{"gene":"FLRT3","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":1999,"finding":"FLRT3 encodes a type I transmembrane protein containing 10 leucine-rich repeats flanked by cysteine-rich regions, a fibronectin/collagen-like domain, and an intracellular tail; when expressed in SF9 and COS-1 cells it is glycosylated and migrates as an ~85-90 kDa protein.","method":"Heterologous expression in SF9 and COS-1 cells; biochemical characterization (glycosylation assay, SDS-PAGE)","journal":"Genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct expression and biochemical characterization in two cell systems, single lab","pmids":["10644439"],"is_preprint":false},{"year":2004,"finding":"FLRT3 is expressed at the cell surface and promotes neurite outgrowth when neurons are plated on CHO cells expressing FLRT3; it does not exhibit homophilic binding.","method":"CHO cell co-culture neurite outgrowth assay; cell-surface expression assay; homophilic binding assay (negative result for homophilic binding)","journal":"Molecular and cellular neurosciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct functional assay with cell-surface expression confirmation and negative result for homophilic binding, single lab","pmids":["15485775"],"is_preprint":false},{"year":2004,"finding":"FLRT3 promotes neurite outgrowth; neurons plated on CHO cells expressing FLRT3 extended significantly longer neurites than those on wild-type CHO cells.","method":"CHO cell co-culture neurite outgrowth assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct functional assay replicated across two independent labs (PMID 15485775 and 14706654)","pmids":["14706654"],"is_preprint":false},{"year":2008,"finding":"Genetic ablation of FLRT3 in mouse disrupts basement membrane integrity in the anterior visceral endoderm (AVE), leading to an EMT-like process in adjacent anterior epiblast cells (loss of cell polarity, ingression, upregulation of Eomes, Brachyury/T, FGF8), without affecting Nodal/Wnt signaling or AP patterning, revealing FLRT3 as a morphogenetic boundary factor.","method":"Mouse genetic knockout; in situ hybridization; immunofluorescence; gene expression analysis","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean in vivo knockout with specific phenotypic readout, multiple orthogonal methods, replicated finding across two independent knockout studies (PMID 19056886 and 18448090)","pmids":["19056886"],"is_preprint":false},{"year":2008,"finding":"FLRT3 null mouse embryos display defects in headfold fusion, definitive endoderm migration, and failure of ventral body wall fusion (cardia bifida), without affecting FGF signaling, demonstrating a key role in cell adhesion and tissue morphogenesis.","method":"Mouse genetic knockout (null allele via gene targeting); developmental phenotype analysis; FGF signaling readouts","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo knockout with defined phenotypic readouts and negative result for FGF signaling effect, independently corroborating the other FLRT3 knockout study","pmids":["18448090"],"is_preprint":false},{"year":2009,"finding":"FLRT3 interacts with the Netrin receptors Unc5B and Unc5D as high-affinity binding partners; Unc5B overexpression phenocopies FLRT3 and both synergize in inducing cell deadhesion in Xenopus embryos; the small GTPase Rnd1 physically and functionally interacts with Unc5B to mediate its effect on cell adhesion.","method":"Expression screen; co-immunoprecipitation; morpholino knockdown; Xenopus cell deadhesion assay","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal functional and physical interaction assays, morpholino knockdown with defined phenotype, single lab","pmids":["19492039"],"is_preprint":false},{"year":2009,"finding":"FLRT3 forms a physical complex with PAPC (paraxial protocadherin) and C-cadherin; PAPC limits the cell-dissociating activity of FLRT3 by inhibiting recruitment of GTPase RND1 to the FLRT3 cytoplasmic domain, thereby calibrating FLRT3's regulation of C-cadherin adhesion for physiological cell sorting.","method":"Co-immunoprecipitation; Xenopus cell adhesion and cell sorting assays; domain mapping","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — physical and functional interaction demonstrated with multiple assays, single lab","pmids":["20027292"],"is_preprint":false},{"year":2011,"finding":"FLRT3 (and FLRT2) ectodomains are shed from neurons and act as repulsive guidance cues for Unc5-positive neurons; Unc5B binds FLRT3 and Unc5D binds specifically FLRT2; deletion of FLRT2 or Unc5D causes premature migration of SVZ-derived neurons toward the cortical plate, while Unc5D overexpression has the opposite effect, placing FLRT2/3–Unc5 signaling as a repulsive mechanism controlling cortical neuron migration.","method":"Mouse genetic knockouts; ectodomain shedding assays; in vitro repulsion/migration assays; in vivo cortical analysis","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple genetic models (KO and OE), in vitro and in vivo assays, defined molecular interaction and phenotypic readout","pmids":["21673655"],"is_preprint":false},{"year":2011,"finding":"FLRT3 was identified as a novel activator of SRF via MAL translocation; FLRT3 is a component of the ABRA-dependent pathway mediating EPEC-induced nuclear accumulation of MAL and actin cytoskeleton signaling to SRF.","method":"Expression screen; MAL-GFP nuclear translocation assay; siRNA knockdown","journal":"PLoS pathogens","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single-lab expression screen with limited mechanistic follow-up on FLRT3 specifically","pmids":["21490959"],"is_preprint":false},{"year":2014,"finding":"FLRT3 is a coreceptor for Robo1 that controls the attractive response to Netrin-1 in thalamic axons; in the presence of Slit1, both Robo1 and FLRT3 are required to induce Netrin-1 attraction by upregulating surface DCC through activation of protein kinase A; thalamic axons lacking FLRT3 are insensitive to Netrin-1.","method":"In vitro axon guidance assays; co-immunoprecipitation; PKA activity assays; in vivo axon guidance analysis in FLRT3 conditional knockout mice","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic loss-of-function with defined in vitro and in vivo phenotypes, identified downstream signaling mechanism (PKA/DCC), multiple orthogonal methods","pmids":["24560577"],"is_preprint":false},{"year":2015,"finding":"LPHN3 binds FLRT3 through its olfactomedin (OLF) domain; the crystal structure of the OLF/FLRT3 complex shows OLF (a 5-bladed β-propeller with a Ca²⁺ ion) binds with high affinity to the concave face of the FLRT3 LRR domain via hydrophobic and charged residues; this interaction mediates glutamatergic synapse development.","method":"Isothermal titration calorimetry; X-ray crystallography (multi-crystal native SAD phasing); domain-deletion mapping","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure of the complex with functional validation by ITC and domain mutagenesis, rigorous structural study","pmids":["26235031"],"is_preprint":false},{"year":2019,"finding":"FLRT3 expression in endothelial cells is rapidly upregulated by VEGF-stimulation of VEGFR2 through transcriptional elongation; siRNA