{"gene":"LRFN2","run_date":"2026-04-28T18:30:27","timeline":{"discoveries":[{"year":2017,"finding":"Lrfn2/SALM1 directly interacts with PSD-95, and this interaction is required for synaptic surface expression of AMPA receptors (GluA1); knockout mice show decreased synaptic PSD-95 and GluA1, structurally immature spines, smaller postsynaptic densities, reduced AMPA/NMDA ratio, and enhanced LTP.","method":"Lrfn2 knockout mice, in vitro interaction assays, electrophysiology, morphological analysis of synapses","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — clean KO with multiple orthogonal methods (behavioral, electrophysiological, biochemical, morphological) and direct in vitro interaction data","pmids":["28604739"],"is_preprint":false},{"year":2018,"finding":"SALM1/LRFN2 regulates excitatory synapse function (NMDAR-dependent synaptic transmission and plasticity) and inhibitory synapse development; Lrfn2-/- CA1 pyramidal neurons show decreased inhibitory synapse density and reduced spontaneous inhibitory synaptic transmission frequency, demonstrating a role in both excitatory and inhibitory circuit organization.","method":"Lrfn2 knockout mice, electrophysiology (whole-cell patch clamp, LTP), immunofluorescence, behavioral assays","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 — independent replication of LRFN2 KO with multiple orthogonal methods, novel finding of inhibitory synapse role","pmids":["29798891"],"is_preprint":false},{"year":2021,"finding":"Sorting nexin-27 (SNX27) directly binds LRFN2 and regulates its endosomal sorting; LRFN2 in turn associates with AMPA receptors, and LRFN2 knockdown decreases surface AMPA receptor expression, reduces synaptic activity, and attenuates hippocampal LTP, revealing an indirect mechanism by which SNX27 controls AMPA receptor-mediated synaptic transmission through LRFN2.","method":"Proteomics in rat primary neurons, Co-IP/pulldown, LRFN2 knockdown, surface biotinylation, electrophysiology (mEPSC, LTP)","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — reciprocal interaction data combined with functional KD experiments and multiple orthogonal readouts","pmids":["34251337"],"is_preprint":false},{"year":2011,"finding":"SALM1/LRFN2 contains a dileucine (DXXXLL) ER retention motif that retains it in the ER; its PDZ-binding motif is required for surface expression in heterologous cells and for dendritic (but not axonal) surface expression in hippocampal neurons. Mutation of the dileucine motif releases LRFN2 from the ER, increases surface expression, and causes formation of irregular enlarged spines and filopodia.","method":"Serial deletion mutagenesis, endoglycosidase H digestion assays, heterologous cell expression, hippocampal neuron transfection, electron microscopy","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — mutagenesis combined with biochemical retention assays and neuronal imaging with multiple orthogonal methods","pmids":["22174418"],"is_preprint":false},{"year":2015,"finding":"LRFN2 protein is localized at synapses of cerebellar and hippocampal rat neurons and is associated with the NR1 subunit of NMDA receptors, as demonstrated by electron microscopy immunogold labeling.","method":"Electron microscopy immunogold labeling in rat neurons","journal":"European journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 — direct ultrastructural localization showing co-association with NMDAR NR1 subunit, single lab","pmids":["26486473"],"is_preprint":false},{"year":2007,"finding":"Lrfn2 expression in colony-forming assays subverts hematopoietic differentiation to increase erythropoiesis and, in cooperation with Myc, leads to erythroblastosis; Lrfn2 expression also promotes outgrowth of a cell type positive for both early hematopoietic and fibroblast markers, indicating a role in hematopoietic cell fate decisions.","method":"In vitro colony-forming assays, transgenic mouse crosses, surface marker staining, mRNA expression studies","journal":"Experimental hematology","confidence":"Medium","confidence_rationale":"Tier 2 — direct gain-of-function in vitro assay with phenotypic readouts, single lab","pmids":["17577922"],"is_preprint":false},{"year":2021,"finding":"Lrfn2-deficient mice exhibit defective NMDA receptor-mediated calcium influx in late erythroblasts, and show altered erythropoiesis including normocytic erythrocythemia, decreased CFU-E progenitors, and altered EPO receptor expression, indicating that Lrfn2 regulates erythropoiesis through modulation of NMDA receptor function in hematopoietic cells.","method":"Lrfn2 KO mice, flow cytometry, peripheral blood tests, CFU assay, calcium influx assay with MK801 NMDAR antagonist","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 — KO mice with multiple functional readouts and pharmacological validation, single lab","pmids":["33481887"],"is_preprint":false},{"year":2024,"finding":"LRFN2 is selectively expressed at cone photoreceptor terminals and identified as a component of the depolarizing bipolar cell (DBC) signaling complex; in LRFN2-deficient mice, cone-mediated