{"gene":"LIN7A","run_date":"2026-06-10T02:59:49","timeline":{"discoveries":[{"year":2001,"finding":"VAM-1, a MAGUK family member, binds directly to human Veli-1 (LIN7A) through a conserved domain, as demonstrated by GST pull-down experiments and blot overlay assays. This interaction suggests LIN7A participates in assembly of multiprotein complexes 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 / Moderate — reciprocal binding shown by two orthogonal biochemical methods (GST pull-down and blot overlay) in a single lab","pmids":["11311936"],"is_preprint":false},{"year":2002,"finding":"MALS-1 (LIN7A) expression in cerebellar granule cells is regulated at the transcriptional level by the Ca²⁺/calcineurin pathway activated through voltage- or ligand-operated Ca²⁺ channels; this regulation does not require de novo protein synthesis and does not occur at the level of mRNA stability.","method":"Pharmacological activation/inhibition of Ca²⁺ channels and calcineurin in cultured cerebellar granule cells; transcriptional reporter and mRNA stability assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple pharmacological perturbations in a defined cellular system, single lab, two mechanistic exclusions (mRNA stability, de novo protein synthesis) strengthen the pathway placement","pmids":["12393911"],"is_preprint":false},{"year":2014,"finding":"LIN7A protein is enriched in the presynaptic fraction of mouse brain (biochemical fractionation). RNAi-mediated knockdown of Lin7A in mouse cortex via in utero electroporation delays neuronal migration (neurons retained in lower cortical plate and intermediate zone at P2) and disrupts interhemispheric axon development.","method":"Biochemical fractionation of mouse brain synaptosomes; in utero electroporation-based RNAi knockdown with histological readout of neuronal migration and axon development","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct loss-of-function in vivo with specific cellular phenotypes, plus subcellular fractionation; single lab","pmids":["24658322"],"is_preprint":false},{"year":2016,"finding":"The α2/β1 form of nitric oxide-sensitive guanylyl cyclase interacts with Lin7a in mouse brain synaptosomes (co-precipitation). In HEK293 cells, the α2/β1 heterodimer (but not the α1/β1 form) is directed to calcium-insensitive cell-cell contacts via the PDZ-binding motif of the α2 subunit; this localization requires heterodimerization with β1 and is mediated through Lin7a and MPP3.","method":"Co-precipitation from mouse brain synaptosomes; overexpression and localization analysis in HEK293 cells; truncation constructs to map the PDZ-binding motif","journal":"Biochemical pharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-precipitation from native tissue plus domain-mapping in cells, single lab, two orthogonal approaches","pmids":["27793718"],"is_preprint":false},{"year":2016,"finding":"LIN7A overexpression in breast epithelial cells causes hyperproliferation, invasion, and complete absence of lumen formation, indicating a direct role in apico-basal polarity maintenance; LIN7A was identified as a Crumbs-complex polarity gene whose dysregulation drives polarity inversion in invasive micropapillary carcinoma.","method":"Gain-of-function overexpression in breast epithelial cells with 3D lumen formation assay, invasion assay, and proliferation readout; gene expression profiling of clinical samples","journal":"Breast cancer research : BCR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — defined cellular phenotypes from gain-of-function with orthogonal readouts (lumen formation, invasion, proliferation); single lab","pmids":["26887652"],"is_preprint":false},{"year":2018,"finding":"LIN7A is a direct target of miR-501-3p in hepatocellular carcinoma cells; re-expression of LIN7A rescues the suppressive effects of miR-501-3p overexpression on cell proliferation, migration, invasion, and EMT, placing LIN7A downstream of miR-501-3p in mediating these processes.","method":"Luciferase reporter assay (implied by 'directly targeted'), gain-of-function and loss-of-function in HCC cell lines, rescue experiments","journal":"Cell death & disease","confidence":"Low","confidence_rationale":"Tier 3 / Weak — pathway placement by rescue experiment in cancer cell lines; direct targeting claim relies on single reporter assay approach; single lab","pmids":["29749382"],"is_preprint":false},{"year":2025,"finding":"Silencing