knockdown of FLRT3 decreases endothelial cell survival and capillary-like structure formation but enhances cell migration, demonstrating a bifunctional role in VEGF-regulated endothelial function.","method":"siRNA knockdown; nascent RNA and mRNA measurement; endothelial tube formation assay; wound healing assay; cell viability assay","journal":"Frontiers in physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct KD with defined cellular phenotypes and transcriptional mechanism, single lab","pmids":["30930791"],"is_preprint":false},{"year":2021,"finding":"FLRT2 and FLRT3 double-knockout mice exhibit abnormal distribution of cortical interneurons within migratory streams and impaired postnatal somatostatin+ interneuron layering; FLRTs act non-cell-autonomously as chemorepellent ligands for developing interneurons in part through Unc5 receptors, confirmed by similar defects in Unc5B/Unc5D double knockouts.","method":"Mouse genetic double knockout; in vitro chemorepulsion assay; immunostaining; in vivo interneuron distribution analysis","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — double-KO and epistasis with Unc5B/Unc5D double-KO, in vitro functional assay, multiple orthogonal methods","pmids":["34301831"],"is_preprint":false},{"year":2022,"finding":"CAF-secreted TGF-β downregulates FLRT3 expression in colorectal cancer cells by activating SMAD4; FLRT3 overexpression inhibits EMT, while FLRT3 silencing promotes EMT, migration, invasion, and suppresses apoptosis; FLRT3 functions as an EMT suppressor downstream of TGF-β/SMAD4.","method":"Ectopic overexpression and siRNA knockdown; western blotting; migration/invasion assays; in vivo xenograft; TGF-β/SMAD4 pathway analysis","journal":"Molecular cancer research : MCR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — gain- and loss-of-function with defined cellular phenotypes, pathway epistasis via SMAD4 activation, single lab","pmids":["35560224"],"is_preprint":false},{"year":2024,"finding":"FLRT3 inhibits T cell activity through the axon guidance receptor UNC5B, which is upregulated on activated human T cells; blocking the FLRT3-UNC5B interaction with a monoclonal antibody reverses tumor immune evasion and restores CAR-T and BiTE+T cell killing in humanized cancer models.","method":"Gain-of-function genetic screen; functional T cell killing assays; humanized cancer models; monoclonal antibody blocking experiment","journal":"Science advances","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — gain-of-function screen plus antibody blocking with defined functional readout, single lab","pmids":["38427724"],"is_preprint":false},{"year":2024,"finding":"TGF-β/SMAD4 signaling directly regulates FLRT3 expression; a direct interaction between FLRT3 and SMAD4 was observed; SMAD4 inhibition increases FLRT3 expression; FLRT3 silencing modulates cardiomyocyte apoptosis, autophagy, and ion channel (SCN5A, KCNIP2, KCND2) expression in an Ang II-stimulated model.","method":"Dual-luciferase reporter assay; ChIP-PCR; western blotting; qRT-PCR; flow cytometry; siRNA knockdown in H9C2 cardiomyocytes","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct physical interaction (ChIP, reporter assay) and KD phenotype with multiple readouts, single lab","pmids":["38509727"],"is_preprint":false},{"year":2025,"finding":"FLRT3 overexpression protects against pulmonary ischemia-reperfusion-induced endothelial barrier dysfunction through interaction with RND3 (Rho family GTPase 3), which prevents RhoA pathway-mediated cytoskeletal disruption; RND3 knockdown in vivo attenuates FLRT3's protective effects; FLRT3 protein undergoes autophagic-lysosomal degradation under hypoxia/reoxygenation.","method":"Lentiviral overexpression and knockdown in vivo; Evans blue extravasation; electron microscopy; endothelial permeability assay; co-immunoprecipitation; RhoA pathway analysis","journal":"Lung","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo and in vitro gain/loss-of-function with defined mechanism (FLRT3–RND3–RhoA), multiple orthogonal methods, single lab","pmids":["40047936"],"is_preprint":false},{"year":2025,"finding":"miR-144-3p directly targets FLRT3 in mandibular bone marrow mesenchymal stem cells, as validated by dual-luciferase reporter assay; miR-144-3p mimic decreases FLRT3 expression and inhibits osteogenesis (reducing BMP2 and RUNX2), while the inhibitor increases FLRT3 and enhances osteogenic differentiation.","method":"Dual-luciferase reporter assay; miRNA mimic/inhibitor functional assays; qRT-PCR; ALP staining; Alizarin Red S staining","journal":"Human genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct target validation by reporter assay plus functional osteogenic phenotype, single lab","pmids":["40653464"],"is_preprint":false}],"current_model":"FLRT3 is a type I transmembrane leucine-rich repeat protein that functions as a cell adhesion molecule, repulsive axon guidance cue, and signaling co-receptor: its shed ectodomain acts as a chemorepellent ligand for Unc5-family receptors (Unc5B/Unc5D) to control cortical neuron and interneuron migration, while at the cell surface it co-operates with Robo1 to gate Netrin-1 attraction via PKA-dependent DCC upregulation, interacts with LPHN3 via a structurally defined LRR–OLF interface to promote glutamatergic synapse development, regulates C-cadherin–mediated adhesion through RND1 recruitment to its cytoplasmic tail, maintains endothelial barrier integrity through RND3–RhoA signaling, and acts as an EMT suppressor whose expression is negatively regulated by TGF-β/SMAD4 signaling."},"narrative":{"mechanistic_narrative":"FLRT3 is a type I transmembrane leucine-rich repeat protein that functions as a cell adhesion molecule and signaling co-receptor governing tissue morphogenesis, axon guidance, neuronal migration, and vascular integrity [PMID:10644439, PMID:19056886, PMID:21673655]. Its shed ectodomain acts as a chemorepellent ligand for the Netrin receptors Unc5B and Unc5D, which it binds with high affinity; this FLRT-Unc5 repulsion controls cortical neuron and interneuron migration in vivo [PMID:19492039, PMID:21673655, PMID:34301831]. At the cell surface, FLRT3 serves as a co-receptor for Robo1 that converts thalamic axons to Netrin-1 attraction by upregulating surface DCC through PKA activation [PMID:24560577], and binds the latrophilin LPHN3 through a defined interface in which the LPHN3 olfactomedin β-propeller docks onto the concave face of the FLRT3 LRR domain to drive glutamatergic synapse development [PMID:26235031]. FLRT3 calibrates cadherin-based adhesion via its cytoplasmic tail, which recruits the small GTPase RND1 to modulate C-cadherin adhesion, an activity restrained by complex formation with PAPC [PMID:20027292]; genetic ablation in mouse disrupts basement membrane integrity and triggers EMT-like behavior, causing headfold, endoderm migration, and ventral body wall fusion defects independently of FGF or Nodal/Wnt signaling [PMID:19056886, PMID:18448090]. In endothelium, FLRT3 is transcriptionally induced by VEGF/VEGFR2 and supports survival and capillary formation [PMID:30930791], and protects the endothelial barrier against ischemia-reperfusion injury by