{"gene":"LGMN","run_date":"2026-04-28T18:30:27","timeline":{"discoveries":[{"year":1996,"finding":"Human LGMN (PRSC1) encodes a 433-amino-acid cysteine protease with sequence identity to hemoglobinases and vacuolar processing cysteine proteases, mapping to chromosome 14q32.1, with strongest expression in kidney.","method":"cDNA cloning, Northern blot, fluorescence in situ hybridization","journal":"Cytogenetics and cell genetics","confidence":"Medium","confidence_rationale":"Tier 2 — direct molecular cloning and chromosomal mapping, single study","pmids":["8893817"],"is_preprint":false},{"year":2020,"finding":"LGMNP1 pseudogene acts as a competitive endogenous RNA (ceRNA) by sponging miR-495-3p, thereby relieving miR-495-3p-mediated repression of LGMN mRNA and upregulating LGMN protein expression to promote GBM cell proliferation and invasion.","method":"Dual-luciferase reporter assay, RNA-induced silencing complex biochemical analysis, miR-495-3p mimic rescue experiments, in vivo xenograft","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2 — luciferase reporter and functional rescue, single lab","pmids":["32711096"],"is_preprint":false},{"year":2021,"finding":"CircLGMN (hsa_circ_0033009) acts as a sponge for miR-127-3p, preventing miR-127-3p-mediated degradation of LGMN mRNA and thereby increasing LGMN protein expression to promote GBM cell proliferation and invasion.","method":"CircRNA overexpression, miR-127-3p mimic rescue, dual-luciferase reporter assay, in vivo xenograft","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2 — luciferase reporter and functional rescue, single lab","pmids":["34582975"],"is_preprint":false},{"year":2022,"finding":"LGMN drives M2-like macrophage polarization; extracellular vesicle-shuttled LGMNP1 pseudogene from ectopic endometrial stromal cells upregulates LGMN mRNA expression in macrophages (THP-1), promoting M2 phenotype (increased CD206, decreased CD86).","method":"EV characterization (nanoparticle tracking, TEM, Western blot), EV internalization fluorescence assay, qRT-PCR and Western blot for M1/M2 markers and LGMN expression","journal":"Human reproduction","confidence":"Medium","confidence_rationale":"Tier 2-3 — multiple orthogonal methods in vitro, single lab, limited patient samples","pmids":["34893848"],"is_preprint":false},{"year":2022,"finding":"Metformin inhibits LGMN expression and induces autophagy via the AKT/mTOR/LC3II signaling pathway in choriocarcinoma cells in a LGMN-dependent manner, suppressing cell proliferation and invasion.","method":"High-throughput sequencing, dose-response qRT-PCR/Western blot, LGMN overexpression rescue, autophagy inhibitor/inducer experiments, subcutaneous xenograft","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal in vitro and in vivo methods, single lab","pmids":["36464174"],"is_preprint":false},{"year":2024,"finding":"LGMN is required for lysosomal/autophagic degradation in breast cancer cells; CRISPR/Cas9-mediated editing of LGMN impairs lysosomal/autophagic function and reduces cancer cell migration, invasion, clone formation in vitro and experimental lung metastasis in vivo.","method":"CRISPR/Cas9 gene editing via lipid nanoparticle delivery of Cas9 mRNA and gRNA, in vitro migration/invasion assays, in vivo experimental lung metastasis model","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — direct loss-of-function with defined cellular phenotypes, single lab","pmids":["38582932"],"is_preprint":false},{"year":2016,"finding":"Knockdown of LGMN reduces breast cancer cell migration, invasion, and colony formation, and downregulates MMP2 and MMP9 expression, linking LGMN to MMP-mediated invasiveness.","method":"shRNA-mediated knockdown, Western blot for MMP2/MMP9, colony formation assay, invasion assay","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2-3 — loss-of-function with defined phenotype and downstream marker changes, single lab","pmids":["27656894"],"is_preprint":false},{"year":2026,"finding":"METTL3-dependent m6A modification of LGMN mRNA is read by YTHDF1, which enhances LGMN translation; elevated LGMN in macrophages promotes ox-LDL-induced ferroptosis and atherosclerosis plaque formation.","method":"RNA sequencing, m6A modification analysis, YTHDF1 binding assay, macrophage-specific METTL3 and LGMN knockdown in vivo (atherosclerosis mouse model), LGMN overexpression rescue","journal":"Journal of molecular and cellular cardiology","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods (m6A mapping, YTHDF1 binding, in vivo KD with rescue), single lab","pmids":["41506595"],"is_preprint":false},{"year":2025,"finding":"LGMN forms a protein complex with ITGA5 and FAPα in osteosarcoma cells, as confirmed by co-immunoprecipitation and immunofluorescence; expression of all three proteins increases dose-dependently with polyethylene microplastic exposure and promotes tumor progression.","method":"Co-immunoprecipitation (Co-IP), immunofluorescence staining, in vivo tumor growth assay with inhibitors","journal":"Ecotoxicology and environmental safety","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP confirms complex, in vivo inhibitor experiments, single lab","pmids":["41086694"],"is_preprint":false},{"year":2025,"finding":"Legumain is required for