of LIN7A in U87 glioblastoma cells increases invasiveness and MMP-2/MMP-9 protease activity, and leads to nuclear accumulation of β-catenin with increased transcriptional activity of β-catenin target genes, suggesting LIN7A suppresses invasion partly by restraining the β-catenin pathway.","method":"Lentiviral RNAi knockdown in U87 cells; real-time cell invasion analysis; zymography for MMP-2/MMP-9; Western blot and immunofluorescence for β-catenin localization; orthotopic xenograft model","journal":"Scientific reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — loss-of-function with multiple phenotypic readouts but β-catenin increase described as 'slight and not statistically significant' for cytoplasmic fraction; single lab, single study","pmids":["40021783"],"is_preprint":false}],"current_model":"LIN7A (MALS-1/Veli-1) is a PDZ-domain scaffold protein that localizes to presynaptic and postsynaptic densities and cell-cell contacts, where it assembles multiprotein complexes by binding partners such as VAM-1 (a MAGUK) and the α2/β1 form of nitric oxide-sensitive guanylyl cyclase (via the α2 PDZ-binding motif), directing them to specific membrane domains; its expression is transcriptionally regulated by the Ca²⁺/calcineurin pathway in neurons; loss of LIN7A disrupts neuronal migration and interhemispheric axon development in vivo, while gain of LIN7A drives polarity defects and invasion in epithelial/tumor cells partly through β-catenin pathway activation."},"narrative":{"mechanistic_narrative":"LIN7A (MALS-1/Veli-1) is a PDZ-domain scaffold protein that assembles membrane-associated multiprotein complexes at neuronal synapses and epithelial cell-cell contacts [PMID:11311936, PMID:27793718]. It binds the MAGUK family member VAM-1 directly through a conserved domain [PMID:11311936], and in brain synaptosomes it captures the α2/β1 form of nitric oxide-sensitive guanylyl cyclase, directing this heterodimer (but not the α1/β1 form) to calcium-insensitive cell-cell contacts via the α2 subunit PDZ-binding motif, an event also requiring MPP3 [PMID:27793718]. In neurons, LIN7A is enriched in the presynaptic fraction, and its transcription is controlled by the Ca²⁺/calcineurin pathway downstream of voltage- and ligand-operated Ca²⁺ channels [PMID:12393911, PMID:24658322]. Functionally, LIN7A is required for proper cortical neuronal migration and interhemispheric axon development in vivo [PMID:24658322], and it maintains epithelial apico-basal polarity as a Crumbs-complex component whose dysregulation drives polarity inversion, hyperproliferation, and invasion [PMID:26887652].","teleology":[{"year":2001,"claim":"Establishing that LIN7A physically engages a MAGUK partner defined it as a scaffold that nucleates multiprotein assemblies rather than acting alone.","evidence":"GST pull-down and blot overlay assays with VAM-1 in heterologous transfection","pmids":["11311936"],"confidence":"Medium","gaps":["Functional consequence of the VAM-1/LIN7A complex not tested","Endogenous interaction in native tissue not shown","Domain on LIN7A mediating binding not mapped"]},{"year":2002,"claim":"Identifying Ca²⁺/calcineurin-dependent transcriptional control answered how LIN7A levels are set in neurons in response to activity.","evidence":"Pharmacological Ca²⁺-channel and calcineurin perturbation in cerebellar granule cells with reporter and mRNA-stability assays","pmids":["12393911"],"confidence":"Medium","gaps":["Transcription factors linking calcineurin to the LIN7A promoter not identified","Physiological stimulus driving this regulation in vivo unresolved"]},{"year":2014,"claim":"In vivo loss-of-function established that LIN7A is required for neuronal migration and axon development, moving it from a binding partner to a developmental effector.","evidence":"Synaptosome fractionation plus in utero electroporation RNAi in mouse cortex with histological migration/axon readouts","pmids":["24658322"],"confidence":"Medium","gaps":["Molecular partners mediating the migration phenotype not defined","RNAi specificity not confirmed by rescue","Mechanism connecting presynaptic localization to migration unclear"]},{"year":2016,"claim":"Mapping the α2/β1 guanylyl cyclase interaction to the α2 PDZ motif and requiring MPP3 demonstrated how LIN7A targets specific signaling enzymes to cell-cell contacts.","evidence":"Co-precipitation from