photopic ERG b-wave amplitude is reduced at bright flash intensities, demonstrating that LRFN2 is required for normal synaptic transmission between cones and cone DBCs.","method":"Unbiased proteomics, immunolocalization, Lrfn2 KO mice, electroretinography (ERG), co-localization with DBC signalplex markers","journal":"eNeuro","confidence":"Medium","confidence_rationale":"Tier 2 — proteomic identification followed by KO functional validation with electrophysiology, single lab","pmids":["38408870"],"is_preprint":false},{"year":2022,"finding":"LRFN2 binds to NMDAR subunit GRIN2B in esophageal squamous cell carcinoma cells; LRFN2 overexpression suppresses cancer cell proliferation, migration, and invasion by downregulating Wnt/β-catenin signaling components (β-catenin, c-Myc, cyclin D1) and NF-κB pathway via a GRIN2B–GSK3β interaction, and these effects are attenuated by the NR2B-selective NMDA antagonist NMDA-IN-1.","method":"Co-IP/binding assay (LRFN2–GRIN2B), overexpression in ESCC cells, western blot, pharmacological antagonism, in vivo tumor growth assay","journal":"Cancer science","confidence":"Medium","confidence_rationale":"Tier 3 — direct binding demonstrated with functional rescue by antagonist, single lab, non-neuronal context","pmids":["35879265"],"is_preprint":false},{"year":2023,"finding":"Tumor-intrinsic LRFN2 inhibits recruitment and functional transition of CD8+ T cells by reducing secretion of pro-inflammatory cytokines and chemokines in bladder cancer; LRFN2 knockdown enhances ICI therapy efficacy in preclinical models.","method":"LRFN2 knockdown in bladder cancer cells, multiplex immunoassay (cytokine/chemokine secretion), in vitro and in vivo functional experiments, single-cell RNA-seq, spatial tissue quantification","journal":"Journal for immunotherapy of cancer","confidence":"Medium","confidence_rationale":"Tier 2 — KD with multiple functional readouts including in vivo, but mechanism (chemokine regulation) not fully resolved at molecular level","pmids":["37802603"],"is_preprint":false}],"current_model":"LRFN2/SALM1 is a postsynaptic transmembrane adhesion molecule that directly binds PSD-95 (via its PDZ-binding motif) and NMDA receptor subunits (NR1/GRIN2B), and associates with AMPA receptors; intracellular trafficking is controlled by a dileucine ER retention motif and regulated by the endosomal adaptor SNX27, which together govern synaptic surface expression of AMPA receptors, excitatory and inhibitory synapse maturation, and NMDA receptor-mediated calcium signaling in both neurons and erythroid cells."},"narrative":{"teleology":[{"year":2007,"claim":"Establishing that LRFN2 functions outside the nervous system, gain-of-function experiments showed LRFN2 expression skews hematopoietic differentiation toward erythropoiesis and cooperates with Myc to cause erythroblastosis, revealing an unexpected role in cell fate decisions.","evidence":"Colony-forming assays with LRFN2 overexpression and transgenic mouse crosses","pmids":["17577922"],"confidence":"Medium","gaps":["Mechanism linking LRFN2 to erythroid lineage commitment not identified","Whether NMDAR signaling mediates this effect was not tested","Single laboratory finding"]},{"year":2011,"claim":"Addressing how LRFN2 surface expression is controlled, mutagenesis revealed a dileucine ER retention motif that restricts LRFN2 to the ER and a PDZ-binding motif required for dendritic (but not axonal) surface delivery, establishing a dual-signal trafficking mechanism that gates LRFN2's synaptic availability.","evidence":"Serial deletion mutagenesis, endoglycosidase H assays, heterologous cell and hippocampal neuron transfection, electron microscopy","pmids":["22174418"],"confidence":"High","gaps":["Identity of PDZ-domain proteins that release ER retention was not determined","Whether trafficking regulation is activity-dependent was not tested"]},{"year":2015,"claim":"Ultrastructural localization confirmed that LRFN2 resides at synapses and associates with the NR1 subunit of NMDA receptors, establishing LRFN2 as a bona fide synaptic NMDAR-associated protein.","evidence":"Electron microscopy immunogold labeling in rat cerebellar and hippocampal neurons","pmids":["26486473"],"confidence":"Medium","gaps":["Single-lab finding without reciprocal biochemical validation of NR1 binding","Functional consequences of the LRFN2–NR1 association were not tested"]},{"year":2017,"claim":"Knockout studies established that LRFN2's direct interaction with PSD-95 is required for synaptic delivery of AMPA receptors (GluA1), normal postsynaptic density structure, and spine maturation, and that loss of LRFN2 reduces the AMPA/NMDA ratio while paradoxically enhancing LTP.","evidence":"Lrfn2 KO mice with in vitro binding assays, electrophysiology, and morphological synapse analysis","pmids":["28604739"],"confidence":"High","gaps":["Whether LRFN2 directly scaffolds AMPA receptors or acts solely through PSD-95 was not resolved","Mechanism of enhanced LTP in KO remained unclear"]},{"year":2018,"claim":"Independent KO studies extended LRFN2's role