processing of cathepsins L, V, B, and D from single-chain to two-chain forms in a legumain-activity-dependent manner; loss of LGMN reduces nuclear cathepsin L levels. N-terminomics revealed putative nuclear substrates of cathepsin L and legumain involved in cell proliferation, cell cycle regulation, inflammation, and ribosomal biogenesis.","method":"Chemical activity-based probes, immunoblots in LGMN−/− cells, recombinant protein in vitro cleavage assay, N-terminomics (NICE pipeline)","journal":"bioRxiv","confidence":"High","confidence_rationale":"Tier 1 — activity-based probes, genetic KO, recombinant protein assay, and unbiased proteomics in single study with multiple orthogonal methods","pmids":["bio_10.1101_2025.08.17.670765"],"is_preprint":true},{"year":2025,"finding":"CST6 (Cystatin 6), a cysteine protease inhibitor, is a high-affinity target/inhibitor of LGMN; administering recombinant CST6 to endothelial cells enhanced LGMN expression in the presence of TNFα, and an inverse relationship between CST6 and LGMN was established in placenta and maternal circulation in preeclampsia.","method":"mRNA expression in human placental tissue, trophoblast stem cell differentiation, hypoxia treatment, recombinant CST6 treatment of endothelial cells, circulating protein measurement","journal":"Scientific reports","confidence":"Low","confidence_rationale":"Tier 3 — functional link between CST6 and LGMN demonstrated in cell models, but mechanistic detail is limited","pmids":["40234537"],"is_preprint":false},{"year":2020,"finding":"miR-642a-5p directly binds the 3'-UTR of LGMN mRNA to suppress LGMN expression; lncRNA PCGEM1 sponges miR-642a-5p, thereby de-repressing LGMN and promoting cervical carcinoma cell proliferation, migration, and invasion.","method":"Luciferase reporter assay, qRT-PCR, LGMN knockdown rescue experiment, PCGEM1 shRNA knockdown","journal":"Experimental and molecular pathology","confidence":"Medium","confidence_rationale":"Tier 2-3 — luciferase reporter plus functional rescue, single lab","pmids":["33121976"],"is_preprint":false}],"current_model":"LGMN (Legumain/AEP) is a lysosomal cysteine endopeptidase that processes multiple cathepsins (L, V, B, D) from single-chain to two-chain forms in an activity-dependent manner, regulates nuclear cathepsin L levels, and cleaves diverse substrates including GPCRs (PAR2, µ-OR1); its expression is post-transcriptionally controlled by ceRNA networks (LGMNP1/miR-495-3p and circLGMN/miR-127-3p) and at the translational level by METTL3/YTHDF1-dependent m6A modification, while functionally it promotes tumor invasion via MMP2/MMP9 upregulation, drives macrophage M2 polarization and ferroptosis, and participates in autophagy regulation through the AKT/mTOR pathway."},"narrative":{"teleology":[{"year":1996,"claim":"Molecular cloning of human LGMN established it as a cysteine protease homologous to plant vacuolar processing enzymes and hemoglobinases, mapping to chromosome 14q32.1 and expressed most abundantly in kidney, providing the foundational gene identity.","evidence":"cDNA cloning, Northern blot, and FISH in human tissues","pmids":["8893817"],"confidence":"Medium","gaps":["Enzymatic activity and substrate specificity not yet characterized","Subcellular localization not experimentally verified","No functional studies performed"]},{"year":2016,"claim":"Loss-of-function experiments first linked LGMN to tumor invasiveness by showing that LGMN knockdown reduced MMP2/MMP9 expression and suppressed breast cancer cell migration, invasion, and colony formation.","evidence":"shRNA knockdown in breast cancer cell lines with Western blot for MMP2/MMP9 and functional invasion assays","pmids":["27656894"],"confidence":"Medium","gaps":["Mechanism connecting LGMN protease activity to MMP2/MMP9 upregulation unclear","No in vivo validation in this study"]},{"year":2020,"claim":"Two independent ceRNA axes were identified that post-transcriptionally control LGMN abundance: the LGMNP1 pseudogene sponges miR-495-3p, and lncRNA PCGEM1 sponges miR-642a-5p, each de-repressing LGMN mRNA to promote cancer cell proliferation and invasion.","evidence":"Dual-luciferase reporter assays, miRNA mimic rescue experiments, and in vivo xenograft models in GBM and cervical carcinoma","pmids":["32711096","33121976"],"confidence":"Medium","gaps":["Relative contribution of each ceRNA axis in physiological versus tumor contexts unknown","No direct measurement of LGMN protein activity changes"]},{"year":2021,"claim":"A third ceRNA circuit was defined: circLGMN sponges miR-127-3p to upregulate LGMN, reinforcing the principle that LGMN is regulated by multiple noncoding RNA sponge mechanisms in GBM.","evidence":"circRNA overexpression, miR-127-3p mimic rescue, dual-luciferase reporter, and xenograft in GBM cells","pmids":["34582975"],"confidence":"Medium","gaps":["Interplay among LGMNP1, circLGMN, and PCGEM1 ceRNA axes not addressed","Tissue specificity of circLGMN regulation unknown"]},{"year":2022,"claim":"LGMN was shown to drive macrophage M2 polarization via extracellular vesicle-mediated transfer of the LGMNP1 pseudogene from ectopic endometrial stromal cells, establishing an immunomodulatory role beyond tumor cell-autonomous functions.","evidence":"EV isolation and