brain synaptosomes plus HEK293 localization and truncation mapping","pmids":["27793718"],"confidence":"Medium","gaps":["Functional output of guanylyl cyclase localization at contacts not measured","Architecture of the LIN7A/MPP3/cyclase complex unresolved"]},{"year":2016,"claim":"Gain-of-function in breast epithelium tied LIN7A to apico-basal polarity maintenance and the Crumbs complex, explaining how its dysregulation drives invasive carcinoma.","evidence":"Overexpression with 3D lumen, invasion and proliferation assays plus clinical expression profiling","pmids":["26887652"],"confidence":"Medium","gaps":["Direct LIN7A interactions within the Crumbs complex not biochemically mapped","Whether the phenotype reflects dosage versus mislocalization unresolved"]},{"year":2018,"claim":"Placing LIN7A downstream of miR-501-3p connected its expression level to proliferation, migration and EMT control in liver cancer cells.","evidence":"Reporter assay, gain/loss-of-function and rescue in HCC cell lines","pmids":["29749382"],"confidence":"Low","gaps":["Direct targeting rests on a single reporter approach","Not independently confirmed","Mechanism by which LIN7A acts in this context not defined"]},{"year":2025,"claim":"Knockdown in glioblastoma linked LIN7A to suppression of invasion via restraint of the β-catenin pathway, implicating it as an invasion brake in tumor cells.","evidence":"Lentiviral RNAi in U87 cells with invasion assays, zymography, β-catenin imaging and orthotopic xenografts","pmids":["40021783"],"confidence":"Low","gaps":["Cytoplasmic β-catenin increase reported as not statistically significant","Direct molecular link between LIN7A and β-catenin not established","Single lab, single study"]},{"year":null,"claim":"How the same scaffold reconciles its presynaptic/migration role with its epithelial polarity and tumor-invasion functions remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unified structural model of LIN7A complexes across tissues","Direct partners in the polarity/Crumbs and β-catenin contexts not biochemically mapped","Whether neuronal and epithelial phenotypes share a common molecular mechanism unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,3]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[3]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[2,4]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[6]}],"complexes":["Crumbs polarity complex"],"partners":["VAM-1","MPP3"],"other_free_text":[]}},"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":"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":23,"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":"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":4,"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":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":"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":"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":8366,"output_tokens":2816,"usd":0.033669,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8894,"output_tokens":2495,"usd":0.053422,"stage2_stop_reason":"end_turn"},"total_usd":0.087091,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"I need to carefully evaluate each paper before extracting discoveries.\n\n**Paper classification:**\n\n1. **PMID:30537154** - lncRNA CASC9/miR-758-3p/LIN7A axis in ovarian cancer. LIN7A is a target here, but the study is about the lncRNA and miRNA regulation of LIN7A expression — not a mechanistic discovery about LIN7A protein function. EXCLUDE (it's about a non-protein regulatory axis targeting LIN7A, not about LIN7A's mechanism).\n\n2. **PMID:29749382** - miR-501-3p targets LIN7A in HCC. LIN7A is the target of a miRNA; the study shows miR-501-3p suppresses metastasis through targeting LIN7A. This does place LIN7A in a pathway (EMT/metastasis) via functional rescue, but the mechanistic detail about LIN7A itself is minimal. Borderline — includes that LIN7A mediates suppression effects on metastasis.\n\n3. **PMID:11311936** - VAM-1 binds to human Veli-1 (VELI1 = LIN7A alias). Direct binding via GST pull-down and blot overlay. INCLUDE.\n\n4. **PMID:26887652** - LIN7A overexpression causes polarity defects in breast carcinoma. Loss-of-function/gain-of-function with cellular phenotype. INCLUDE.\n\n5. **PMID:24658322** - LIN7A RNAi in mouse cortex delays neuronal migration and axonal growth. Biochemical fractionation shows presynaptic enrichment. INCLUDE.