interacting with RND3 to block RhoA-mediated cytoskeletal disruption [PMID:40047936]. FLRT3 also acts as an EMT suppressor whose expression is directly repressed by TGF-β/SMAD4 signaling in colorectal cancer cells [PMID:35560224], and inhibits T cell activity through UNC5B such that antibody blockade restores anti-tumor killing [PMID:38427724].","teleology":[{"year":1999,"claim":"Established the molecular architecture of FLRT3, defining it as a glycosylated type I transmembrane LRR protein and setting the structural framework for its later ligand and adhesion roles.","evidence":"Heterologous expression and biochemical characterization in SF9 and COS-1 cells","pmids":["10644439"],"confidence":"Medium","gaps":["No function assigned at this stage","Localization and binding partners undefined"]},{"year":2004,"claim":"Showed FLRT3 is a functional cell-surface molecule that promotes neurite outgrowth without homophilic binding, implying it acts through a heterophilic partner rather than self-association.","evidence":"CHO cell co-culture neurite outgrowth assays and homophilic binding tests, replicated across two labs","pmids":["15485775","14706654"],"confidence":"Medium","gaps":["Receptor mediating neurite outgrowth not identified","Signaling mechanism unknown"]},{"year":2008,"claim":"In vivo knockouts established FLRT3 as a morphogenetic boundary and adhesion factor whose loss disrupts basement membrane integrity and provokes EMT-like ingression, independent of FGF/Nodal/Wnt patterning.","evidence":"Two independent mouse null alleles with developmental phenotyping, in situ hybridization, and pathway readouts","pmids":["19056886","18448090"],"confidence":"High","gaps":["Molecular partner mediating adhesion control not yet defined","Mechanism linking FLRT3 to basement membrane integrity unresolved"]},{"year":2009,"claim":"Identified Unc5B/Unc5D as high-affinity FLRT3 partners and linked the FLRT3 cytoplasmic tail to RND1-dependent adhesion control, providing the receptor and GTPase modules for FLRT3 signaling.","evidence":"Expression screen, co-immunoprecipitation, morpholino knockdown, and Xenopus cell deadhesion assays","pmids":["19492039","20027292"],"confidence":"Medium","gaps":["Single organism (Xenopus) for adhesion mechanism","PAPC regulation tested in embryonic context only"]},{"year":2011,"claim":"Demonstrated that shed FLRT2/FLRT3 ectodomains act as repulsive guidance cues for Unc5-positive neurons, defining a paracrine repulsion mechanism that controls cortical neuron migration timing.","evidence":"Mouse genetic knockouts and overexpression, ectodomain shedding assays, and in vitro/in vivo migration analysis","pmids":["21673655"],"confidence":"High","gaps":["Protease responsible for shedding not defined here","FLRT3-specific Unc5 partner specificity vs FLRT2 incompletely resolved"]},{"year":2014,"claim":"Revealed a distinct cell-surface role: FLRT3 partners with Robo1 to switch thalamic axons toward Netrin-1 attraction via PKA-driven surface DCC upregulation.","evidence":"In vitro and in vivo axon guidance assays in conditional knockouts, co-immunoprecipitation, and PKA activity assays","pmids":["24560577"],"confidence":"High","gaps":["How Slit1/Robo1 engagement is coupled to PKA not fully mapped","Generalizability beyond thalamic axons untested"]},{"year":2015,"claim":"Provided the atomic-resolution basis for FLRT3 synaptic function by solving the LPHN3 OLF–FLRT3 LRR complex structure, defining a high-affinity heterophilic interface driving glutamatergic synapse development.","evidence":"X-ray crystallography, isothermal titration calorimetry, and domain-deletion mapping","pmids":["26235031"],"confidence":"High","gaps":["Cellular signaling downstream of the FLRT3–LPHN3 complex not detailed","Interplay with Unc5 binding on the same LRR face unresolved"]},{"year":2019,"claim":"Extended FLRT3 function to vasculature, showing it is VEGF/VEGFR2-inducible via transcriptional elongation and bifunctionally regulates endothelial survival, tube formation, and migration.","evidence":"siRNA knockdown, nascent RNA measurement, and endothelial tube/migration/viability assays","pmids":["30930791"],"confidence":"Medium","gaps":["Receptor/effector mediating endothelial effects not identified here","Single endothelial cell system"]},{"year":2021,"claim":"Confirmed FLRT–Unc5 repulsion operates non-cell-autonomously on cortical interneurons, with epistasis to Unc5B/Unc5D establishing the receptor specificity of the migration phenotype.","evidence":"FLRT2/FLRT3 and Unc5B/Unc5D double-knockout mice, in vitro chemorepulsion, and in vivo interneuron mapping","pmids":["34301831"],"confidence":"High","gaps":["Relative contribution of FLRT3 vs FLRT2 to interneuron guidance not separated","Layer-specific cues remaining unidentified"]},{"year":2022,"claim":"Positioned FLRT3 as an EMT suppressor in cancer that is transcriptionally silenced by stromal TGF-β/SMAD4 signaling, linking its adhesion role to tumor invasion control.","evidence":"Gain- and loss-of-function with migration/invasion assays, xenografts, and TGF-β/SMAD4 pathway epistasis","pmids":["35560224"],"confidence":"Medium","gaps":["Direct vs indirect SMAD4 regulation of FLRT3 not fully resolved here","Single tumor type"]},{"year":2024,"claim":"Identified FLRT3 as an immune checkpoint-like ligand that suppresses T cell activity via UNC5B, providing a therapeutically actionable interaction in tumor immune evasion.","evidence":"Gain-of-function genetic screen, T cell killing assays, humanized cancer models, and monoclonal antibody blockade","pmids":["38427724"],"confidence":"Medium","gaps":["Signaling within T cells downstream of UNC5B not detailed","Single-lab finding"]},{"year":2024,"claim":"Documented direct SMAD4 regulation of FLRT3 and a FLRT3-dependent program controlling cardiomyocyte apoptosis, autophagy, and ion channel expression, broadening its tissue context.","evidence":"Dual-luciferase reporter, ChIP-PCR, knockdown, and apoptosis/ion-channel readouts in Ang II-stimulated H9C2 cardiomyocytes","pmids":["38509727"],"confidence":"Medium","gaps":["Mechanism linking FLRT3 to ion channel genes unknown","Cell-line model only"]},{"year":2025,"claim":"Defined a vascular protective mechanism in which FLRT3 binds RND3 to suppress RhoA-mediated cytoskeletal disruption and maintain endothelial barrier integrity, with FLRT3 turnover by autophagic-lysosomal degradation under stress.","evidence":"In vivo lentiviral gain/loss-of-function, Evans blue extravasation, electron microscopy, co-immunoprecipitation, and RhoA pathway analysis","pmids":["40047936"],"confidence":"Medium","gaps":["Direct vs indirect FLRT3–RND3 binding not crystallographically defined","Single-lab finding"]},{"year":null,"claim":"How FLRT3 integrates its multiple competing partners (Unc5, Robo1, LPHN3, cadherins, Rnd-family GTPases) at a single surface to produce context-specific adhesion, repulsion, or attraction outputs remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model of partner selection across tissues","Regulation of ectodomain shedding vs cell-surface retention not defined","Cytoplasmic signaling output remains poorly mapped"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098631","term_label":"cell