to inhibitory synapse development, showing that Lrfn2-/- CA1 neurons have decreased inhibitory synapse density and reduced spontaneous inhibitory transmission, establishing LRFN2 as a bidirectional organizer of excitatory–inhibitory circuit balance.","evidence":"Lrfn2 KO mice, whole-cell patch clamp, immunofluorescence, behavioral assays","pmids":["29798891"],"confidence":"High","gaps":["Whether the inhibitory synapse phenotype is cell-autonomous or circuit-level was not distinguished","Molecular partners mediating the inhibitory synapse role were not identified"]},{"year":2021,"claim":"Identification of SNX27 as an endosomal sorting partner for LRFN2 revealed the mechanism by which LRFN2 surface levels are regulated post-ER, and demonstrated that LRFN2 indirectly controls AMPA receptor surface expression and hippocampal LTP through this trafficking pathway.","evidence":"Proteomics in rat primary neurons, Co-IP/pulldown, LRFN2 knockdown, surface biotinylation, mEPSC and LTP recordings","pmids":["34251337"],"confidence":"High","gaps":["Whether SNX27 and PSD-95 compete for the same PDZ-binding motif on LRFN2 was not tested","Recycling kinetics and activity dependence of LRFN2 endosomal sorting were not measured"]},{"year":2021,"claim":"KO mice demonstrated that LRFN2 regulates NMDA receptor-mediated calcium influx in late erythroblasts, connecting the synaptic adhesion molecule to erythropoiesis control through NMDAR function in hematopoietic cells.","evidence":"Lrfn2 KO mice, flow cytometry, peripheral blood analysis, CFU assay, calcium influx assay with MK801","pmids":["33481887"],"confidence":"Medium","gaps":["Single-lab finding; independent replication needed","Direct physical interaction between LRFN2 and NMDAR in erythroblasts was not demonstrated biochemically","Downstream signaling from NMDAR calcium influx to EPO receptor regulation not mapped"]},{"year":2022,"claim":"Co-immunoprecipitation established a direct LRFN2–GRIN2B interaction in cancer cells, and overexpression experiments showed LRFN2 suppresses Wnt/β-catenin and NF-κB signaling through a GRIN2B–GSK3β axis, demonstrating a tumor-suppressive signaling function outside the nervous system.","evidence":"Co-IP in ESCC cells, overexpression/western blot, pharmacological antagonism with NMDA-IN-1, in vivo tumor growth assay","pmids":["35879265"],"confidence":"Medium","gaps":["Single-lab finding in one cancer type","Whether endogenous LRFN2 levels are sufficient to engage this pathway in normal tissue unknown","Structural basis of LRFN2–GRIN2B interaction not resolved"]},{"year":2023,"claim":"Knockdown experiments in bladder cancer revealed that tumor-intrinsic LRFN2 suppresses pro-inflammatory cytokine/chemokine secretion, inhibiting CD8+ T cell recruitment and enabling immune evasion, identifying LRFN2 as a regulator of the tumor immune microenvironment.","evidence":"LRFN2 knockdown in bladder cancer cells, multiplex immunoassay, in vivo models, single-cell RNA-seq, spatial tissue analysis","pmids":["37802603"],"confidence":"Medium","gaps":["Molecular mechanism connecting LRFN2 to cytokine/chemokine transcription or secretion machinery not identified","Whether NMDAR signaling mediates the immune-evasion phenotype was not tested"]},{"year":2024,"claim":"Proteomics and KO studies identified LRFN2 as a component of the cone photoreceptor–depolarizing bipolar cell signaling complex, demonstrating that LRFN2 is required for normal cone-mediated synaptic transmission in the retina.","evidence":"Unbiased proteomics, immunolocalization at cone terminals, Lrfn2 KO mice, photopic ERG","pmids":["38408870"],"confidence":"Medium","gaps":["Single-lab finding; specific binding partners at cone terminals not identified","Whether LRFN2 functions as a trans-synaptic adhesion molecule at ribbon synapses was not tested"]},{"year":null,"claim":"The trans-synaptic binding partners of LRFN2, the structural basis of its interactions with NMDAR subunits and PSD-95, and the molecular mechanism by which LRFN2 controls cytokine secretion and immune evasion in tumors remain unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No trans-synaptic ligand identified for LRFN2","No crystal/cryo-EM structure of LRFN2 or its complexes","Mechanism linking LRFN2 to cytokine/chemokine regulation in cancer is unknown","Whether neuronal and non-neuronal functions share a unified NMDAR-dependent mechanism is untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098631","term_label":"cell adhesion mediator activity","supporting_discovery_ids":[0,1,7]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,2]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,2,3,7]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[3]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[0,1,2,4]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[8,9]},{"term_id":"R-HSA-9709957","term_label":"Sensory Perception","supporting_discovery_ids":[7]}],"complexes":[],"partners":["DLG4","GRIN1","GRIN2B","SNX27","GRIA1"],"other_free_text":[]},"mechanistic_narrative":"LRFN2 (SALM1) is a