characterization (NTA, TEM), EV internalization assay, qRT-PCR/Western blot for M1/M2 markers in THP-1 macrophages","pmids":["34893848"],"confidence":"Medium","gaps":["Whether LGMN protease activity is required for M2 polarization not tested","Limited patient samples; in vivo validation lacking"]},{"year":2022,"claim":"Metformin was found to suppress LGMN expression and induce autophagy through the AKT/mTOR/LC3II axis in a LGMN-dependent manner, positioning LGMN as a functional node linking autophagy regulation to cell proliferation.","evidence":"Dose-response Western blot, LGMN overexpression rescue, autophagy inhibitor/inducer experiments, and xenograft in choriocarcinoma cells","pmids":["36464174"],"confidence":"Medium","gaps":["Mechanism by which LGMN modulates AKT/mTOR signaling not defined","Whether this pathway operates in non-cancer cells unknown"]},{"year":2024,"claim":"CRISPR/Cas9-mediated disruption of LGMN confirmed its requirement for lysosomal/autophagic degradation and demonstrated that LGMN loss reduces breast cancer migration, invasion, and experimental lung metastasis in vivo.","evidence":"CRISPR/Cas9 editing via lipid nanoparticle delivery, in vitro migration/invasion assays, in vivo lung metastasis model","pmids":["38582932"],"confidence":"Medium","gaps":["Specific lysosomal substrates affected by LGMN loss not identified in this study","Off-target CRISPR effects not fully ruled out"]},{"year":2025,"claim":"Biochemical and proteomic analyses demonstrated that legumain directly processes cathepsins L, V, B, and D to their mature two-chain forms and controls nuclear cathepsin L levels, with N-terminomics revealing putative nuclear substrates involved in proliferation, cell cycle, and ribosomal biogenesis.","evidence":"(preprint) Activity-based probes, immunoblots in LGMN-knockout cells, recombinant in vitro cleavage assays, and NICE N-terminomics pipeline","pmids":["bio_10.1101_2025.08.17.670765"],"confidence":"High","gaps":["Preprint; awaits peer review","Functional consequences of individual cathepsin processing events not dissected","Nuclear substrates identified by proteomics require individual validation"]},{"year":2025,"claim":"Co-immunoprecipitation revealed that LGMN forms a complex with ITGA5 and FAPα in osteosarcoma cells, suggesting a cell-surface or pericellular signaling role beyond its lysosomal protease function.","evidence":"Co-IP, immunofluorescence colocalization, and in vivo tumor growth assay with inhibitors in osteosarcoma cells","pmids":["41086694"],"confidence":"Medium","gaps":["Reciprocal Co-IP and stoichiometry not fully established","Functional consequence of LGMN–ITGA5–FAPα complex on protease activity unknown","Context-dependence on polyethylene microplastic exposure limits generalizability"]},{"year":2026,"claim":"METTL3-deposited m6A modification on LGMN mRNA, read by YTHDF1, enhances LGMN translation in macrophages, and elevated LGMN promotes oxidized-LDL-induced ferroptosis and atherosclerotic plaque formation, establishing an epitranscriptomic layer of LGMN regulation with cardiovascular disease relevance.","evidence":"m6A mapping, YTHDF1 binding assays, macrophage-specific METTL3 and LGMN knockdown in atherosclerosis mouse model, LGMN overexpression rescue","pmids":["41506595"],"confidence":"High","gaps":["Mechanism by which LGMN induces ferroptosis not fully elucidated","Whether m6A regulation of LGMN operates in non-macrophage cell types unknown"]},{"year":null,"claim":"The direct substrates of legumain beyond cathepsins remain poorly validated, the structural basis for its substrate specificity is unresolved, and the mechanism connecting LGMN protease activity to downstream signaling events (MMP upregulation, AKT/mTOR modulation, ferroptosis induction) has not been defined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No crystal structure of human legumain in complex with a natural substrate","Causal chain from LGMN activity to MMP2/MMP9 transcription not delineated","In vivo contribution of nuclear versus lysosomal LGMN pools unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[9,6,5]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,9]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[5,9]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[9]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[9,5]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[4,5]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[3,7]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[6,5,1]}],"complexes":["LGMN–ITGA5–FAPα"],"partners":["CTSL","CTSV","CTSB","CTSD","ITGA5","FAP","CST6","YTHDF1"],"other_free_text":[]},"mechanistic_narrative":"LGMN encodes legumain (also called asparaginyl endopeptidase, AEP), a lysosomal cysteine endopeptidase that processes cathepsins L, V, B, and D from single-chain to two-chain mature forms in an activity-dependent manner and regulates nuclear cathepsin L levels, thereby influencing downstream proteolytic cascades involved in cell proliferation, cell cycle control, and inflammation [PMID:bio_10.1101_2025.08.17.670765]. LGMN promotes tumor cell invasion and metastasis by upregulating MMP2 and MMP9 expression, and its loss impairs lysosomal/autophagic degradation, reducing cancer cell migration and experimental lung metastasis [PMID:27656894, PMID:38582932]. LGMN expression is post-transcriptionally regulated by multiple competing endogenous RNA axes—including the LGMNP1 pseudogene/miR-495-3p, circLGMN/miR-127-3p, and PCGEM1/miR-642a-5p circuits—and at the translational level by METTL3-mediated m6A modification read by YTHDF1 [PMID:32711096, PMID:34582975, PMID:33121976, PMID:41506595]. In macrophages, LGMN drives M2-like polarization and oxidized-LDL-induced ferroptosis contributing to atherosclerotic plaque formation [PMID:34893848, PMID:41506595]."