{"gene":"LIN7A","run_date":"2026-04-28T18:30:27","timeline":{"discoveries":[{"year":2001,"finding":"VAM-1 (a MAGUK family member) contains a conserved domain that directly binds to Veli-1 (human LIN7A homologue), as demonstrated by GST pull-down experiments and blot overlay assays, suggesting VAM-1 promotes assembly of a Veli-1-containing protein complex in neuronal and epithelial cells.","method":"GST pull-down, blot overlay assay, heterologous transfection","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal binding demonstrated by two orthogonal in vitro methods (GST pull-down + blot overlay), single study","pmids":["11311936"],"is_preprint":false},{"year":2002,"finding":"MALS-1/Veli-1 (LIN7A) expression in cerebellar granule cells is regulated at the transcriptional level by Ca²⁺ entry through voltage- or ligand-operated Ca²⁺ channels acting via the calcineurin pathway, without requiring de novo protein synthesis or altered mRNA stability.","method":"Pharmacological activation/inhibition of Ca²⁺/calcineurin pathway in cultured cerebellar granule cells, transcriptional assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — multiple pharmacological interventions with mechanistic dissection (mRNA stability and protein synthesis ruled out), single lab","pmids":["12393911"],"is_preprint":false},{"year":2014,"finding":"Lin-7A localizes to the presynaptic fraction in mouse brain (biochemical fractionation), and its RNAi-mediated suppression via in utero electroporation delays neuronal migration and disrupts interhemispheric axon development in the cerebral cortex, establishing a required role in cortical neurodevelopment.","method":"Biochemical fractionation, RNAi knockdown by in utero electroporation, immunohistochemistry","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 — direct loss-of-function with defined cellular phenotype (neuronal migration delay, axon growth defect) plus subcellular fractionation; single lab","pmids":["24658322"],"is_preprint":false},{"year":2016,"finding":"LIN7A overexpression in breast epithelial cells causes hyperproliferation, invasion, and complete absence of lumen formation, revealing a direct role in apico-basal polarity regulation as a Crumbs-complex component; gene expression profiling identified LIN7A as one of the most differentially overexpressed polarity genes in invasive micropapillary carcinomas.","method":"Gain-of-function overexpression assay, 3D lumen-formation assay, gene expression profiling","journal":"Breast cancer research : BCR","confidence":"Medium","confidence_rationale":"Tier 2 — overexpression with specific polarity/invasion phenotypic readout; single lab with multiple assays","pmids":["26887652"],"is_preprint":false},{"year":2016,"finding":"Lin7a interacts with the α2/β1 form of nitric oxide-sensitive guanylyl cyclase in mouse brain synaptosomes (co-precipitation), and directs this heterodimer to calcium-insensitive cell-cell contacts in HEK293 cells via its PDZ domain; the PDZ-binding motif of the α2 subunit is accessible only in the heterodimer conformation, and Lin7a links the complex to nectin-based cell-cell contacts via MPP3.","method":"Co-precipitation from brain synaptosomes, overexpression in HEK293 cells, truncation/domain mutant analysis, immunofluorescence localization","journal":"Biochemical pharmacology","confidence":"Medium","confidence_rationale":"Tier 2 — co-precipitation from native tissue plus domain-mapping in cells with multiple truncation constructs; single lab","pmids":["27793718"],"is_preprint":false},{"year":2025,"finding":"Lentiviral silencing of LIN7A in U87 glioblastoma cells increases invasiveness, elevates MMP-2 and MMP-9 protease activity, and causes nuclear accumulation of β-catenin with increased transcriptional activity of β-catenin target genes, indicating LIN7A suppresses invasion partly by restraining the β-catenin pathway and maintaining cell polarity and intercellular junctions.","method":"Lentiviral knockdown, real-time cell invasion assay, spheroid invasion assay, zymography, Western blotting, immunofluorescence, orthotopic xenograft","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — loss-of-function with multiple mechanistic readouts (proteases, β-catenin pathway) and in vivo validation; single lab","pmids":["40021783"],"is_preprint":false}],"current_model":"LIN7A (Veli-1/MALS-1) is a PDZ-domain scaffold protein that localizes to presynaptic and cell-cell contact sites, where it assembles multiprotein complexes (including MAGUK partners such as VAM-1/MPP3 and transmembrane cargo such as the α2/β1 nitric oxide-sensitive guanylyl cyclase) to maintain apico-basal cell polarity, support neuronal migration and axon development, and suppress invasion by restraining MMP activity and nuclear β-catenin signaling; its transcription is regulated by Ca²⁺/calcineurin signaling in neurons."