leucine-rich repeat transmembrane adhesion molecule that organizes postsynaptic signaling complexes to control excitatory and inhibitory synapse development, synaptic plasticity, and NMDA receptor-mediated calcium signaling in both neuronal and non-neuronal contexts. LRFN2 directly binds PSD-95 via its PDZ-binding motif and NMDA receptor subunits (NR1, GRIN2B), and its interaction with PSD-95 is required for synaptic surface expression of AMPA receptors (GluA1), normal postsynaptic density size, and spine maturation; knockout mice exhibit reduced AMPA/NMDA ratio, enhanced LTP, decreased inhibitory synapse density, and behavioral abnormalities [PMID:28604739, PMID:29798891]. Intracellular trafficking of LRFN2 is governed by a dileucine ER retention motif that restricts surface expression and by the endosomal adaptor SNX27, which sorts LRFN2 to the surface and thereby indirectly controls AMPA receptor-mediated synaptic transmission [PMID:22174418, PMID:34251337]. Beyond the central nervous system, LRFN2 modulates NMDA receptor-dependent calcium influx in erythroblasts to regulate erythropoiesis, is a component of the cone photoreceptor–depolarizing bipolar cell signaling complex required for normal photopic vision, and suppresses Wnt/β-catenin and NF-κB signaling through GRIN2B–GSK3β interaction in cancer cells [PMID:33481887, PMID:38408870, PMID:35879265]."},"prefetch_data":{"uniprot":{"accession":"Q9ULH4","full_name":"Leucine-rich repeat and fibronectin type-III domain-containing protein 2","aliases":["Synaptic adhesion-like molecule 1"],"length_aa":789,"mass_kda":84.7,"function":"Promotes neurite outgrowth in hippocampal neurons. Enhances the cell surface expression of 2 NMDA receptor subunits GRIN1 and GRIN2A. May play a role in redistributing DLG4 to the cell periphery (By similarity)","subcellular_location":"Membrane; Synapse; Postsynaptic cell membrane","url":"https://www.uniprot.org/uniprotkb/Q9ULH4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/LRFN2","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/LRFN2","total_profiled":1310},"omim":[{"mim_id":"612811","title":"LEUCINE-RICH REPEAT AND FIBRONECTIN TYPE III DOMAIN-CONTAINING PROTEIN 5; LRFN5","url":"https://www.omim.org/entry/612811"},{"mim_id":"612809","title":"LEUCINE-RICH REPEAT AND FIBRONECTIN TYPE III DOMAIN-CONTAINING PROTEIN 3; LRFN3","url":"https://www.omim.org/entry/612809"},{"mim_id":"612808","title":"LEUCINE-RICH REPEAT AND FIBRONECTIN TYPE III DOMAIN-CONTAINING PROTEIN 2; LRFN2","url":"https://www.omim.org/entry/612808"},{"mim_id":"612807","title":"LEUCINE-RICH REPEAT AND FIBRONECTIN TYPE III DOMAIN-CONTAINING PROTEIN 1; LRFN1","url":"https://www.omim.org/entry/612807"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Plasma membrane","reliability":"Supported"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"brain","ntpm":6.3},{"tissue":"retina","ntpm":2.9}],"url":"https://www.proteinatlas.org/search/LRFN2"},"hgnc":{"alias_symbol":["FIGLER2"],"prev_symbol":["KIAA1246","SALM1"]},"alphafold":{"accession":"Q9ULH4","domains":[{"cath_id":"2.60.40.10","chopping":"288-378","consensus_level":"high","plddt":94.2402,"start":288,"end":378},{"cath_id":"2.60.40.10","chopping":"427-515","consensus_level":"high","plddt":83.0997,"start":427,"end":515}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULH4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULH4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULH4-F1-predicted_aligned_error_v6.png","plddt_mean":69.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LRFN2","jax_strain_url":"https://www.jax.org/strain/search?query=LRFN2"},"sequence":{"accession":"Q9ULH4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9ULH4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9ULH4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULH4"}},"corpus_meta":[{"pmid":"28604739","id":"PMC_28604739","title":"Autism-like behaviours and enhanced memory formation and synaptic plasticity in Lrfn2/SALM1-deficient mice.","date":"2017","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/28604739","citation_count":64,"is_preprint":false},{"pmid":"31605628","id":"PMC_31605628","title":"Genetic variants of DNAH11 and LRFN2 genes and their association with ovarian and breast cancer.","date":"2019","source":"International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics","url":"https://pubmed.ncbi.nlm.nih.gov/31605628","citation_count":25,"is_preprint":false},{"pmid":"29798891","id":"PMC_29798891","title":"Lrfn2-Mutant Mice Display Suppressed Synaptic Plasticity and Inhibitory Synapse Development and Abnormal Social Communication and Startle Response.","date":"2018","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/29798891","citation_count":24,"is_preprint":false},{"pmid":"37802603","id":"PMC_37802603","title":"Bladder cancer intrinsic LRFN2 drives anticancer immunotherapy resistance by attenuating CD8+ T cell infiltration and functional transition.","date":"2023","source":"Journal for immunotherapy