},"prefetch_data":{"uniprot":{"accession":"Q99538","full_name":"Legumain","aliases":["Asparaginyl endopeptidase","AEP","Protease, cysteine 1"],"length_aa":433,"mass_kda":49.4,"function":"Has a strict specificity for hydrolysis of asparaginyl bonds (PubMed:23776206). Can also cleave aspartyl bonds slowly, especially under acidic conditions (PubMed:23776206). Involved in the processing of proteins for MHC class II antigen presentation in the lysosomal/endosomal system (PubMed:9872320). Also involved in MHC class I antigen presentation in cross-presenting dendritic cells by mediating cleavage and maturation of Perforin-2 (MPEG1), thereby promoting antigen translocation in the cytosol (By similarity). Required for normal lysosomal protein degradation in renal proximal tubules (By similarity). Required for normal degradation of internalized EGFR (By similarity). Plays a role in the regulation of cell proliferation via its role in EGFR degradation (By similarity)","subcellular_location":"Lysosome","url":"https://www.uniprot.org/uniprotkb/Q99538/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/LGMN","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CANX","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/LGMN","total_profiled":1310},"omim":[{"mim_id":"605476","title":"ARF GTPase-ACTIVATING PROTEIN WITH GTPase DOMAIN, ANKYRIN REPEAT, AND PLECKSTRIN HOMOLOGY DOMAIN 2; AGAP2","url":"https://www.omim.org/entry/605476"},{"mim_id":"602620","title":"LEGUMAIN; LGMN","url":"https://www.omim.org/entry/602620"},{"mim_id":"600960","title":"SET NUCLEAR PROTOONCOGENE; SET","url":"https://www.omim.org/entry/600960"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Vesicles","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/LGMN"},"hgnc":{"alias_symbol":["LGMN1"],"prev_symbol":["PRSC1"]},"alphafold":{"accession":"Q99538","domains":[{"cath_id":"3.40.50.1460","chopping":"30-306","consensus_level":"high","plddt":97.6534,"start":30,"end":306},{"cath_id":"1.10.132.130","chopping":"323-431","consensus_level":"high","plddt":96.0019,"start":323,"end":431}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q99538","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q99538-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q99538-F1-predicted_aligned_error_v6.png","plddt_mean":94.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LGMN","jax_strain_url":"https://www.jax.org/strain/search?query=LGMN"},"sequence":{"accession":"Q99538","fasta_url":"https://rest.uniprot.org/uniprotkb/Q99538.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q99538/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q99538"}},"corpus_meta":[{"pmid":"34893848","id":"PMC_34893848","title":"The extracellular vesicular pseudogene LGMNP1 induces M2-like macrophage polarization by upregulating LGMN and serves as a novel promising predictive biomarker for ovarian endometriosis recurrence.","date":"2022","source":"Human reproduction (Oxford, England)","url":"https://pubmed.ncbi.nlm.nih.gov/34893848","citation_count":42,"is_preprint":false},{"pmid":"34582975","id":"PMC_34582975","title":"Circular RNA circLGMN facilitates glioblastoma progression by targeting miR-127-3p/LGMN axis.","date":"2021","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/34582975","citation_count":33,"is_preprint":false},{"pmid":"36825203","id":"PMC_36825203","title":"Role of LGMN in tumor development and its progression and connection with the tumor microenvironment.","date":"2023","source":"Frontiers in molecular biosciences","url":"https://pubmed.ncbi.nlm.nih.gov/36825203","citation_count":32,"is_preprint":false},{"pmid":"32711096","id":"PMC_32711096","title":"The LGMN pseudogene promotes tumor progression by acting as a miR-495-3p sponge in glioblastoma.","date":"2020","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/32711096","citation_count":30,"is_preprint":false},{"pmid":"8893817","id":"PMC_8893817","title":"Molecular cloning of a human cDNA encoding putative cysteine protease (PRSC1) and its chromosome assignment to 14q32.1.","date":"1996","source":"Cytogenetics and cell genetics","url":"https://pubmed.ncbi.nlm.nih.gov/8893817","citation_count":16,"is_preprint":false},{"pmid":"38057699","id":"PMC_38057699","title":"Integrative analysis of TBI data reveals Lgmn as a key player in immune cell-mediated ferroptosis.","date":"2023","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/38057699","citation_count":12,"is_preprint":false},{"pmid":"38582932","id":"PMC_38582932","title":"Co-delivery of Cas9 mRNA and guide RNAs for editing of LGMN gene represses breast cancer cell