adhesion mediator activity","supporting_discovery_ids":[3,4,6]},{"term_id":"GO:0048018","term_label":"receptor ligand activity","supporting_discovery_ids":[5,7,12]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[9,6]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[1,7,9]},{"term_id":"GO:0005576","term_label":"extracellular region","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[3,4,7,12]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[9,16]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[13,14]}],"complexes":[],"partners":["UNC5B","UNC5D","ROBO1","LPHN3","RND1","RND3","CDH3","SMAD4"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NZU0","full_name":"Leucine-rich repeat transmembrane protein FLRT3","aliases":["Fibronectin-like domain-containing leucine-rich transmembrane protein 3"],"length_aa":649,"mass_kda":73.0,"function":"Functions in cell-cell adhesion, cell migration and axon guidance, exerting an attractive or repulsive role depending on its interaction partners. Plays a role in the spatial organization of brain neurons. Plays a role in vascular development in the retina (By similarity). Plays a role in cell-cell adhesion via its interaction with ADGRL3 and probably also other latrophilins that are expressed at the surface of adjacent cells (PubMed:26235030). Interaction with the intracellular domain of ROBO1 mediates axon attraction towards cells expressing NTN1. Mediates axon growth cone collapse and plays a repulsive role in neuron guidance via its interaction with UNC5B, and possibly also other UNC-5 family members (By similarity). Promotes neurite outgrowth (in vitro) (PubMed:14706654). Mediates cell-cell contacts that promote an increase both in neurite number and in neurite length. Plays a role in the regulation of the density of glutamaergic synapses. Plays a role in fibroblast growth factor-mediated signaling cascades. Required for normal morphogenesis during embryonic development, but not for normal embryonic patterning. Required for normal ventral closure, headfold fusion and definitive endoderm migration during embryonic development. Required for the formation of a normal basement membrane and the maintenance of a normal anterior visceral endoderm during embryonic development (By similarity)","subcellular_location":"Cell membrane; Presynaptic cell membrane; Endoplasmic reticulum membrane; Cell junction, focal adhesion; Secreted; Cell projection, axon; Cell projection, growth cone membrane","url":"https://www.uniprot.org/uniprotkb/Q9NZU0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FLRT3","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/FLRT3","total_profiled":1310},"omim":[{"mim_id":"616417","title":"ADHESION G PROTEIN-COUPLED RECEPTOR L3; ADGRL3","url":"https://www.omim.org/entry/616417"},{"mim_id":"616416","title":"ADHESION G PROTEIN-COUPLED RECEPTOR L1; ADGRL1","url":"https://www.omim.org/entry/616416"},{"mim_id":"615271","title":"HYPOGONADOTROPIC HYPOGONADISM 21 WITH OR WITHOUT ANOSMIA; HH21","url":"https://www.omim.org/entry/615271"},{"mim_id":"615270","title":"HYPOGONADOTROPIC HYPOGONADISM 20 WITH OR WITHOUT ANOSMIA; HH20","url":"https://www.omim.org/entry/615270"},{"mim_id":"615269","title":"HYPOGONADOTROPIC HYPOGONADISM 19 WITH OR WITHOUT ANOSMIA; HH19","url":"https://www.omim.org/entry/615269"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Plasma membrane","reliability":"Supported"},{"location":"Vesicles","reliability":"Additional"},{"location":"Cell Junctions","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"kidney","ntpm":21.7}],"url":"https://www.proteinatlas.org/search/FLRT3"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q9NZU0","domains":[{"cath_id":"3.80.10.10","chopping":"30-165","consensus_level":"medium","plddt":96.734,"start":30,"end":165},{"cath_id":"2.60.40.10","chopping":"410-499","consensus_level":"high","plddt":78.6812,"start":410,"end":499}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NZU0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NZU0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NZU0-F1-predicted_aligned_error_v6.png","plddt_mean":74.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FLRT3","jax_strain_url":"https://www.jax.org/strain/search?query=FLRT3"},"sequence":{"accession":"Q9NZU0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NZU0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NZU0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NZU0"}},"corpus_meta":[{"pmid":"23643382","id":"PMC_23643382","title":"Mutations in FGF17, IL17RD, DUSP6, SPRY4, and FLRT3 are identified in individuals with congenital hypogonadotropic hypogonadism.","date":"2013","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23643382","citation_count":202,"is_preprint":false},{"pmid":"21673655","id":"PMC_21673655","title":"FLRT2 and FLRT3 act as repulsive guidance cues for Unc5-positive neurons.","date":"2011","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/21673655","citation_count":123,"is_preprint":false},{"pmid":"10644439","id":"PMC_10644439","title":"Identification of FLRT1, FLRT2, and FLRT3: a novel family of transmembrane leucine-rich repeat proteins.","date":"1999","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/10644439","citation_count":103,"is_preprint":false},{"pmid":"24560577","id":"PMC_24560577","title":"FLRT3 is a Robo1-interacting protein that determines Netrin-1 attraction in developing axons.","date":"2014","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/24560577","citation_count":70,"is_preprint":false},{"pmid":"19056886","id":"PMC_19056886","title":"Genetic ablation of FLRT3 reveals a novel morphogenetic function for the anterior visceral endoderm in suppressing mesoderm differentiation.","date":"2008","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/19056886","citation_count":57,"is_preprint":false},{"pmid":"14706654","id":"PMC_14706654","title":"FLRT3, a cell surface molecule containing LRR repeats and a FNIII domain, promotes neurite outgrowth.","date":"2004","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/14706654","citation_count":50,"is_preprint":false},{"pmid":"18448090","id":"PMC_18448090","title":"Ventral closure, headfold fusion and definitive endoderm migration defects in mouse embryos lacking the fibronectin leucine-rich transmembrane protein FLRT3.","date":"2008","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/18448090","citation_count":48,"is_preprint":false},{"pmid":"19492039","id":"PMC_19492039","title":"Unc5B interacts with FLRT3 and Rnd1 to modulate cell adhesion in Xenopus embryos.","date":"2009","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/19492039","citation_count":47,"is_preprint":false},{"pmid":"20027292","id":"PMC_20027292","title":"A protocadherin-cadherin-FLRT3 complex controls cell adhesion and morphogenesis.","date":"2009","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/20027292","citation_count":45,"is_preprint":false},{"pmid":"15485775","id":"PMC_15485775","title":"FLRT3 is expressed in sensory neurons after peripheral nerve injury and regulates neurite outgrowth.","date":"2004","source":"Molecular and cellular