},"narrative":{"teleology":[{"year":2001,"claim":"Identifying a direct MAGUK-family binding partner for LIN7A established that Veli-1 participates in scaffolded protein complexes in neuronal and epithelial cells, raising the question of what cargo these complexes recruit.","evidence":"GST pull-down and blot overlay assays demonstrating VAM-1–Veli-1 direct binding","pmids":["11311936"],"confidence":"Medium","gaps":["No in vivo validation of the VAM-1–Veli-1 interaction","Functional consequence of complex formation not tested","Other MAGUK partners not compared"]},{"year":2002,"claim":"Demonstrating that LIN7A transcription is controlled by Ca²⁺ influx through the calcineurin pathway in neurons revealed how synaptic activity could dynamically regulate this scaffold, but the downstream transcription factor remained unidentified.","evidence":"Pharmacological activation/inhibition of Ca²⁺/calcineurin signaling in cultured cerebellar granule cells with transcriptional readouts","pmids":["12393911"],"confidence":"Medium","gaps":["Transcription factor mediating calcineurin-dependent LIN7A expression not identified","In vivo relevance of activity-dependent regulation not tested"]},{"year":2014,"claim":"Loss-of-function experiments in vivo showed that LIN7A is required for cortical neuronal migration and axon pathfinding, moving it from a biochemical scaffold to a functionally required neurodevelopmental factor.","evidence":"RNAi knockdown via in utero electroporation in mouse cortex with immunohistochemical analysis of migration and axon tracts","pmids":["24658322"],"confidence":"Medium","gaps":["Molecular mechanism linking LIN7A to migration machinery not defined","Rescue experiment not reported","Presynaptic localization shown biochemically but functional role at synapses not tested"]},{"year":2016,"claim":"Two studies expanded LIN7A's role beyond neurons: overexpression in breast epithelial cells disrupted lumen formation and drove invasion, establishing LIN7A as a dosage-sensitive polarity regulator, while PDZ-domain-mediated recruitment of NO-sensitive guanylyl cyclase to nectin-based cell-cell contacts via MPP3 provided a concrete cargo-delivery mechanism.","evidence":"3D lumen-formation and invasion assays in breast epithelial cells; co-precipitation from brain synaptosomes and domain-mapping in HEK293 cells with truncation mutants","pmids":["26887652","27793718"],"confidence":"Medium","gaps":["Whether lumen-formation defect operates through the same β-catenin or MMP pathways identified later is unknown","Structural basis of PDZ-dependent heterodimer selectivity not resolved","In vivo validation of guanylyl cyclase targeting not performed"]},{"year":2025,"claim":"Silencing LIN7A in glioblastoma cells identified a specific invasion-suppressive mechanism: LIN7A restrains MMP-2/9 activity and prevents nuclear β-catenin accumulation, linking its polarity-scaffold function to Wnt/β-catenin pathway control.","evidence":"Lentiviral knockdown in U87 cells with zymography, β-catenin immunofluorescence, invasion assays, and orthotopic xenograft","pmids":["40021783"],"confidence":"Medium","gaps":["Direct physical link between LIN7A and β-catenin retention at junctions not shown","Whether MMP upregulation is a direct or indirect consequence of polarity loss is unresolved","Single cell line (U87) limits generalizability"]},{"year":null,"claim":"The direct molecular mechanism by which LIN7A restrains β-catenin nuclear translocation and MMP expression, and whether its neurodevelopmental and tumor-suppressive roles share a common polarity-dependent signaling axis, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of LIN7A in complex with its partners","No genetic knockout mouse phenotype reported","Relationship between calcineurin-dependent transcriptional regulation and polarity/invasion functions not connected"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,4]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[4,5]},{"term_id":"GO:0043226","term_label":"organelle","supporting_discovery_ids":[2]}],"pathway":[],"complexes":["Crumbs polarity complex"],"partners":["MPP3","GUCY1A2","GUCY1B1"],"other_free_text":[]},"mechanistic_narrative":"LIN7A (Veli-1/MALS-1) is a PDZ-domain scaffold protein that assembles multiprotein complexes at cell-cell contacts and synapses to maintain apico-basal polarity, support neuronal development, and restrain cellular invasion. It directly binds MAGUK family partners such as VAM-1/MPP3 and recruits transmembrane cargo including the α2/β1 nitric oxide-sensitive guanylyl cyclase to nectin-based cell-cell contacts via its PDZ domain [PMID:11311936, PMID:27793718]. In the brain, LIN7A localizes to presynaptic fractions and is required for cortical neuronal migration and interhemispheric axon development, with its transcription regulated by Ca²⁺/calcineurin signaling [PMID:24658322, PMID:12393911]. Loss of LIN7A promotes glioblastoma invasion by elevating MMP-2/MMP-9 activity and triggering nuclear β-catenin accumulation, while its overexpression in breast epithelial cells disrupts lumen formation, demonstrating that precise LIN7A dosage is critical for polarity and invasion control [PMID:40021783, PMID:26887652]."