\n\n6. **PMID:36864492** - LIN7A methylation/expression in AML; in vitro knockdown affects apoptosis with decitabine. Some functional mechanism. INCLUDE (limited mechanistic content).\n\n7. **PMID:27793718** - α2/β1 guanylyl cyclase interacts with Lin7a in brain synaptosomes; Lin7a directs complex to cell-cell contacts via MPP3. Co-precipitation and localization experiments. INCLUDE.\n\n8. **PMID:39480871** - C. elegans MALS-1 in this paper refers to MALSU1 (mitoribosomal assembly factor), NOT LIN7A (MALS-1 alias). The alias \"MALS-1\" for LIN7A is different from \"MALSU1.\" This is a SYMBOL COLLISION — the C. elegans MALS-1 here is the MALSU1 ortholog, not LIN7A. EXCLUDE.\n\n9. **PMID:40021783** - LIN7A silencing in U87 glioblastoma cells; increases invasion via β-catenin pathway, MMP-2/9 activity. INCLUDE.\n\n10. **PMID:12393911** - MALS-1/MALS-2 expression regulated by Ca²⁺/calcineurin pathway in cerebellar granule cells. MALS-1 = LIN7A alias. INCLUDE.\n\n11. **PMID:38957040** - Bioinformatic/WGCNA study; miR-29b-3p identified as regulator of LIN7A. Validated in blood samples by qRT-PCR and ELISA. Mostly biomarker/bioinformatic. Limited mechanistic content. EXCLUDE (computational prediction with expression validation only).\n\n12. **PMID:37873356** - Preprint version of PMID:39480871 paper about C. elegans MALS-1 = MALSU1. Same SYMBOL COLLISION as #8. EXCLUDE.\n\nNow extracting discoveries:\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"VAM-1, a MAGUK family member, binds directly to human Veli-1 (LIN7A) through a conserved domain, as demonstrated by GST pull-down experiments and blot overlay assays. This interaction suggests LIN7A participates in assembly of multiprotein complexes 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 / Moderate — reciprocal binding shown by two orthogonal biochemical methods (GST pull-down and blot overlay) in a single lab\",\n      \"pmids\": [\"11311936\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"MALS-1 (LIN7A) expression in cerebellar granule cells is regulated at the transcriptional level by the Ca²⁺/calcineurin pathway activated through voltage- or ligand-operated Ca²⁺ channels; this regulation does not require de novo protein synthesis and does not occur at the level of mRNA stability.\",\n      \"method\": \"Pharmacological activation/inhibition of Ca²⁺ channels and calcineurin in cultured cerebellar granule cells; transcriptional reporter and mRNA stability assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple pharmacological perturbations in a defined cellular system, single lab, two mechanistic exclusions (mRNA stability, de novo protein synthesis) strengthen the pathway placement\",\n      \"pmids\": [\"12393911\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"LIN7A protein is enriched in the presynaptic fraction of mouse brain (biochemical fractionation). RNAi-mediated knockdown of Lin7A in mouse cortex via in utero electroporation delays neuronal migration (neurons retained in lower cortical plate and intermediate zone at P2) and disrupts interhemispheric axon development.\",\n      \"method\": \"Biochemical fractionation of mouse brain synaptosomes; in utero electroporation-based RNAi knockdown with histological readout of neuronal migration and axon development\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct loss-of-function in vivo with specific cellular phenotypes, plus subcellular fractionation; single lab\",\n      \"pmids\": [\"24658322\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The α2/β1 form of nitric oxide-sensitive guanylyl cyclase interacts with Lin7a in mouse brain synaptosomes (co-precipitation). In HEK293 cells, the α2/β1 heterodimer (but not the α1/β1 form) is directed to calcium-insensitive cell-cell contacts via the PDZ-binding motif of the α2 subunit; this localization requires heterodimerization with β1 and is mediated through Lin7a and MPP3.\",\n      \"method\": \"Co-precipitation from mouse brain synaptosomes; overexpression and localization analysis in HEK293 cells; truncation constructs to map the PDZ-binding motif\",\n      \"journal\": \"Biochemical pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-precipitation from native tissue plus domain-mapping in cells, single lab, two orthogonal approaches\",\n      \"pmids\": [\"27793718\"],\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, indicating a direct role in apico-basal polarity maintenance; LIN7A was identified as a Crumbs-complex polarity gene whose dysregulation drives polarity inversion in invasive micropapillary carcinoma.