neurosciences","url":"https://pubmed.ncbi.nlm.nih.gov/15485775","citation_count":43,"is_preprint":false},{"pmid":"26235031","id":"PMC_26235031","title":"Structural and Mechanistic Insights into the Latrophilin3-FLRT3 Complex that Mediates Glutamatergic Synapse Development.","date":"2015","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/26235031","citation_count":42,"is_preprint":false},{"pmid":"38225404","id":"PMC_38225404","title":"A protein-encoding CCDC7 circular RNA inhibits the progression of prostate cancer by up-regulating FLRT3.","date":"2024","source":"NPJ precision oncology","url":"https://pubmed.ncbi.nlm.nih.gov/38225404","citation_count":27,"is_preprint":false},{"pmid":"19635589","id":"PMC_19635589","title":"Flrt2 and Flrt3 have overlapping and non-overlapping expression during craniofacial development.","date":"2009","source":"Gene expression patterns : GEP","url":"https://pubmed.ncbi.nlm.nih.gov/19635589","citation_count":26,"is_preprint":false},{"pmid":"35560224","id":"PMC_35560224","title":"TGF-β-Induced FLRT3 Attenuation Is Essential for Cancer-Associated Fibroblast-Mediated Epithelial-Mesenchymal Transition in Colorectal Cancer.","date":"2022","source":"Molecular cancer research : MCR","url":"https://pubmed.ncbi.nlm.nih.gov/35560224","citation_count":26,"is_preprint":false},{"pmid":"30930791","id":"PMC_30930791","title":"Axon Guidance-Related Factor FLRT3 Regulates VEGF-Signaling and Endothelial Cell Function.","date":"2019","source":"Frontiers in physiology","url":"https://pubmed.ncbi.nlm.nih.gov/30930791","citation_count":19,"is_preprint":false},{"pmid":"21575622","id":"PMC_21575622","title":"FLRT3 as a key player on chick limb development.","date":"2011","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/21575622","citation_count":18,"is_preprint":false},{"pmid":"34301831","id":"PMC_34301831","title":"FLRT2 and FLRT3 Cooperate in Maintaining the Tangential Migratory Streams of Cortical Interneurons during Development.","date":"2021","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/34301831","citation_count":17,"is_preprint":false},{"pmid":"37330168","id":"PMC_37330168","title":"Serum exosomal m6A demethylase FTO promotes gefitinib resistance in non-small cell lung cancer by up-regulating FLRT3, PTGIS and SIRPα expression.","date":"2023","source":"Pulmonary pharmacology & therapeutics","url":"https://pubmed.ncbi.nlm.nih.gov/37330168","citation_count":10,"is_preprint":false},{"pmid":"17051480","id":"PMC_17051480","title":"The expression of Flrt3 during chick limb development.","date":"2006","source":"The International journal of developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/17051480","citation_count":10,"is_preprint":false},{"pmid":"33711669","id":"PMC_33711669","title":"Variants in FLRT3 and SLC35E2B identified using exome sequencing in seven high myopia families from Central Europe.","date":"2021","source":"Advances in medical sciences","url":"https://pubmed.ncbi.nlm.nih.gov/33711669","citation_count":8,"is_preprint":false},{"pmid":"21490959","id":"PMC_21490959","title":"Bacterial and host determinants of MAL activation upon EPEC infection: the roles of Tir, ABRA, and FLRT3.","date":"2011","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/21490959","citation_count":7,"is_preprint":false},{"pmid":"38509727","id":"PMC_38509727","title":"FLRT3 and TGF-β/SMAD4 signalling: Impacts on apoptosis, autophagy and ion channels in supraventricular tachycardia.","date":"2024","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38509727","citation_count":6,"is_preprint":false},{"pmid":"34955746","id":"PMC_34955746","title":"FLRT3 Marks Direction-Selective Retinal Ganglion Cells That Project to the Medial Terminal Nucleus.","date":"2021","source":"Frontiers in molecular neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/34955746","citation_count":5,"is_preprint":false},{"pmid":"38427724","id":"PMC_38427724","title":"The FLRT3-UNC5B checkpoint pathway inhibits T cell-based cancer immunotherapies.","date":"2024","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/38427724","citation_count":2,"is_preprint":false},{"pmid":"40047936","id":"PMC_40047936","title":"FLRT3 Overexpression Attenuates Ischemia-Reperfusion Induced Vascular Hyperpermeability and Lung Injury Through RND3.","date":"2025","source":"Lung","url":"https://pubmed.ncbi.nlm.nih.gov/40047936","citation_count":2,"is_preprint":false},{"pmid":"40653464","id":"PMC_40653464","title":"miR-144-3p targeting FLRT3 in osteogenic differentiation of mandibular bone marrow mesenchymal stem cells.","date":"2025","source":"Human genomics","url":"https://pubmed.ncbi.nlm.nih.gov/40653464","citation_count":1,"is_preprint":false},{"pmid":"39995192","id":"PMC_39995192","title":"Effect of FLRT3 on epithelial-mesenchymal transition in clear cell renal cell carcinoma.","date":"2025","source":"Urologia","url":"https://pubmed.ncbi.nlm.nih.gov/39995192","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15516,"output_tokens":4471,"usd":0.056807,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12432,"output_tokens":4309,"usd":0.084943,"stage2_stop_reason":"end_turn"},"total_usd":0.14175,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1999,\n      \"finding\": \"FLRT3 encodes a type I transmembrane protein containing 10 leucine-rich repeats flanked by cysteine-rich regions, a fibronectin/collagen-like domain, and an intracellular tail; when expressed in SF9 and COS-1 cells it is glycosylated and migrates as an ~85-90 kDa protein.\",\n      \"method\": \"Heterologous expression in SF9 and COS-1 cells; biochemical characterization (glycosylation assay, SDS-PAGE)\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct expression and biochemical characterization in two cell systems, single lab\",\n      \"pmids\": [\"10644439\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"FLRT3 is expressed at the cell surface and promotes neurite outgrowth when neurons are plated on CHO cells expressing FLRT3; it does not exhibit homophilic binding.\",\n      \"method\": \"CHO cell co-culture neurite outgrowth assay; cell-surface expression assay; homophilic binding assay (negative result for homophilic binding)\",\n      \"journal\": \"Molecular and cellular neurosciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct functional assay with cell-surface expression confirmation and negative result for homophilic binding, single lab\",\n      \"pmids\": [\"15485775\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"FLRT3 promotes neurite outgrowth; neurons plated on CHO cells expressing FLRT3 extended significantly longer neurites than those on wild-type CHO cells.\",\n      \"method\": \"CHO cell co-culture neurite outgrowth assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct functional assay replicated across two independent labs (PMID 15485775 and 14706654)\",\n      \"pmids\": [\"14706654\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Genetic ablation of FLRT3 in mouse disrupts basement membrane integrity in the anterior visceral endoderm (AVE), leading to an EMT-like process in adjacent anterior epiblast cells (loss of cell polarity, ingression, upregulation of Eomes, Brachyury/T, FGF8), without affecting Nodal/Wnt signaling or AP patterning, revealing FLRT3 as a morphogenetic boundary factor.