},"prefetch_data":{"uniprot":{"accession":"O14910","full_name":"Protein lin-7 homolog A","aliases":["Mammalian lin-seven protein 1","MALS-1","Tax interaction protein 33","TIP-33","Vertebrate lin-7 homolog 1","Veli-1"],"length_aa":233,"mass_kda":26.0,"function":"Plays a role in establishing and maintaining the asymmetric distribution of channels and receptors at the plasma membrane of polarized cells. Forms membrane-associated multiprotein complexes that may regulate delivery and recycling of proteins to the correct membrane domains. The tripartite complex composed of LIN7 (LIN7A, LIN7B or LIN7C), CASK and APBA1 associates with the motor protein KIF17 to transport vesicles containing N-methyl-D-aspartate (NMDA) receptor subunit NR2B along microtubules (By similarity). This complex may have the potential to couple synaptic vesicle exocytosis to cell adhesion in brain. Ensures the proper localization of GRIN2B (subunit 2B of the NMDA receptor) to neuronal postsynaptic density and may function in localizing synaptic vesicles at synapses where it is recruited by beta-catenin and cadherin. Required to localize Kir2 channels, GABA transporter (SLC6A12) and EGFR/ERBB1, ERBB2, ERBB3 and ERBB4 to the basolateral membrane of epithelial cells","subcellular_location":"Cell membrane; Basolateral cell membrane; Cell junction; Postsynaptic density membrane; Cell junction, tight junction","url":"https://www.uniprot.org/uniprotkb/O14910/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/LIN7A","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":[{"gene":"CTTN","stoichiometry":4.0},{"gene":"CALM3","stoichiometry":0.2},{"gene":"CAPZB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/LIN7A","total_profiled":1310},"omim":[{"mim_id":"616484","title":"TAX1-BINDING PROTEIN 3; TAX1BP3","url":"https://www.omim.org/entry/616484"},{"mim_id":"612332","title":"LIN7 HOMOLOG C, CRUMBS CELL POLARITY COMPLEX COMPONENT; LIN7C","url":"https://www.omim.org/entry/612332"},{"mim_id":"612331","title":"LIN7 HOMOLOG B, CRUMBS CELL POLARITY COMPLEX COMPONENT; LIN7B","url":"https://www.omim.org/entry/612331"},{"mim_id":"610973","title":"MEMBRANE PROTEIN, PALMITOYLATED 7; MPP7","url":"https://www.omim.org/entry/610973"},{"mim_id":"603380","title":"LIN7 HOMOLOG A, CRUMBS CELL POLARITY COMPLEX COMPONENT; LIN7A","url":"https://www.omim.org/entry/603380"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"bone marrow","ntpm":26.3},{"tissue":"retina","ntpm":24.6}],"url":"https://www.proteinatlas.org/search/LIN7A"},"hgnc":{"alias_symbol":["MALS-1","TIP-33","LIN-7A","VELI1"],"prev_symbol":[]},"alphafold":{"accession":"O14910","domains":[{"cath_id":"1.20.1270.460","chopping":"24-89","consensus_level":"high","plddt":82.2038,"start":24,"end":89},{"cath_id":"2.30.42.10","chopping":"108-191","consensus_level":"high","plddt":95.4051,"start":108,"end":191}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O14910","model_url":"https://alphafold.ebi.ac.uk/files/AF-O14910-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O14910-F1-predicted_aligned_error_v6.png","plddt_mean":80.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LIN7A","jax_strain_url":"https://www.jax.org/strain/search?query=LIN7A"},"sequence":{"accession":"O14910","fasta_url":"https://rest.uniprot.org/uniprotkb/O14910.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O14910/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O14910"}},"corpus_meta":[{"pmid":"30537154","id":"PMC_30537154","title":"Long noncoding RNA CASC9 promotes LIN7A expression via miR-758-3p to facilitate the malignancy of ovarian cancer.","date":"2018","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/30537154","citation_count":55,"is_preprint":false},{"pmid":"29749382","id":"PMC_29749382","title":"microRNA-501-3p suppresses metastasis and progression of hepatocellular carcinoma through targeting LIN7A.","date":"2018","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/29749382","citation_count":42,"is_preprint":false},{"pmid":"11311936","id":"PMC_11311936","title":"VAM-1: a new member of the MAGUK family binds to human Veli-1 through a conserved domain.","date":"2001","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/11311936","citation_count":37,"is_preprint":false},{"pmid":"24658322","id":"PMC_24658322","title":"LIN7A depletion disrupts cerebral cortex development, contributing to intellectual disability in 12q21-deletion syndrome.