": [\"41884003\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"SEMA3E vs SEMA3F contributions not disentangled\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single Sema3E-PlexinD1 axis selects among opposing outputs (repulsion vs attraction vs survival vs invasion) across cell types remains unresolved at the level of shared molecular switches.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying structural model linking receptor context (Neuropilin-1, furin cleavage, GAP activity) to output selection\", \"Cross-tissue comparison of effector usage lacking\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0048018\", \"supporting_discovery_ids\": [0, 2, 4, 7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [6, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [1, 15]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [0, 2, 13]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [4, 7, 8]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [6, 8]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [1, 3, 7]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PLXND1\", \"NRP1\", \"ERBB2\", \"Tuba\", \"Mtss1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}