\",\n      \"method\": \"Mouse genetic knockout; in situ hybridization; immunofluorescence; gene expression analysis\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean in vivo knockout with specific phenotypic readout, multiple orthogonal methods, replicated finding across two independent knockout studies (PMID 19056886 and 18448090)\",\n      \"pmids\": [\"19056886\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"FLRT3 null mouse embryos display defects in headfold fusion, definitive endoderm migration, and failure of ventral body wall fusion (cardia bifida), without affecting FGF signaling, demonstrating a key role in cell adhesion and tissue morphogenesis.\",\n      \"method\": \"Mouse genetic knockout (null allele via gene targeting); developmental phenotype analysis; FGF signaling readouts\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo knockout with defined phenotypic readouts and negative result for FGF signaling effect, independently corroborating the other FLRT3 knockout study\",\n      \"pmids\": [\"18448090\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"FLRT3 interacts with the Netrin receptors Unc5B and Unc5D as high-affinity binding partners; Unc5B overexpression phenocopies FLRT3 and both synergize in inducing cell deadhesion in Xenopus embryos; the small GTPase Rnd1 physically and functionally interacts with Unc5B to mediate its effect on cell adhesion.\",\n      \"method\": \"Expression screen; co-immunoprecipitation; morpholino knockdown; Xenopus cell deadhesion assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal functional and physical interaction assays, morpholino knockdown with defined phenotype, single lab\",\n      \"pmids\": [\"19492039\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"FLRT3 forms a physical complex with PAPC (paraxial protocadherin) and C-cadherin; PAPC limits the cell-dissociating activity of FLRT3 by inhibiting recruitment of GTPase RND1 to the FLRT3 cytoplasmic domain, thereby calibrating FLRT3's regulation of C-cadherin adhesion for physiological cell sorting.\",\n      \"method\": \"Co-immunoprecipitation; Xenopus cell adhesion and cell sorting assays; domain mapping\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — physical and functional interaction demonstrated with multiple assays, single lab\",\n      \"pmids\": [\"20027292\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"FLRT3 (and FLRT2) ectodomains are shed from neurons and act as repulsive guidance cues for Unc5-positive neurons; Unc5B binds FLRT3 and Unc5D binds specifically FLRT2; deletion of FLRT2 or Unc5D causes premature migration of SVZ-derived neurons toward the cortical plate, while Unc5D overexpression has the opposite effect, placing FLRT2/3–Unc5 signaling as a repulsive mechanism controlling cortical neuron migration.\",\n      \"method\": \"Mouse genetic knockouts; ectodomain shedding assays; in vitro repulsion/migration assays; in vivo cortical analysis\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple genetic models (KO and OE), in vitro and in vivo assays, defined molecular interaction and phenotypic readout\",\n      \"pmids\": [\"21673655\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"FLRT3 was identified as a novel activator of SRF via MAL translocation; FLRT3 is a component of the ABRA-dependent pathway mediating EPEC-induced nuclear accumulation of MAL and actin cytoskeleton signaling to SRF.\",\n      \"method\": \"Expression screen; MAL-GFP nuclear translocation assay; siRNA knockdown\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single-lab expression screen with limited mechanistic follow-up on FLRT3 specifically\",\n      \"pmids\": [\"21490959\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"FLRT3 is a coreceptor for Robo1 that controls the attractive response to Netrin-1 in thalamic axons; in the presence of Slit1, both Robo1 and FLRT3 are required to induce Netrin-1 attraction by upregulating surface DCC through activation of protein kinase A; thalamic axons lacking FLRT3 are insensitive to Netrin-1.\",\n      \"method\": \"In vitro axon guidance assays; co-immunoprecipitation; PKA activity assays; in vivo axon guidance analysis in FLRT3 conditional knockout mice\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic loss-of-function with defined in vitro and in vivo phenotypes, identified downstream signaling mechanism (PKA/DCC), multiple orthogonal methods\",\n      \"pmids\": [\"24560577\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"LPHN3 binds FLRT3 through its olfactomedin (OLF) domain; the crystal structure of the OLF/FLRT3 complex shows OLF (a 5-bladed β-propeller with a Ca²⁺ ion) binds with high affinity to the concave face of the FLRT3 LRR domain via hydrophobic and charged residues; this interaction mediates glutamatergic synapse development.\",\n      \"method\": \"Isothermal titration calorimetry; X-ray crystallography (multi-crystal native SAD phasing); domain-deletion mapping\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure of the complex with functional validation by ITC and domain mutagenesis, rigorous structural study\",\n      \"pmids\": [\"26235031\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"FLRT3 expression in endothelial cells is rapidly upregulated by VEGF-stimulation of VEGFR2 through transcriptional elongation; siRNA knockdown of FLRT3 decreases endothelial cell survival and capillary-like structure formation but enhances cell migration, demonstrating a bifunctional role in VEGF-regulated endothelial function.\",\n      \"method\": \"siRNA knockdown; nascent RNA and mRNA measurement; endothelial tube formation assay; wound healing assay; cell viability assay\",\n      \"journal\": \"Frontiers in physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct KD with defined cellular phenotypes and transcriptional mechanism, single lab\",\n      \"pmids\": [\"30930791\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"FLRT2 and FLRT3 double-knockout mice exhibit abnormal distribution of cortical interneurons within migratory streams and impaired postnatal somatostatin+ interneuron layering; FLRTs act non-cell-autonomously as chemorepellent ligands for developing interneurons in part through Unc5 receptors, confirmed by similar defects in Unc5B/Unc5D double knockouts.\",\n      \"method\": \"Mouse genetic double knockout; in vitro chemorepulsion assay; immunostaining; in vivo interneuron distribution analysis\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — double-KO and epistasis with Unc5B/Unc5D double-KO, in vitro functional assay, multiple orthogonal methods\",\n      \"pmids\": [\"34301831\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CAF-secreted TGF-β downregulates FLRT3 expression in colorectal cancer cells by activating SMAD4; FLRT3 overexpression inhibits EMT, while FLRT3 silencing promotes EMT, migration, invasion, and suppresses apoptosis; FLRT3 functions as an EMT suppressor downstream of TGF-β/SMAD4.