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24658322","citation_count":23,"is_preprint":false},{"pmid":"26887652","id":"PMC_26887652","title":"LIN7A is a major determinant of cell-polarity defects in breast carcinomas.","date":"2016","source":"Breast cancer research : BCR","url":"https://pubmed.ncbi.nlm.nih.gov/26887652","citation_count":22,"is_preprint":false},{"pmid":"36864492","id":"PMC_36864492","title":"DNA methylation landscape reveals LIN7A as a decitabine-responsive marker in patients with t(8;21) acute myeloid leukemia.","date":"2023","source":"Clinical epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/36864492","citation_count":9,"is_preprint":false},{"pmid":"27793718","id":"PMC_27793718","title":"Heterodimerization with the β1 subunit directs the α2 subunit of nitric oxide-sensitive guanylyl cyclase to calcium-insensitive cell-cell contacts in HEK293 cells: Interaction with Lin7a.","date":"2016","source":"Biochemical pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/27793718","citation_count":7,"is_preprint":false},{"pmid":"39480871","id":"PMC_39480871","title":"Ortholog of autism candidate gene RBM27 regulates mitoribosomal assembly factor MALS-1 to protect against mitochondrial dysfunction and axon degeneration during neurodevelopment.","date":"2024","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/39480871","citation_count":3,"is_preprint":false},{"pmid":"38957040","id":"PMC_38957040","title":"Identification and validation of miR-29b-3p and LIN7A as important diagnostic markers for bone non-union by WGCNA.","date":"2024","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38957040","citation_count":2,"is_preprint":false},{"pmid":"12393911","id":"PMC_12393911","title":"The expression of the PDZ protein MALS-1/velis is regulated by calcium and calcineurin in cerebellar granule cells.","date":"2002","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12393911","citation_count":2,"is_preprint":false},{"pmid":"40021783","id":"PMC_40021783","title":"Impact of LIN7A silencing on U87 cell invasion and its clinical significance in glioblastoma.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/40021783","citation_count":1,"is_preprint":false},{"pmid":"37873356","id":"PMC_37873356","title":"Autism candidate gene rbm-26 (RBM26/27) regulates MALS-1 to protect against mitochondrial dysfunction and axon degeneration during neurodevelopment.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37873356","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7591,"output_tokens":1560,"usd":0.023086},"stage2":{"model":"claude-opus-4-6","input_tokens":4848,"output_tokens":3377,"usd":0.162997},"total_usd":0.186083,"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\": 2001,\n      \"finding\": \"VAM-1 (a MAGUK family member) contains a conserved domain that directly binds to Veli-1 (human LIN7A homologue), as demonstrated by GST pull-down experiments and blot overlay assays, suggesting VAM-1 promotes assembly of a Veli-1-containing protein complex in neuronal and epithelial cells.\",\n      \"method\": \"GST pull-down, blot overlay assay, heterologous transfection\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal binding demonstrated by two orthogonal in vitro methods (GST pull-down + blot overlay), single study\",\n      \"pmids\": [\"11311936\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"MALS-1/Veli-1 (LIN7A) expression in cerebellar granule cells is regulated at the transcriptional level by Ca²⁺ entry through voltage- or ligand-operated Ca²⁺ channels acting via the calcineurin pathway, without requiring de novo protein synthesis or altered mRNA stability.\",\n      \"method\": \"Pharmacological activation/inhibition of Ca²⁺/calcineurin pathway in cultured cerebellar granule cells, transcriptional assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple pharmacological interventions with mechanistic dissection (mRNA stability and protein synthesis ruled out), single lab\",\n      \"pmids\": [\"12393911\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Lin-7A localizes to the presynaptic fraction in mouse brain (biochemical fractionation), and its RNAi-mediated suppression via in utero electroporation delays neuronal migration and disrupts interhemispheric axon development in the cerebral cortex, establishing a required role in cortical neurodevelopment.