of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/37802603","citation_count":22,"is_preprint":false},{"pmid":"26486473","id":"PMC_26486473","title":"Heterozygous deletion of the LRFN2 gene is associated with working memory deficits.","date":"2015","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/26486473","citation_count":18,"is_preprint":false},{"pmid":"34251337","id":"PMC_34251337","title":"Sorting nexin-27 regulates AMPA receptor trafficking through the synaptic adhesion protein LRFN2.","date":"2021","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/34251337","citation_count":16,"is_preprint":false},{"pmid":"17577922","id":"PMC_17577922","title":"Regulation of erythropoiesis by the neuronal transmembrane protein Lrfn2.","date":"2007","source":"Experimental hematology","url":"https://pubmed.ncbi.nlm.nih.gov/17577922","citation_count":12,"is_preprint":false},{"pmid":"22174418","id":"PMC_22174418","title":"Dileucine and PDZ-binding motifs mediate synaptic adhesion-like molecule 1 (SALM1) trafficking in hippocampal neurons.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/22174418","citation_count":12,"is_preprint":false},{"pmid":"35879265","id":"PMC_35879265","title":"LRFN2 binding to NMDAR inhibits the progress of ESCC via regulating the Wnt/β-Catenin and NF-κB signaling pathway.","date":"2022","source":"Cancer science","url":"https://pubmed.ncbi.nlm.nih.gov/35879265","citation_count":10,"is_preprint":false},{"pmid":"33481887","id":"PMC_33481887","title":"Dysregulation of erythropoiesis and altered erythroblastic NMDA receptor-mediated calcium influx in Lrfn2-deficient mice.","date":"2021","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/33481887","citation_count":4,"is_preprint":false},{"pmid":"38408870","id":"PMC_38408870","title":"Cone Synaptic function is modulated by the leucine rich repeat (LRR) adhesion molecule LRFN2.","date":"2024","source":"eNeuro","url":"https://pubmed.ncbi.nlm.nih.gov/38408870","citation_count":4,"is_preprint":false},{"pmid":"32880595","id":"PMC_32880595","title":"LRFN2 gene variant rs2494938 provides susceptibility to esophageal cancer in the population of Jammu and Kashmir.","date":"2020","source":"Journal of cancer research and therapeutics","url":"https://pubmed.ncbi.nlm.nih.gov/32880595","citation_count":2,"is_preprint":false},{"pmid":"32904533","id":"PMC_32904533","title":"Genetic variant rs2494938 of LRFN2 gene is associated with non-small cell lung cancer risk in North-Indian population.","date":"2020","source":"3 Biotech","url":"https://pubmed.ncbi.nlm.nih.gov/32904533","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8654,"output_tokens":2559,"usd":0.032174},"stage2":{"model":"claude-opus-4-6","input_tokens":5890,"output_tokens":3015,"usd":0.157238},"total_usd":0.189412,"stage1_batch_id":"msgbatch_01Mgbec4vM6c9vXht7JVJzss","stage2_batch_id":"msgbatch_01JkuuH5RB2BdJNsgnhjbC6s","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"Lrfn2/SALM1 directly interacts with PSD-95, and this interaction is required for synaptic surface expression of AMPA receptors (GluA1); knockout mice show decreased synaptic PSD-95 and GluA1, structurally immature spines, smaller postsynaptic densities, reduced AMPA/NMDA ratio, and enhanced LTP.\",\n      \"method\": \"Lrfn2 knockout mice, in vitro interaction assays, electrophysiology, morphological analysis of synapses\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with multiple orthogonal methods (behavioral, electrophysiological, biochemical, morphological) and direct in vitro interaction data\",\n      \"pmids\": [\"28604739\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"SALM1/LRFN2 regulates excitatory synapse function (NMDAR-dependent synaptic transmission and plasticity) and inhibitory synapse development; Lrfn2-/- CA1 pyramidal neurons show decreased inhibitory synapse density and reduced spontaneous inhibitory synaptic transmission frequency, demonstrating a role in both excitatory and inhibitory circuit organization.\",\n      \"method\": \"Lrfn2 knockout mice, electrophysiology (whole-cell patch clamp, LTP), immunofluorescence, behavioral assays\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — independent replication of LRFN2 KO with multiple orthogonal methods, novel finding of inhibitory synapse role\",\n      \"pmids\": [\"29798891\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Sorting nexin-27 (SNX27) directly binds LRFN2 and regulates its endosomal sorting; LRFN2 in turn associates with AMPA receptors, and LRFN2 knockdown decreases surface AMPA receptor expression, reduces synaptic activity, and attenuates hippocampal LTP, revealing an indirect mechanism by which SNX27 controls AMPA receptor-mediated synaptic transmission through LRFN2.