\",\n      \"method\": \"Ectopic overexpression and siRNA knockdown; western blotting; migration/invasion assays; in vivo xenograft; TGF-β/SMAD4 pathway analysis\",\n      \"journal\": \"Molecular cancer research : MCR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — gain- and loss-of-function with defined cellular phenotypes, pathway epistasis via SMAD4 activation, single lab\",\n      \"pmids\": [\"35560224\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"FLRT3 inhibits T cell activity through the axon guidance receptor UNC5B, which is upregulated on activated human T cells; blocking the FLRT3-UNC5B interaction with a monoclonal antibody reverses tumor immune evasion and restores CAR-T and BiTE+T cell killing in humanized cancer models.\",\n      \"method\": \"Gain-of-function genetic screen; functional T cell killing assays; humanized cancer models; monoclonal antibody blocking experiment\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — gain-of-function screen plus antibody blocking with defined functional readout, single lab\",\n      \"pmids\": [\"38427724\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TGF-β/SMAD4 signaling directly regulates FLRT3 expression; a direct interaction between FLRT3 and SMAD4 was observed; SMAD4 inhibition increases FLRT3 expression; FLRT3 silencing modulates cardiomyocyte apoptosis, autophagy, and ion channel (SCN5A, KCNIP2, KCND2) expression in an Ang II-stimulated model.\",\n      \"method\": \"Dual-luciferase reporter assay; ChIP-PCR; western blotting; qRT-PCR; flow cytometry; siRNA knockdown in H9C2 cardiomyocytes\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct physical interaction (ChIP, reporter assay) and KD phenotype with multiple readouts, single lab\",\n      \"pmids\": [\"38509727\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FLRT3 overexpression protects against pulmonary ischemia-reperfusion-induced endothelial barrier dysfunction through interaction with RND3 (Rho family GTPase 3), which prevents RhoA pathway-mediated cytoskeletal disruption; RND3 knockdown in vivo attenuates FLRT3's protective effects; FLRT3 protein undergoes autophagic-lysosomal degradation under hypoxia/reoxygenation.\",\n      \"method\": \"Lentiviral overexpression and knockdown in vivo; Evans blue extravasation; electron microscopy; endothelial permeability assay; co-immunoprecipitation; RhoA pathway analysis\",\n      \"journal\": \"Lung\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo and in vitro gain/loss-of-function with defined mechanism (FLRT3–RND3–RhoA), multiple orthogonal methods, single lab\",\n      \"pmids\": [\"40047936\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"miR-144-3p directly targets FLRT3 in mandibular bone marrow mesenchymal stem cells, as validated by dual-luciferase reporter assay; miR-144-3p mimic decreases FLRT3 expression and inhibits osteogenesis (reducing BMP2 and RUNX2), while the inhibitor increases FLRT3 and enhances osteogenic differentiation.\",\n      \"method\": \"Dual-luciferase reporter assay; miRNA mimic/inhibitor functional assays; qRT-PCR; ALP staining; Alizarin Red S staining\",\n      \"journal\": \"Human genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct target validation by reporter assay plus functional osteogenic phenotype, single lab\",\n      \"pmids\": [\"40653464\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FLRT3 is a type I transmembrane leucine-rich repeat protein that functions as a cell adhesion molecule, repulsive axon guidance cue, and signaling co-receptor: its shed ectodomain acts as a chemorepellent ligand for Unc5-family receptors (Unc5B/Unc5D) to control cortical neuron and interneuron migration, while at the cell surface it co-operates with Robo1 to gate Netrin-1 attraction via PKA-dependent DCC upregulation, interacts with LPHN3 via a structurally defined LRR–OLF interface to promote glutamatergic synapse development, regulates C-cadherin–mediated adhesion through RND1 recruitment to its cytoplasmic tail, maintains endothelial barrier integrity through RND3–RhoA signaling, and acts as an EMT suppressor whose expression is negatively regulated by TGF-β/SMAD4 signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"FLRT3 is a type I transmembrane leucine-rich repeat protein that functions as a cell adhesion molecule and signaling co-receptor governing tissue morphogenesis, axon guidance, neuronal migration, and vascular integrity [#0, #3, #7]. Its shed ectodomain acts as a chemorepellent ligand for the Netrin receptors Unc5B and Unc5D, which it binds with high affinity; this FLRT-Unc5 repulsion controls cortical neuron and interneuron migration in vivo [#5, #7, #12]. At the cell surface, FLRT3 serves as a co-receptor for Robo1 that converts thalamic axons to Netrin-1 attraction by upregulating surface DCC through PKA activation [#9], and binds the latrophilin LPHN3 through a defined interface in which the LPHN3 olfactomedin β-propeller docks onto the concave face of the FLRT3 LRR domain to drive glutamatergic synapse development [#10]. FLRT3 calibrates cadherin-based adhesion via its cytoplasmic tail, which recruits the small GTPase RND1 to modulate C-cadherin adhesion, an activity restrained by complex formation with PAPC [#6]; genetic ablation in mouse disrupts basement membrane integrity and triggers EMT-like behavior, causing headfold, endoderm migration, and ventral body wall fusion defects independently of FGF or Nodal/Wnt signaling [#3, #4]. In endothelium, FLRT3 is transcriptionally induced by VEGF/VEGFR2 and supports survival and capillary formation [#11], and protects the endothelial barrier against ischemia-reperfusion injury by interacting with RND3 to block RhoA-mediated cytoskeletal disruption [#16]. FLRT3 also acts as an EMT suppressor whose expression is directly repressed by TGF-β/SMAD4 signaling in colorectal cancer cells [#13], and inhibits T cell activity through UNC5B such that antibody blockade restores anti-tumor killing [#14].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Established the molecular architecture of FLRT3, defining it as a glycosylated type I transmembrane LRR protein and setting the structural framework for its later ligand and adhesion roles.\",\n      \"evidence\": \"Heterologous expression and biochemical characterization in SF9 and COS-1 cells\",\n      \"pmids\": [\"10644439\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No function assigned at this stage\", \"Localization and binding partners undefined\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Showed FLRT3 is a functional cell-surface molecule that promotes neurite outgrowth without homophilic binding, implying it acts through a heterophilic partner rather than self-association.\",\n      \"evidence\": \"CHO cell co-culture neurite outgrowth assays and homophilic binding tests, replicated across two labs\",\n      \"pmids\": [\"15485775\", \"14706654\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Receptor mediating neurite outgrowth not identified\", \"Signaling mechanism unknown\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"In vivo knockouts established FLRT3 as a morphogenetic boundary and adhesion factor whose loss disrupts basement membrane integrity and provokes EMT-like ingression, independent of FGF/Nodal/Wnt patterning.