\",\n      \"method\": \"Biochemical fractionation, RNAi knockdown by in utero electroporation, immunohistochemistry\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct loss-of-function with defined cellular phenotype (neuronal migration delay, axon growth defect) plus subcellular fractionation; single lab\",\n      \"pmids\": [\"24658322\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"LIN7A overexpression in breast epithelial cells causes hyperproliferation, invasion, and complete absence of lumen formation, revealing a direct role in apico-basal polarity regulation as a Crumbs-complex component; gene expression profiling identified LIN7A as one of the most differentially overexpressed polarity genes in invasive micropapillary carcinomas.\",\n      \"method\": \"Gain-of-function overexpression assay, 3D lumen-formation assay, gene expression profiling\",\n      \"journal\": \"Breast cancer research : BCR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — overexpression with specific polarity/invasion phenotypic readout; single lab with multiple assays\",\n      \"pmids\": [\"26887652\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Lin7a interacts with the α2/β1 form of nitric oxide-sensitive guanylyl cyclase in mouse brain synaptosomes (co-precipitation), and directs this heterodimer to calcium-insensitive cell-cell contacts in HEK293 cells via its PDZ domain; the PDZ-binding motif of the α2 subunit is accessible only in the heterodimer conformation, and Lin7a links the complex to nectin-based cell-cell contacts via MPP3.\",\n      \"method\": \"Co-precipitation from brain synaptosomes, overexpression in HEK293 cells, truncation/domain mutant analysis, immunofluorescence localization\",\n      \"journal\": \"Biochemical pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — co-precipitation from native tissue plus domain-mapping in cells with multiple truncation constructs; single lab\",\n      \"pmids\": [\"27793718\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Lentiviral silencing of LIN7A in U87 glioblastoma cells increases invasiveness, elevates MMP-2 and MMP-9 protease activity, and causes nuclear accumulation of β-catenin with increased transcriptional activity of β-catenin target genes, indicating LIN7A suppresses invasion partly by restraining the β-catenin pathway and maintaining cell polarity and intercellular junctions.\",\n      \"method\": \"Lentiviral knockdown, real-time cell invasion assay, spheroid invasion assay, zymography, Western blotting, immunofluorescence, orthotopic xenograft\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function with multiple mechanistic readouts (proteases, β-catenin pathway) and in vivo validation; single lab\",\n      \"pmids\": [\"40021783\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LIN7A (Veli-1/MALS-1) is a PDZ-domain scaffold protein that localizes to presynaptic and cell-cell contact sites, where it assembles multiprotein complexes (including MAGUK partners such as VAM-1/MPP3 and transmembrane cargo such as the α2/β1 nitric oxide-sensitive guanylyl cyclase) to maintain apico-basal cell polarity, support neuronal migration and axon development, and suppress invasion by restraining MMP activity and nuclear β-catenin signaling; its transcription is regulated by Ca²⁺/calcineurin signaling in neurons.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"LIN7A (Veli-1/MALS-1) is a PDZ-domain scaffold protein that assembles multiprotein complexes at cell-cell contacts and synapses to maintain apico-basal polarity, support neuronal development, and restrain cellular invasion. It directly binds MAGUK family partners such as VAM-1/MPP3 and recruits transmembrane cargo including the α2/β1 nitric oxide-sensitive guanylyl cyclase to nectin-based cell-cell contacts via its PDZ domain [PMID:11311936, PMID:27793718]. In the brain, LIN7A localizes to presynaptic fractions and is required for cortical neuronal migration and interhemispheric axon development, with its transcription regulated by Ca²⁺/calcineurin signaling [PMID:24658322, PMID:12393911]. Loss of LIN7A promotes glioblastoma invasion by elevating MMP-2/MMP-9 activity and triggering nuclear β-catenin accumulation, while its overexpression in breast epithelial cells disrupts lumen formation, demonstrating that precise LIN7A dosage is critical for polarity and invasion control [PMID:40021783, PMID:26887652].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Identifying a direct MAGUK-family binding partner for LIN7A established that Veli-1 participates in scaffolded protein complexes in neuronal and epithelial cells, raising the question of what cargo these complexes recruit.\",\n      \"evidence\": \"GST pull-down and blot overlay assays demonstrating VAM-1–Veli-1 direct binding\",\n      \"pmids\": [\"11311936\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No in vivo validation of the VAM-1–Veli-1 interaction\", \"Functional consequence of complex formation not tested\", \"Other MAGUK partners not compared\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Demonstrating that LIN7A transcription is controlled by Ca²⁺ influx through the calcineurin pathway in neurons revealed how synaptic activity could dynamically regulate this scaffold, but the downstream transcription factor remained unidentified.