\",\n      \"method\": \"Proteomics in rat primary neurons, Co-IP/pulldown, LRFN2 knockdown, surface biotinylation, electrophysiology (mEPSC, LTP)\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal interaction data combined with functional KD experiments and multiple orthogonal readouts\",\n      \"pmids\": [\"34251337\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"SALM1/LRFN2 contains a dileucine (DXXXLL) ER retention motif that retains it in the ER; its PDZ-binding motif is required for surface expression in heterologous cells and for dendritic (but not axonal) surface expression in hippocampal neurons. Mutation of the dileucine motif releases LRFN2 from the ER, increases surface expression, and causes formation of irregular enlarged spines and filopodia.\",\n      \"method\": \"Serial deletion mutagenesis, endoglycosidase H digestion assays, heterologous cell expression, hippocampal neuron transfection, electron microscopy\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — mutagenesis combined with biochemical retention assays and neuronal imaging with multiple orthogonal methods\",\n      \"pmids\": [\"22174418\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"LRFN2 protein is localized at synapses of cerebellar and hippocampal rat neurons and is associated with the NR1 subunit of NMDA receptors, as demonstrated by electron microscopy immunogold labeling.\",\n      \"method\": \"Electron microscopy immunogold labeling in rat neurons\",\n      \"journal\": \"European journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct ultrastructural localization showing co-association with NMDAR NR1 subunit, single lab\",\n      \"pmids\": [\"26486473\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Lrfn2 expression in colony-forming assays subverts hematopoietic differentiation to increase erythropoiesis and, in cooperation with Myc, leads to erythroblastosis; Lrfn2 expression also promotes outgrowth of a cell type positive for both early hematopoietic and fibroblast markers, indicating a role in hematopoietic cell fate decisions.\",\n      \"method\": \"In vitro colony-forming assays, transgenic mouse crosses, surface marker staining, mRNA expression studies\",\n      \"journal\": \"Experimental hematology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct gain-of-function in vitro assay with phenotypic readouts, single lab\",\n      \"pmids\": [\"17577922\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Lrfn2-deficient mice exhibit defective NMDA receptor-mediated calcium influx in late erythroblasts, and show altered erythropoiesis including normocytic erythrocythemia, decreased CFU-E progenitors, and altered EPO receptor expression, indicating that Lrfn2 regulates erythropoiesis through modulation of NMDA receptor function in hematopoietic cells.\",\n      \"method\": \"Lrfn2 KO mice, flow cytometry, peripheral blood tests, CFU assay, calcium influx assay with MK801 NMDAR antagonist\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO mice with multiple functional readouts and pharmacological validation, single lab\",\n      \"pmids\": [\"33481887\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"LRFN2 is selectively expressed at cone photoreceptor terminals and identified as a component of the depolarizing bipolar cell (DBC) signaling complex; in LRFN2-deficient mice, cone-mediated photopic ERG b-wave amplitude is reduced at bright flash intensities, demonstrating that LRFN2 is required for normal synaptic transmission between cones and cone DBCs.\",\n      \"method\": \"Unbiased proteomics, immunolocalization, Lrfn2 KO mice, electroretinography (ERG), co-localization with DBC signalplex markers\",\n      \"journal\": \"eNeuro\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — proteomic identification followed by KO functional validation with electrophysiology, single lab\",\n      \"pmids\": [\"38408870\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"LRFN2 binds to NMDAR subunit GRIN2B in esophageal squamous cell carcinoma cells; LRFN2 overexpression suppresses cancer cell proliferation, migration, and invasion by downregulating Wnt/β-catenin signaling components (β-catenin, c-Myc, cyclin D1) and NF-κB pathway via a GRIN2B–GSK3β interaction, and these effects are attenuated by the NR2B-selective NMDA antagonist NMDA-IN-1.\",\n      \"method\": \"Co-IP/binding assay (LRFN2–GRIN2B), overexpression in ESCC cells, western blot, pharmacological antagonism, in vivo tumor growth assay\",\n      \"journal\": \"Cancer science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — direct binding demonstrated with functional rescue by antagonist, single lab, non-neuronal context\",\n      \"pmids\": [\"35879265\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Tumor-intrinsic LRFN2 inhibits recruitment and functional transition of CD8+ T cells by reducing secretion of pro-inflammatory cytokines and chemokines in bladder cancer; LRFN2 knockdown enhances ICI therapy efficacy in preclinical models.