\",\n      \"evidence\": \"Two independent mouse null alleles with developmental phenotyping, in situ hybridization, and pathway readouts\",\n      \"pmids\": [\"19056886\", \"18448090\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular partner mediating adhesion control not yet defined\", \"Mechanism linking FLRT3 to basement membrane integrity unresolved\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Identified Unc5B/Unc5D as high-affinity FLRT3 partners and linked the FLRT3 cytoplasmic tail to RND1-dependent adhesion control, providing the receptor and GTPase modules for FLRT3 signaling.\",\n      \"evidence\": \"Expression screen, co-immunoprecipitation, morpholino knockdown, and Xenopus cell deadhesion assays\",\n      \"pmids\": [\"19492039\", \"20027292\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single organism (Xenopus) for adhesion mechanism\", \"PAPC regulation tested in embryonic context only\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Demonstrated that shed FLRT2/FLRT3 ectodomains act as repulsive guidance cues for Unc5-positive neurons, defining a paracrine repulsion mechanism that controls cortical neuron migration timing.\",\n      \"evidence\": \"Mouse genetic knockouts and overexpression, ectodomain shedding assays, and in vitro/in vivo migration analysis\",\n      \"pmids\": [\"21673655\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Protease responsible for shedding not defined here\", \"FLRT3-specific Unc5 partner specificity vs FLRT2 incompletely resolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Revealed a distinct cell-surface role: FLRT3 partners with Robo1 to switch thalamic axons toward Netrin-1 attraction via PKA-driven surface DCC upregulation.\",\n      \"evidence\": \"In vitro and in vivo axon guidance assays in conditional knockouts, co-immunoprecipitation, and PKA activity assays\",\n      \"pmids\": [\"24560577\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How Slit1/Robo1 engagement is coupled to PKA not fully mapped\", \"Generalizability beyond thalamic axons untested\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Provided the atomic-resolution basis for FLRT3 synaptic function by solving the LPHN3 OLF–FLRT3 LRR complex structure, defining a high-affinity heterophilic interface driving glutamatergic synapse development.\",\n      \"evidence\": \"X-ray crystallography, isothermal titration calorimetry, and domain-deletion mapping\",\n      \"pmids\": [\"26235031\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cellular signaling downstream of the FLRT3–LPHN3 complex not detailed\", \"Interplay with Unc5 binding on the same LRR face unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Extended FLRT3 function to vasculature, showing it is VEGF/VEGFR2-inducible via transcriptional elongation and bifunctionally regulates endothelial survival, tube formation, and migration.\",\n      \"evidence\": \"siRNA knockdown, nascent RNA measurement, and endothelial tube/migration/viability assays\",\n      \"pmids\": [\"30930791\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Receptor/effector mediating endothelial effects not identified here\", \"Single endothelial cell system\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Confirmed FLRT–Unc5 repulsion operates non-cell-autonomously on cortical interneurons, with epistasis to Unc5B/Unc5D establishing the receptor specificity of the migration phenotype.\",\n      \"evidence\": \"FLRT2/FLRT3 and Unc5B/Unc5D double-knockout mice, in vitro chemorepulsion, and in vivo interneuron mapping\",\n      \"pmids\": [\"34301831\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contribution of FLRT3 vs FLRT2 to interneuron guidance not separated\", \"Layer-specific cues remaining unidentified\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Positioned FLRT3 as an EMT suppressor in cancer that is transcriptionally silenced by stromal TGF-β/SMAD4 signaling, linking its adhesion role to tumor invasion control.\",\n      \"evidence\": \"Gain- and loss-of-function with migration/invasion assays, xenografts, and TGF-β/SMAD4 pathway epistasis\",\n      \"pmids\": [\"35560224\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect SMAD4 regulation of FLRT3 not fully resolved here\", \"Single tumor type\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified FLRT3 as an immune checkpoint-like ligand that suppresses T cell activity via UNC5B, providing a therapeutically actionable interaction in tumor immune evasion.\",\n      \"evidence\": \"Gain-of-function genetic screen, T cell killing assays, humanized cancer models, and monoclonal antibody blockade\",\n      \"pmids\": [\"38427724\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Signaling within T cells downstream of UNC5B not detailed\", \"Single-lab finding\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Documented direct SMAD4 regulation of FLRT3 and a FLRT3-dependent program controlling cardiomyocyte apoptosis, autophagy, and ion channel expression, broadening its tissue context.\",\n      \"evidence\": \"Dual-luciferase reporter, ChIP-PCR, knockdown, and apoptosis/ion-channel readouts in Ang II-stimulated H9C2 cardiomyocytes\",\n      \"pmids\": [\"38509727\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking FLRT3 to ion channel genes unknown\", \"Cell-line model only\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined a vascular protective mechanism in which FLRT3 binds RND3 to suppress RhoA-mediated cytoskeletal disruption and maintain endothelial barrier integrity, with FLRT3 turnover by autophagic-lysosomal degradation under stress.\",\n      \"evidence\": \"In vivo lentiviral gain/loss-of-function, Evans blue extravasation, electron microscopy, co-immunoprecipitation, and RhoA pathway analysis\",\n      \"pmids\": [\"40047936\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect FLRT3–RND3 binding not crystallographically defined\", \"Single-lab finding\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How FLRT3 integrates its multiple competing partners (Unc5, Robo1, LPHN3, cadherins, Rnd-family GTPases) at a single surface to produce context-specific adhesion, repulsion, or attraction outputs remains unresolved.\",\n      \"evidence\": null,\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model of partner selection across tissues\", \"Regulation of ectodomain shedding vs cell-surface retention not defined\", \"Cytoplasmic signaling output remains poorly mapped\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098631\", \"supporting_discovery_ids\": [3, 4, 6]},\n      {\"term_id\": \"GO:0048018\", \"supporting_discovery_ids\": [5, 7, 12]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [9, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [1, 7, 9]},\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [3, 4, 7, 12]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [9, 16]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [13, 14]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"UNC5B\", \"UNC5D\", \"ROBO1\", \"LPHN3\", \"RND1\", \"RND3\", \"CDH3\", \"SMAD4\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}