metastasis.","date":"2024","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/38582932","citation_count":12,"is_preprint":false},{"pmid":"33121976","id":"PMC_33121976","title":"Down-regulation of lncRNA PCGEM1 inhibits cervical carcinoma by modulating the miR-642a-5p/LGMN axis.","date":"2020","source":"Experimental and molecular pathology","url":"https://pubmed.ncbi.nlm.nih.gov/33121976","citation_count":11,"is_preprint":false},{"pmid":"36464174","id":"PMC_36464174","title":"Metformin regulates autophagy via LGMN to inhibit choriocarcinoma.","date":"2022","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/36464174","citation_count":6,"is_preprint":false},{"pmid":"32506655","id":"PMC_32506655","title":"Lack of association between LGMN and Alzheimer's disease in the Southern Han Chinese population.","date":"2020","source":"The European journal of neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/32506655","citation_count":6,"is_preprint":false},{"pmid":"27656894","id":"PMC_27656894","title":"MiRNA-Embedded ShRNAs for Radiation-Inducible LGMN Knockdown and the Antitumor Effects on Breast Cancer.","date":"2016","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/27656894","citation_count":4,"is_preprint":false},{"pmid":"38081528","id":"PMC_38081528","title":"Immune modulation of goat monocytes by Fasciola gigantica Legumain-1 protein (Fg-LGMN-1).","date":"2023","source":"Experimental parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/38081528","citation_count":3,"is_preprint":false},{"pmid":"40234537","id":"PMC_40234537","title":"Cystatin 6 (CST6) and Legumain (LGMN) are potential mediators in the pathogenesis of preeclampsia.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/40234537","citation_count":2,"is_preprint":false},{"pmid":"41506595","id":"PMC_41506595","title":"METTL3-dependent N6-methyladenosine modification on LGMN mRNA promotes macrophage ferroptosis and atherosclerosis.","date":"2026","source":"Journal of molecular and cellular cardiology","url":"https://pubmed.ncbi.nlm.nih.gov/41506595","citation_count":0,"is_preprint":false},{"pmid":"41410717","id":"PMC_41410717","title":"Comparing the Interactions of Trichomonas vaginalis/gallinae Legumain-Like Cysteine Protease 1 (LEGU-1) and Human Legumain (LGMN) Protein Sequences with Proton Pump Inhibitor Drugs (Lansoprazole, Omeprazole, and Esomeprazole) by Bioinformatics Analyses.","date":"2025","source":"Acta parasitologica","url":"https://pubmed.ncbi.nlm.nih.gov/41410717","citation_count":0,"is_preprint":false},{"pmid":"41086694","id":"PMC_41086694","title":"Polyethylene microplastics trigger osteosarcoma progression via ITGA5/FAPα/LGMN cancer promoting complex: A novel environmental cancer promoting mechanism.","date":"2025","source":"Ecotoxicology and environmental safety","url":"https://pubmed.ncbi.nlm.nih.gov/41086694","citation_count":0,"is_preprint":false},{"pmid":"41792098","id":"PMC_41792098","title":"Lgmn targets two distinct GPCRs, PAR2 and µ-OR1, and induces cell death in acute lymphoblastic leukemia through an intracellular Ca²⁺ imbalance triggered by ER Ca²⁺ release.","date":"2026","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/41792098","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.08.17.670765","title":"Legumain drives processing of cathepsins and nuclear localisation of cathepsin L","date":"2025-08-19","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.17.670765","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11982,"output_tokens":2802,"usd":0.038988},"stage2":{"model":"claude-opus-4-6","input_tokens":6164,"output_tokens":2901,"usd":0.155018},"total_usd":0.194006,"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\": 1996,\n      \"finding\": \"Human LGMN (PRSC1) encodes a 433-amino-acid cysteine protease with sequence identity to hemoglobinases and vacuolar processing cysteine proteases, mapping to chromosome 14q32.1, with strongest expression in kidney.\",\n      \"method\": \"cDNA cloning, Northern blot, fluorescence in situ hybridization\",\n      \"journal\": \"Cytogenetics and cell genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct molecular cloning and chromosomal mapping, single study\",\n      \"pmids\": [\"8893817\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"LGMNP1 pseudogene acts as a competitive endogenous RNA (ceRNA) by sponging miR-495-3p, thereby relieving miR-495-3p-mediated repression of LGMN mRNA and upregulating LGMN protein expression to promote GBM cell proliferation and invasion.\",\n      \"method\": \"Dual-luciferase reporter assay, RNA-induced silencing complex biochemical analysis, miR-495-3p mimic rescue experiments, in vivo xenograft\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — luciferase reporter and functional rescue, single lab\",\n      \"pmids\": [\"32711096\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CircLGMN (hsa_circ_0033009) acts as a sponge for miR-127-3p, preventing miR-127-3p-mediated degradation of LGMN mRNA and thereby increasing LGMN protein expression to promote GBM cell proliferation and invasion.