\",\n      \"method\": \"Gain-of-function overexpression in breast epithelial cells with 3D lumen formation assay, invasion assay, and proliferation readout; gene expression profiling of clinical samples\",\n      \"journal\": \"Breast cancer research : BCR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined cellular phenotypes from gain-of-function with orthogonal readouts (lumen formation, invasion, proliferation); single lab\",\n      \"pmids\": [\"26887652\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"LIN7A is a direct target of miR-501-3p in hepatocellular carcinoma cells; re-expression of LIN7A rescues the suppressive effects of miR-501-3p overexpression on cell proliferation, migration, invasion, and EMT, placing LIN7A downstream of miR-501-3p in mediating these processes.\",\n      \"method\": \"Luciferase reporter assay (implied by 'directly targeted'), gain-of-function and loss-of-function in HCC cell lines, rescue experiments\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — pathway placement by rescue experiment in cancer cell lines; direct targeting claim relies on single reporter assay approach; single lab\",\n      \"pmids\": [\"29749382\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Silencing of LIN7A in U87 glioblastoma cells increases invasiveness and MMP-2/MMP-9 protease activity, and leads to nuclear accumulation of β-catenin with increased transcriptional activity of β-catenin target genes, suggesting LIN7A suppresses invasion partly by restraining the β-catenin pathway.\",\n      \"method\": \"Lentiviral RNAi knockdown in U87 cells; real-time cell invasion analysis; zymography for MMP-2/MMP-9; Western blot and immunofluorescence for β-catenin localization; orthotopic xenograft model\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — loss-of-function with multiple phenotypic readouts but β-catenin increase described as 'slight and not statistically significant' for cytoplasmic fraction; single lab, single study\",\n      \"pmids\": [\"40021783\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LIN7A (MALS-1/Veli-1) is a PDZ-domain scaffold protein that localizes to presynaptic and postsynaptic densities and cell-cell contacts, where it assembles multiprotein complexes by binding partners such as VAM-1 (a MAGUK) and the α2/β1 form of nitric oxide-sensitive guanylyl cyclase (via the α2 PDZ-binding motif), directing them to specific membrane domains; its expression is transcriptionally regulated by the Ca²⁺/calcineurin pathway in neurons; loss of LIN7A disrupts neuronal migration and interhemispheric axon development in vivo, while gain of LIN7A drives polarity defects and invasion in epithelial/tumor cells partly through β-catenin pathway activation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LIN7A (MALS-1/Veli-1) is a PDZ-domain scaffold protein that assembles membrane-associated multiprotein complexes at neuronal synapses and epithelial cell-cell contacts [#0, #3]. It binds the MAGUK family member VAM-1 directly through a conserved domain [#0], and in brain synaptosomes it captures the \\u03b12/\\u03b21 form of nitric oxide-sensitive guanylyl cyclase, directing this heterodimer (but not the \\u03b11/\\u03b21 form) to calcium-insensitive cell-cell contacts via the \\u03b12 subunit PDZ-binding motif, an event also requiring MPP3 [#3]. In neurons, LIN7A is enriched in the presynaptic fraction, and its transcription is controlled by the Ca\\u00b2\\u207a/calcineurin pathway downstream of voltage- and ligand-operated Ca\\u00b2\\u207a channels [#1, #2]. Functionally, LIN7A is required for proper cortical neuronal migration and interhemispheric axon development in vivo [#2], and it maintains epithelial apico-basal polarity as a Crumbs-complex component whose dysregulation drives polarity inversion, hyperproliferation, and invasion [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Establishing that LIN7A physically engages a MAGUK partner defined it as a scaffold that nucleates multiprotein assemblies rather than acting alone.