\",\n      \"method\": \"LRFN2 knockdown in bladder cancer cells, multiplex immunoassay (cytokine/chemokine secretion), in vitro and in vivo functional experiments, single-cell RNA-seq, spatial tissue quantification\",\n      \"journal\": \"Journal for immunotherapy of cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KD with multiple functional readouts including in vivo, but mechanism (chemokine regulation) not fully resolved at molecular level\",\n      \"pmids\": [\"37802603\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LRFN2/SALM1 is a postsynaptic transmembrane adhesion molecule that directly binds PSD-95 (via its PDZ-binding motif) and NMDA receptor subunits (NR1/GRIN2B), and associates with AMPA receptors; intracellular trafficking is controlled by a dileucine ER retention motif and regulated by the endosomal adaptor SNX27, which together govern synaptic surface expression of AMPA receptors, excitatory and inhibitory synapse maturation, and NMDA receptor-mediated calcium signaling in both neurons and erythroid cells.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"LRFN2 (SALM1) is a leucine-rich repeat transmembrane adhesion molecule that organizes postsynaptic signaling complexes to control excitatory and inhibitory synapse development, synaptic plasticity, and NMDA receptor-mediated calcium signaling in both neuronal and non-neuronal contexts. LRFN2 directly binds PSD-95 via its PDZ-binding motif and NMDA receptor subunits (NR1, GRIN2B), and its interaction with PSD-95 is required for synaptic surface expression of AMPA receptors (GluA1), normal postsynaptic density size, and spine maturation; knockout mice exhibit reduced AMPA/NMDA ratio, enhanced LTP, decreased inhibitory synapse density, and behavioral abnormalities [PMID:28604739, PMID:29798891]. Intracellular trafficking of LRFN2 is governed by a dileucine ER retention motif that restricts surface expression and by the endosomal adaptor SNX27, which sorts LRFN2 to the surface and thereby indirectly controls AMPA receptor-mediated synaptic transmission [PMID:22174418, PMID:34251337]. Beyond the central nervous system, LRFN2 modulates NMDA receptor-dependent calcium influx in erythroblasts to regulate erythropoiesis, is a component of the cone photoreceptor–depolarizing bipolar cell signaling complex required for normal photopic vision, and suppresses Wnt/β-catenin and NF-κB signaling through GRIN2B–GSK3β interaction in cancer cells [PMID:33481887, PMID:38408870, PMID:35879265].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Establishing that LRFN2 functions outside the nervous system, gain-of-function experiments showed LRFN2 expression skews hematopoietic differentiation toward erythropoiesis and cooperates with Myc to cause erythroblastosis, revealing an unexpected role in cell fate decisions.\",\n      \"evidence\": \"Colony-forming assays with LRFN2 overexpression and transgenic mouse crosses\",\n      \"pmids\": [\"17577922\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking LRFN2 to erythroid lineage commitment not identified\", \"Whether NMDAR signaling mediates this effect was not tested\", \"Single laboratory finding\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Addressing how LRFN2 surface expression is controlled, mutagenesis revealed a dileucine ER retention motif that restricts LRFN2 to the ER and a PDZ-binding motif required for dendritic (but not axonal) surface delivery, establishing a dual-signal trafficking mechanism that gates LRFN2's synaptic availability.\",\n      \"evidence\": \"Serial deletion mutagenesis, endoglycosidase H assays, heterologous cell and hippocampal neuron transfection, electron microscopy\",\n      \"pmids\": [\"22174418\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of PDZ-domain proteins that release ER retention was not determined\", \"Whether trafficking regulation is activity-dependent was not tested\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Ultrastructural localization confirmed that LRFN2 resides at synapses and associates with the NR1 subunit of NMDA receptors, establishing LRFN2 as a bona fide synaptic NMDAR-associated protein.\",\n      \"evidence\": \"Electron microscopy immunogold labeling in rat cerebellar and hippocampal neurons\",\n      \"pmids\": [\"26486473\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab finding without reciprocal biochemical validation of NR1 binding\", \"Functional consequences of the LRFN2–NR1 association were not tested\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Knockout studies established that LRFN2's direct interaction with PSD-95 is required for synaptic delivery of AMPA receptors (GluA1), normal postsynaptic density structure, and spine maturation, and that loss of LRFN2 reduces the AMPA/NMDA ratio while paradoxically enhancing LTP.\",\n      \"evidence\": \"Lrfn2 KO mice with in vitro binding assays, electrophysiology, and morphological synapse analysis\",\n      \"pmids\": [\"28604739\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether LRFN2 directly scaffolds AMPA receptors or acts solely through PSD-95 was not resolved\", \"Mechanism of enhanced LTP in KO remained unclear\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Independent KO studies extended LRFN2's role to inhibitory synapse development, showing that Lrfn2-/- CA1 neurons have decreased inhibitory synapse density and reduced spontaneous inhibitory transmission, establishing LRFN2 as a bidirectional organizer of excitatory–inhibitory circuit balance.