\",\n      \"method\": \"CircRNA overexpression, miR-127-3p mimic rescue, dual-luciferase reporter assay, in vivo xenograft\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — luciferase reporter and functional rescue, single lab\",\n      \"pmids\": [\"34582975\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"LGMN drives M2-like macrophage polarization; extracellular vesicle-shuttled LGMNP1 pseudogene from ectopic endometrial stromal cells upregulates LGMN mRNA expression in macrophages (THP-1), promoting M2 phenotype (increased CD206, decreased CD86).\",\n      \"method\": \"EV characterization (nanoparticle tracking, TEM, Western blot), EV internalization fluorescence assay, qRT-PCR and Western blot for M1/M2 markers and LGMN expression\",\n      \"journal\": \"Human reproduction\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — multiple orthogonal methods in vitro, single lab, limited patient samples\",\n      \"pmids\": [\"34893848\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Metformin inhibits LGMN expression and induces autophagy via the AKT/mTOR/LC3II signaling pathway in choriocarcinoma cells in a LGMN-dependent manner, suppressing cell proliferation and invasion.\",\n      \"method\": \"High-throughput sequencing, dose-response qRT-PCR/Western blot, LGMN overexpression rescue, autophagy inhibitor/inducer experiments, subcutaneous xenograft\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal in vitro and in vivo methods, single lab\",\n      \"pmids\": [\"36464174\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"LGMN is required for lysosomal/autophagic degradation in breast cancer cells; CRISPR/Cas9-mediated editing of LGMN impairs lysosomal/autophagic function and reduces cancer cell migration, invasion, clone formation in vitro and experimental lung metastasis in vivo.\",\n      \"method\": \"CRISPR/Cas9 gene editing via lipid nanoparticle delivery of Cas9 mRNA and gRNA, in vitro migration/invasion assays, in vivo experimental lung metastasis model\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct loss-of-function with defined cellular phenotypes, single lab\",\n      \"pmids\": [\"38582932\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Knockdown of LGMN reduces breast cancer cell migration, invasion, and colony formation, and downregulates MMP2 and MMP9 expression, linking LGMN to MMP-mediated invasiveness.\",\n      \"method\": \"shRNA-mediated knockdown, Western blot for MMP2/MMP9, colony formation assay, invasion assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — loss-of-function with defined phenotype and downstream marker changes, single lab\",\n      \"pmids\": [\"27656894\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"METTL3-dependent m6A modification of LGMN mRNA is read by YTHDF1, which enhances LGMN translation; elevated LGMN in macrophages promotes ox-LDL-induced ferroptosis and atherosclerosis plaque formation.\",\n      \"method\": \"RNA sequencing, m6A modification analysis, YTHDF1 binding assay, macrophage-specific METTL3 and LGMN knockdown in vivo (atherosclerosis mouse model), LGMN overexpression rescue\",\n      \"journal\": \"Journal of molecular and cellular cardiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods (m6A mapping, YTHDF1 binding, in vivo KD with rescue), single lab\",\n      \"pmids\": [\"41506595\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"LGMN forms a protein complex with ITGA5 and FAPα in osteosarcoma cells, as confirmed by co-immunoprecipitation and immunofluorescence; expression of all three proteins increases dose-dependently with polyethylene microplastic exposure and promotes tumor progression.\",\n      \"method\": \"Co-immunoprecipitation (Co-IP), immunofluorescence staining, in vivo tumor growth assay with inhibitors\",\n      \"journal\": \"Ecotoxicology and environmental safety\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP confirms complex, in vivo inhibitor experiments, single lab\",\n      \"pmids\": [\"41086694\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Legumain is required for processing of cathepsins L, V, B, and D from single-chain to two-chain forms in a legumain-activity-dependent manner; loss of LGMN reduces nuclear cathepsin L levels. N-terminomics revealed putative nuclear substrates of cathepsin L and legumain involved in cell proliferation, cell cycle regulation, inflammation, and ribosomal biogenesis.\",\n      \"method\": \"Chemical activity-based probes, immunoblots in LGMN−/− cells, recombinant protein in vitro cleavage assay, N-terminomics (NICE pipeline)\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — activity-based probes, genetic KO, recombinant protein assay, and unbiased proteomics in single study with multiple orthogonal methods\",\n      \"pmids\": [\"bio_10.1101_2025.08.17.670765\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CST6 (Cystatin 6), a cysteine protease inhibitor, is a high-affinity target/inhibitor of LGMN; administering recombinant CST6 to endothelial cells enhanced LGMN expression in the presence of TNFα, and an inverse relationship between CST6 and LGMN was established in placenta and maternal circulation in preeclampsia.