\",\n      \"evidence\": \"GST pull-down and blot overlay assays with VAM-1 in heterologous transfection\",\n      \"pmids\": [\"11311936\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of the VAM-1/LIN7A complex not tested\", \"Endogenous interaction in native tissue not shown\", \"Domain on LIN7A mediating binding not mapped\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Identifying Ca\\u00b2\\u207a/calcineurin-dependent transcriptional control answered how LIN7A levels are set in neurons in response to activity.\",\n      \"evidence\": \"Pharmacological Ca\\u00b2\\u207a-channel and calcineurin perturbation in cerebellar granule cells with reporter and mRNA-stability assays\",\n      \"pmids\": [\"12393911\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Transcription factors linking calcineurin to the LIN7A promoter not identified\", \"Physiological stimulus driving this regulation in vivo unresolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"In vivo loss-of-function established that LIN7A is required for neuronal migration and axon development, moving it from a binding partner to a developmental effector.\",\n      \"evidence\": \"Synaptosome fractionation plus in utero electroporation RNAi in mouse cortex with histological migration/axon readouts\",\n      \"pmids\": [\"24658322\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular partners mediating the migration phenotype not defined\", \"RNAi specificity not confirmed by rescue\", \"Mechanism connecting presynaptic localization to migration unclear\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Mapping the \\u03b12/\\u03b21 guanylyl cyclase interaction to the \\u03b12 PDZ motif and requiring MPP3 demonstrated how LIN7A targets specific signaling enzymes to cell-cell contacts.\",\n      \"evidence\": \"Co-precipitation from brain synaptosomes plus HEK293 localization and truncation mapping\",\n      \"pmids\": [\"27793718\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional output of guanylyl cyclase localization at contacts not measured\", \"Architecture of the LIN7A/MPP3/cyclase complex unresolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Gain-of-function in breast epithelium tied LIN7A to apico-basal polarity maintenance and the Crumbs complex, explaining how its dysregulation drives invasive carcinoma.\",\n      \"evidence\": \"Overexpression with 3D lumen, invasion and proliferation assays plus clinical expression profiling\",\n      \"pmids\": [\"26887652\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct LIN7A interactions within the Crumbs complex not biochemically mapped\", \"Whether the phenotype reflects dosage versus mislocalization unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Placing LIN7A downstream of miR-501-3p connected its expression level to proliferation, migration and EMT control in liver cancer cells.\",\n      \"evidence\": \"Reporter assay, gain/loss-of-function and rescue in HCC cell lines\",\n      \"pmids\": [\"29749382\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Direct targeting rests on a single reporter approach\", \"Not independently confirmed\", \"Mechanism by which LIN7A acts in this context not defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Knockdown in glioblastoma linked LIN7A to suppression of invasion via restraint of the \\u03b2-catenin pathway, implicating it as an invasion brake in tumor cells.\",\n      \"evidence\": \"Lentiviral RNAi in U87 cells with invasion assays, zymography, \\u03b2-catenin imaging and orthotopic xenografts\",\n      \"pmids\": [\"40021783\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Cytoplasmic \\u03b2-catenin increase reported as not statistically significant\", \"Direct molecular link between LIN7A and \\u03b2-catenin not established\", \"Single lab, single study\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the same scaffold reconciles its presynaptic/migration role with its epithelial polarity and tumor-invasion functions remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unified structural model of LIN7A complexes across tissues\", \"Direct partners in the polarity/Crumbs and \\u03b2-catenin contexts not biochemically mapped\", \"Whether neuronal and epithelial phenotypes share a common molecular mechanism unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [2, 4]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\"Crumbs polarity complex\"],\n    \"partners\": [\"VAM-1\", \"MPP3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}