\",\n      \"evidence\": \"Pharmacological activation/inhibition of Ca²⁺/calcineurin signaling in cultured cerebellar granule cells with transcriptional readouts\",\n      \"pmids\": [\"12393911\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Transcription factor mediating calcineurin-dependent LIN7A expression not identified\", \"In vivo relevance of activity-dependent regulation not tested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Loss-of-function experiments in vivo showed that LIN7A is required for cortical neuronal migration and axon pathfinding, moving it from a biochemical scaffold to a functionally required neurodevelopmental factor.\",\n      \"evidence\": \"RNAi knockdown via in utero electroporation in mouse cortex with immunohistochemical analysis of migration and axon tracts\",\n      \"pmids\": [\"24658322\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism linking LIN7A to migration machinery not defined\", \"Rescue experiment not reported\", \"Presynaptic localization shown biochemically but functional role at synapses not tested\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Two studies expanded LIN7A's role beyond neurons: overexpression in breast epithelial cells disrupted lumen formation and drove invasion, establishing LIN7A as a dosage-sensitive polarity regulator, while PDZ-domain-mediated recruitment of NO-sensitive guanylyl cyclase to nectin-based cell-cell contacts via MPP3 provided a concrete cargo-delivery mechanism.\",\n      \"evidence\": \"3D lumen-formation and invasion assays in breast epithelial cells; co-precipitation from brain synaptosomes and domain-mapping in HEK293 cells with truncation mutants\",\n      \"pmids\": [\"26887652\", \"27793718\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether lumen-formation defect operates through the same β-catenin or MMP pathways identified later is unknown\", \"Structural basis of PDZ-dependent heterodimer selectivity not resolved\", \"In vivo validation of guanylyl cyclase targeting not performed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Silencing LIN7A in glioblastoma cells identified a specific invasion-suppressive mechanism: LIN7A restrains MMP-2/9 activity and prevents nuclear β-catenin accumulation, linking its polarity-scaffold function to Wnt/β-catenin pathway control.\",\n      \"evidence\": \"Lentiviral knockdown in U87 cells with zymography, β-catenin immunofluorescence, invasion assays, and orthotopic xenograft\",\n      \"pmids\": [\"40021783\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct physical link between LIN7A and β-catenin retention at junctions not shown\", \"Whether MMP upregulation is a direct or indirect consequence of polarity loss is unresolved\", \"Single cell line (U87) limits generalizability\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct molecular mechanism by which LIN7A restrains β-catenin nuclear translocation and MMP expression, and whether its neurodevelopmental and tumor-suppressive roles share a common polarity-dependent signaling axis, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of LIN7A in complex with its partners\", \"No genetic knockout mouse phenotype reported\", \"Relationship between calcineurin-dependent transcriptional regulation and polarity/invasion functions not connected\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [4, 5]},\n      {\"term_id\": \"GO:0043226\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": []}\n    ],\n    \"complexes\": [\"Crumbs polarity complex\"],\n    \"partners\": [\"MPP3\", \"GUCY1A2\", \"GUCY1B1\"],\n    \"other_free_text\": []\n  }\n}\n```\n\nWait, I made an error in the pathway slot — I used a GO term instead of a Reactome term. Let me fix that.\n\n```json\n{\n  \"mechanistic_narrative\": \"LIN7A (Veli-1/MALS-1) is a PDZ-domain scaffold protein that assembles multiprotein complexes at cell-cell contacts and synapses to maintain apico-basal polarity, support neuronal development, and restrain cellular invasion. It directly binds MAGUK family partners such as VAM-1/MPP3 and recruits transmembrane cargo including the α2/β1 nitric oxide-sensitive guanylyl cyclase to nectin-based cell-cell contacts via its PDZ domain [PMID:11311936, PMID:27793718]. In the brain, LIN7A localizes to presynaptic fractions and is required for cortical neuronal migration and interhemispheric axon development, with its transcription regulated by Ca²⁺/calcineurin signaling [PMID:24658322, PMID:12393911]. Loss of LIN7A promotes glioblastoma invasion by elevating MMP-2/MMP-9 activity and triggering nuclear β-catenin accumulation, while its overexpression in breast epithelial cells disrupts lumen formation, demonstrating that precise LIN7A dosage is critical for polarity and invasion control [PMID:40021783, PMID:26887652].