\",\n      \"method\": \"mRNA expression in human placental tissue, trophoblast stem cell differentiation, hypoxia treatment, recombinant CST6 treatment of endothelial cells, circulating protein measurement\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — functional link between CST6 and LGMN demonstrated in cell models, but mechanistic detail is limited\",\n      \"pmids\": [\"40234537\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"miR-642a-5p directly binds the 3'-UTR of LGMN mRNA to suppress LGMN expression; lncRNA PCGEM1 sponges miR-642a-5p, thereby de-repressing LGMN and promoting cervical carcinoma cell proliferation, migration, and invasion.\",\n      \"method\": \"Luciferase reporter assay, qRT-PCR, LGMN knockdown rescue experiment, PCGEM1 shRNA knockdown\",\n      \"journal\": \"Experimental and molecular pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — luciferase reporter plus functional rescue, single lab\",\n      \"pmids\": [\"33121976\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LGMN (Legumain/AEP) is a lysosomal cysteine endopeptidase that processes multiple cathepsins (L, V, B, D) from single-chain to two-chain forms in an activity-dependent manner, regulates nuclear cathepsin L levels, and cleaves diverse substrates including GPCRs (PAR2, µ-OR1); its expression is post-transcriptionally controlled by ceRNA networks (LGMNP1/miR-495-3p and circLGMN/miR-127-3p) and at the translational level by METTL3/YTHDF1-dependent m6A modification, while functionally it promotes tumor invasion via MMP2/MMP9 upregulation, drives macrophage M2 polarization and ferroptosis, and participates in autophagy regulation through the AKT/mTOR pathway.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"LGMN encodes legumain (also called asparaginyl endopeptidase, AEP), a lysosomal cysteine endopeptidase that processes cathepsins L, V, B, and D from single-chain to two-chain mature forms in an activity-dependent manner and regulates nuclear cathepsin L levels, thereby influencing downstream proteolytic cascades involved in cell proliferation, cell cycle control, and inflammation [PMID:bio_10.1101_2025.08.17.670765]. LGMN promotes tumor cell invasion and metastasis by upregulating MMP2 and MMP9 expression, and its loss impairs lysosomal/autophagic degradation, reducing cancer cell migration and experimental lung metastasis [PMID:27656894, PMID:38582932]. LGMN expression is post-transcriptionally regulated by multiple competing endogenous RNA axes—including the LGMNP1 pseudogene/miR-495-3p, circLGMN/miR-127-3p, and PCGEM1/miR-642a-5p circuits—and at the translational level by METTL3-mediated m6A modification read by YTHDF1 [PMID:32711096, PMID:34582975, PMID:33121976, PMID:41506595]. In macrophages, LGMN drives M2-like polarization and oxidized-LDL-induced ferroptosis contributing to atherosclerotic plaque formation [PMID:34893848, PMID:41506595].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Molecular cloning of human LGMN established it as a cysteine protease homologous to plant vacuolar processing enzymes and hemoglobinases, mapping to chromosome 14q32.1 and expressed most abundantly in kidney, providing the foundational gene identity.\",\n      \"evidence\": \"cDNA cloning, Northern blot, and FISH in human tissues\",\n      \"pmids\": [\"8893817\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Enzymatic activity and substrate specificity not yet characterized\", \"Subcellular localization not experimentally verified\", \"No functional studies performed\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Loss-of-function experiments first linked LGMN to tumor invasiveness by showing that LGMN knockdown reduced MMP2/MMP9 expression and suppressed breast cancer cell migration, invasion, and colony formation.\",\n      \"evidence\": \"shRNA knockdown in breast cancer cell lines with Western blot for MMP2/MMP9 and functional invasion assays\",\n      \"pmids\": [\"27656894\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting LGMN protease activity to MMP2/MMP9 upregulation unclear\", \"No in vivo validation in this study\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Two independent ceRNA axes were identified that post-transcriptionally control LGMN abundance: the LGMNP1 pseudogene sponges miR-495-3p, and lncRNA PCGEM1 sponges miR-642a-5p, each de-repressing LGMN mRNA to promote cancer cell proliferation and invasion.\",\n      \"evidence\": \"Dual-luciferase reporter assays, miRNA mimic rescue experiments, and in vivo xenograft models in GBM and cervical carcinoma\",\n      \"pmids\": [\"32711096\", \"33121976\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relative contribution of each ceRNA axis in physiological versus tumor contexts unknown\", \"No direct measurement of LGMN protein activity changes\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"A third ceRNA circuit was defined: circLGMN sponges miR-127-3p to upregulate LGMN, reinforcing the principle that LGMN is regulated by multiple noncoding RNA sponge mechanisms in GBM.\",\n      \"evidence\": \"circRNA overexpression, miR-127-3p mimic rescue, dual-luciferase reporter, and xenograft in GBM cells\",\n      \"pmids\": [\"34582975\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Interplay among LGMNP1, circLGMN, and PCGEM1 ceRNA axes not addressed\", \"Tissue specificity of circLGMN regulation unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"LGMN was shown to drive macrophage M2 polarization via extracellular vesicle-mediated transfer of the LGMNP1 pseudogene from ectopic endometrial stromal cells, establishing an immunomodulatory role beyond tumor cell-autonomous functions.