\",\n      \"evidence\": \"Lrfn2 KO mice, whole-cell patch clamp, immunofluorescence, behavioral assays\",\n      \"pmids\": [\"29798891\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the inhibitory synapse phenotype is cell-autonomous or circuit-level was not distinguished\", \"Molecular partners mediating the inhibitory synapse role were not identified\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identification of SNX27 as an endosomal sorting partner for LRFN2 revealed the mechanism by which LRFN2 surface levels are regulated post-ER, and demonstrated that LRFN2 indirectly controls AMPA receptor surface expression and hippocampal LTP through this trafficking pathway.\",\n      \"evidence\": \"Proteomics in rat primary neurons, Co-IP/pulldown, LRFN2 knockdown, surface biotinylation, mEPSC and LTP recordings\",\n      \"pmids\": [\"34251337\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether SNX27 and PSD-95 compete for the same PDZ-binding motif on LRFN2 was not tested\", \"Recycling kinetics and activity dependence of LRFN2 endosomal sorting were not measured\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"KO mice demonstrated that LRFN2 regulates NMDA receptor-mediated calcium influx in late erythroblasts, connecting the synaptic adhesion molecule to erythropoiesis control through NMDAR function in hematopoietic cells.\",\n      \"evidence\": \"Lrfn2 KO mice, flow cytometry, peripheral blood analysis, CFU assay, calcium influx assay with MK801\",\n      \"pmids\": [\"33481887\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab finding; independent replication needed\", \"Direct physical interaction between LRFN2 and NMDAR in erythroblasts was not demonstrated biochemically\", \"Downstream signaling from NMDAR calcium influx to EPO receptor regulation not mapped\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Co-immunoprecipitation established a direct LRFN2–GRIN2B interaction in cancer cells, and overexpression experiments showed LRFN2 suppresses Wnt/β-catenin and NF-κB signaling through a GRIN2B–GSK3β axis, demonstrating a tumor-suppressive signaling function outside the nervous system.\",\n      \"evidence\": \"Co-IP in ESCC cells, overexpression/western blot, pharmacological antagonism with NMDA-IN-1, in vivo tumor growth assay\",\n      \"pmids\": [\"35879265\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab finding in one cancer type\", \"Whether endogenous LRFN2 levels are sufficient to engage this pathway in normal tissue unknown\", \"Structural basis of LRFN2–GRIN2B interaction not resolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Knockdown experiments in bladder cancer revealed that tumor-intrinsic LRFN2 suppresses pro-inflammatory cytokine/chemokine secretion, inhibiting CD8+ T cell recruitment and enabling immune evasion, identifying LRFN2 as a regulator of the tumor immune microenvironment.\",\n      \"evidence\": \"LRFN2 knockdown in bladder cancer cells, multiplex immunoassay, in vivo models, single-cell RNA-seq, spatial tissue analysis\",\n      \"pmids\": [\"37802603\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism connecting LRFN2 to cytokine/chemokine transcription or secretion machinery not identified\", \"Whether NMDAR signaling mediates the immune-evasion phenotype was not tested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Proteomics and KO studies identified LRFN2 as a component of the cone photoreceptor–depolarizing bipolar cell signaling complex, demonstrating that LRFN2 is required for normal cone-mediated synaptic transmission in the retina.\",\n      \"evidence\": \"Unbiased proteomics, immunolocalization at cone terminals, Lrfn2 KO mice, photopic ERG\",\n      \"pmids\": [\"38408870\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab finding; specific binding partners at cone terminals not identified\", \"Whether LRFN2 functions as a trans-synaptic adhesion molecule at ribbon synapses was not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The trans-synaptic binding partners of LRFN2, the structural basis of its interactions with NMDAR subunits and PSD-95, and the molecular mechanism by which LRFN2 controls cytokine secretion and immune evasion in tumors remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No trans-synaptic ligand identified for LRFN2\", \"No crystal/cryo-EM structure of LRFN2 or its complexes\", \"Mechanism linking LRFN2 to cytokine/chemokine regulation in cancer is unknown\", \"Whether neuronal and non-neuronal functions share a unified NMDAR-dependent mechanism is untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098631\", \"supporting_discovery_ids\": [0, 1, 7]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 2, 3, 7]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [0, 1, 2, 4]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [8, 9]},\n      {\"term_id\": \"R-HSA-9709957\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"DLG4\", \"GRIN1\", \"GRIN2B\", \"SNX27\", \"GRIA1\"],\n    \"other_free_text\": []\n  }\n}\n```"}