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Identifying a direct MAGUK-family binding partner for LIN7A established that Veli-1 participates in scaffolded protein complexes in neuronal and epithelial cells, raising the question of what cargo these complexes recruit.\",\n      \"evidence\": \"GST pull-down and blot overlay assays demonstrating VAM-1–Veli-1 direct binding\",\n      \"pmids\": [\"11311936\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No in vivo validation of the VAM-1–Veli-1 interaction\", \"Functional consequence of complex formation not tested\", \"Other MAGUK partners not compared\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Demonstrating that LIN7A transcription is controlled by Ca²⁺ influx through the calcineurin pathway in neurons revealed how synaptic activity could dynamically regulate this scaffold, but the downstream transcription factor remained unidentified.\",\n      \"evidence\": \"Pharmacological activation/inhibition of Ca²⁺/calcineurin signaling in cultured cerebellar granule cells with transcriptional readouts\",\n      \"pmids\": [\"12393911\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Transcription factor mediating calcineurin-dependent LIN7A expression not identified\", \"In vivo relevance of activity-dependent regulation not tested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Loss-of-function experiments in vivo showed that LIN7A is required for cortical neuronal migration and axon pathfinding, moving it from a biochemical scaffold to a functionally required neurodevelopmental factor.\",\n      \"evidence\": \"RNAi knockdown via in utero electroporation in mouse cortex with immunohistochemical analysis of migration and axon tracts\",\n      \"pmids\": [\"24658322\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism linking LIN7A to migration machinery not defined\", \"Rescue experiment not reported\", \"Presynaptic localization shown biochemically but functional role at synapses not tested\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Two studies expanded LIN7A's role beyond neurons: overexpression in breast epithelial cells disrupted lumen formation and drove invasion, establishing LIN7A as a dosage-sensitive polarity regulator, while PDZ-domain-mediated recruitment of NO-sensitive guanylyl cyclase to nectin-based cell-cell contacts via MPP3 provided a concrete cargo-delivery mechanism.\",\n      \"evidence\": \"3D lumen-formation and invasion assays in breast epithelial cells; co-precipitation from brain synaptosomes and domain-mapping in HEK293 cells with truncation mutants\",\n      \"pmids\": [\"26887652\", \"27793718\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether lumen-formation defect operates through the same β-catenin or MMP pathways identified later is unknown\", \"Structural basis of PDZ-dependent heterodimer selectivity not resolved\", \"In vivo validation of guanylyl cyclase targeting not performed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Silencing LIN7A in glioblastoma cells identified a specific invasion-suppressive mechanism: LIN7A restrains MMP-2/9 activity and prevents nuclear β-catenin accumulation, linking its polarity-scaffold function to Wnt/β-catenin pathway control.\",\n      \"evidence\": \"Lentiviral knockdown in U87 cells with zymography, β-catenin immunofluorescence, invasion assays, and orthotopic xenograft\",\n      \"pmids\": [\"40021783\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct physical link between LIN7A and β-catenin retention at junctions not shown\", \"Whether MMP upregulation is a direct or indirect consequence of polarity loss is unresolved\", \"Single cell line (U87) limits generalizability\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct molecular mechanism by which LIN7A restrains β-catenin nuclear translocation and MMP expression, and whether its neurodevelopmental and tumor-suppressive roles share a common polarity-dependent signaling axis, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of LIN7A in complex with its partners\", \"No genetic knockout mouse phenotype reported\", \"Relationship between calcineurin-dependent transcriptional regulation and polarity/invasion functions not connected\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"R-HSA-1500931\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"complexes\": [\"Crumbs polarity complex\"],\n    \"partners\": [\"MPP3\", \"GUCY1A2\", \"GUCY1B1\"],\n    \"other_free_text\": []\n  }\n}\n```"}