\",\n      \"evidence\": \"EV isolation and characterization (NTA, TEM), EV internalization assay, qRT-PCR/Western blot for M1/M2 markers in THP-1 macrophages\",\n      \"pmids\": [\"34893848\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether LGMN protease activity is required for M2 polarization not tested\", \"Limited patient samples; in vivo validation lacking\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Metformin was found to suppress LGMN expression and induce autophagy through the AKT/mTOR/LC3II axis in a LGMN-dependent manner, positioning LGMN as a functional node linking autophagy regulation to cell proliferation.\",\n      \"evidence\": \"Dose-response Western blot, LGMN overexpression rescue, autophagy inhibitor/inducer experiments, and xenograft in choriocarcinoma cells\",\n      \"pmids\": [\"36464174\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which LGMN modulates AKT/mTOR signaling not defined\", \"Whether this pathway operates in non-cancer cells unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"CRISPR/Cas9-mediated disruption of LGMN confirmed its requirement for lysosomal/autophagic degradation and demonstrated that LGMN loss reduces breast cancer migration, invasion, and experimental lung metastasis in vivo.\",\n      \"evidence\": \"CRISPR/Cas9 editing via lipid nanoparticle delivery, in vitro migration/invasion assays, in vivo lung metastasis model\",\n      \"pmids\": [\"38582932\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific lysosomal substrates affected by LGMN loss not identified in this study\", \"Off-target CRISPR effects not fully ruled out\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Biochemical and proteomic analyses demonstrated that legumain directly processes cathepsins L, V, B, and D to their mature two-chain forms and controls nuclear cathepsin L levels, with N-terminomics revealing putative nuclear substrates involved in proliferation, cell cycle, and ribosomal biogenesis.\",\n      \"evidence\": \"(preprint) Activity-based probes, immunoblots in LGMN-knockout cells, recombinant in vitro cleavage assays, and NICE N-terminomics pipeline\",\n      \"pmids\": [\"bio_10.1101_2025.08.17.670765\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Preprint; awaits peer review\", \"Functional consequences of individual cathepsin processing events not dissected\", \"Nuclear substrates identified by proteomics require individual validation\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Co-immunoprecipitation revealed that LGMN forms a complex with ITGA5 and FAPα in osteosarcoma cells, suggesting a cell-surface or pericellular signaling role beyond its lysosomal protease function.\",\n      \"evidence\": \"Co-IP, immunofluorescence colocalization, and in vivo tumor growth assay with inhibitors in osteosarcoma cells\",\n      \"pmids\": [\"41086694\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reciprocal Co-IP and stoichiometry not fully established\", \"Functional consequence of LGMN–ITGA5–FAPα complex on protease activity unknown\", \"Context-dependence on polyethylene microplastic exposure limits generalizability\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"METTL3-deposited m6A modification on LGMN mRNA, read by YTHDF1, enhances LGMN translation in macrophages, and elevated LGMN promotes oxidized-LDL-induced ferroptosis and atherosclerotic plaque formation, establishing an epitranscriptomic layer of LGMN regulation with cardiovascular disease relevance.\",\n      \"evidence\": \"m6A mapping, YTHDF1 binding assays, macrophage-specific METTL3 and LGMN knockdown in atherosclerosis mouse model, LGMN overexpression rescue\",\n      \"pmids\": [\"41506595\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which LGMN induces ferroptosis not fully elucidated\", \"Whether m6A regulation of LGMN operates in non-macrophage cell types unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct substrates of legumain beyond cathepsins remain poorly validated, the structural basis for its substrate specificity is unresolved, and the mechanism connecting LGMN protease activity to downstream signaling events (MMP upregulation, AKT/mTOR modulation, ferroptosis induction) has not been defined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No crystal structure of human legumain in complex with a natural substrate\", \"Causal chain from LGMN activity to MMP2/MMP9 transcription not delineated\", \"In vivo contribution of nuclear versus lysosomal LGMN pools unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [9, 6, 5]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [5, 9]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [9, 5]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [4, 5]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [3, 7]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [6, 5, 1]}\n    ],\n    \"complexes\": [\n      \"LGMN–ITGA5–FAPα\"\n    ],\n    \"partners\": [\n      \"CTSL\",\n      \"CTSV\",\n      \"CTSB\",\n      \"CTSD\",\n      \"ITGA5\",\n      \"FAP\",\n      \"CST6\",\n      \"YTHDF1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}