{"gene":"LGMN","run_date":"2026-06-10T02:59:49","timeline":{"discoveries":[{"year":1996,"finding":"LGMN (PRSC1) encodes a novel human cysteine protease of 433 amino acids with 40% sequence identity to Schistosoma japonicum hemoglobinase and 36% identity to a soybean vacuolar-processing cysteine protease, establishing it as a conserved cysteine protease family member; chromosomal location determined at 14q32.1 by fluorescence in situ hybridization.","method":"cDNA cloning, sequence analysis, northern blot, fluorescence in situ hybridization","journal":"Cytogenetics and cell genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — molecular cloning with sequence characterization and chromosomal mapping; single lab, multiple orthogonal methods but no enzymatic validation","pmids":["8893817"],"is_preprint":false},{"year":2016,"finding":"Knockdown of LGMN in breast cancer cells downregulates MMP2 and MMP9 expression and impairs colony formation, migration, and invasion, placing LGMN upstream of matrix metalloproteinases in breast cancer invasiveness.","method":"shRNA-mediated knockdown, western blotting, colony formation assay, invasion assay","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — defined cellular phenotype (migration/invasion) with downstream molecular readout (MMP2/MMP9), single lab, multiple assays","pmids":["27656894"],"is_preprint":false},{"year":2022,"finding":"Metformin induces autophagy in choriocarcinoma cells by suppressing LGMN expression through the AKT/mTOR/LC3II signaling pathway; LGMN knockdown phenocopies metformin-induced inhibition of proliferation and invasion, placing LGMN within the AKT/mTOR autophagy axis.","method":"siRNA knockdown, western blotting, high-throughput sequencing, autophagy inhibitor/inducer pharmacological experiments, xenograft model","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — pathway placement via epistasis (KD phenocopies drug, overexpression rescues), single lab, in vitro and in vivo concordant results","pmids":["36464174"],"is_preprint":false},{"year":2024,"finding":"CRISPR/Cas9-mediated editing of LGMN impairs lysosomal/autophagic degradation and reduces migration, invasion, and experimental lung metastasis of breast cancer cells, demonstrating that LGMN is required for lysosomal/autophagic function and metastatic capacity.","method":"CRISPR/Cas9 gene editing via lipid nanoparticle delivery of Cas9 mRNA + gRNA, invasion/migration assays, experimental lung metastasis model","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined cellular and in vivo phenotype; single lab, in vitro and in vivo orthogonal methods","pmids":["38582932"],"is_preprint":false},{"year":2025,"finding":"LGMN is required for processing of cathepsins L, V, B, and D from single-chain to two-chain form in cells; in LGMN-knockout cells this processing is abrogated. The mechanism is indirect since recombinant legumain does not directly cleave cathepsins in vitro. Loss of LGMN also reduces nuclear localization of cathepsin L (which preferentially exists in double-chain form in the nucleus). N-terminomics (NICE pipeline) identified putative nuclear substrates of LGMN and cathepsin L, suggesting roles in cell proliferation, cell cycle regulation, inflammation, and ribosomal biogenesis.","method":"LGMN-knockout cell lines, chemical activity-based probes, immunoblots, recombinant protein cleavage assay (negative for direct cleavage), chemical N-terminomics (NICE pipeline)","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — multiple orthogonal methods (activity probes, KO cells, in vitro reconstitution negative, N-terminomics), single lab preprint not yet peer-reviewed","pmids":["bio_10.1101_2025.08.17.670765"],"is_preprint":true},{"year":2026,"finding":"METTL3-dependent N6-methyladenosine (m6A) modification of LGMN mRNA enhances its translation via YTHDF1 binding to m6A-methylated LGMN mRNA; elevated LGMN in macrophages promotes ox-LDL-induced ferroptosis, lipid deposition, and inflammatory responses, driving atherosclerosis plaque formation. Macrophage-specific LGMN knockdown reduces plaque formation and ferroptosis in vivo.","method":"RNA-sequencing, m6A modification analysis, YTHDF1 binding assay, macrophage-specific LGMN knockdown (in vivo and in vitro), METTL3 knockdown/overexpression, ferroptosis assays, lipid deposition assays, mouse atherosclerosis model","journal":"Journal of molecular and cellular cardiology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (m6A assay, YTHDF1 binding, KD, rescue with LGMN overexpression, in vivo macrophage-specific KO), mechanistic pathway fully traced from writer (METTL3) to reader (YTHDF1) to effector (LGMN) to phenotype (ferroptosis/AS)","pmids":["41506595"],"is_preprint":false},{"year":2026,"finding":"Macrophage-specific conditional knockout of LGMN (LGMNflox/flox; Lyz2-Cre) inhibits gastric cancer tumor growth by reprogramming TAMs toward an anti-tumor phenotype, reducing Treg cell infiltration, enhancing CD8+ T cell infiltration, and inhibiting tumor angiogenesis by downregulating VEGF-A expression.","method":"Macrophage-specific conditional knockout mouse model, subcutaneous xenograft model, immunofluorescence, tube formation assay, scRNA-seq, bulk RNA-seq analysis","journal":"Frontiers in immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cell-type-specific in vivo KO with defined mechanistic readouts (VEGF-A, Treg, CD8+ T cells); single lab, multiple orthogonal methods","pmids":["42058204"],"is_preprint":false},{"year":2026,"finding":"LGMN is elevated in M2 macrophages and co-localizes with CD206 in fibrotic lung tissue; pharmacological inhibition of LGMN with RR-11a reduces TGF-β1 secretion from M2 macrophages, thereby diminishing macrophage-fibroblast crosstalk and alleviating bleomycin-induced pulmonary fibrosis in mice.","method":"LGMN inhibitor (RR-11a) treatment, immunofluorescence co-localization, TGF-β1 secretion assay, bleomycin pulmonary fibrosis mouse model, in vitro M2 macrophage culture","journal":"Frontiers in immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pharmacological inhibition with defined downstream molecular readout (TGF-β1) and in vivo disease model; single lab, in vitro and in vivo concordant","pmids":["42051490"],"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; polyethylene microplastic exposure upregulates ITGA5, which promotes assembly of this complex and drives cancer progression in a dose-dependent manner. Inhibitors targeting ITGA5, FAPα, or LGMN individually partially alleviate tumor growth in vivo.","method":"Co-immunoprecipitation (Co-IP), immunofluorescence staining, high-throughput sequencing, subcutaneous xenograft mouse model, pharmacological inhibition","journal":"Ecotoxicology and environmental safety","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — reciprocal Co-IP confirms complex formation, but mechanistic dissection of how the complex drives progression is limited; single lab","pmids":["41086694"],"is_preprint":false},{"year":2025,"finding":"CST6 (Cystatin 6), a cysteine protease inhibitor, is a high-affinity target interaction partner of LGMN in the placenta; administration of recombinant CST6 to endothelial cells enhances endothelial dysfunction markers and LGMN expression in the presence of TNFα, suggesting a regulatory relationship between CST6 and LGMN activity.","method":"mRNA expression analysis, recombinant protein treatment, endothelial cell dysfunction assays (TNFα model), human trophoblast stem cell differentiation model","journal":"Scientific reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — indirect evidence of interaction via expression changes after recombinant protein treatment; no direct binding assay performed; single lab","pmids":["40234537"],"is_preprint":false}],"current_model":"LGMN (legumain/asparagine endopeptidase) is a lysosomal cysteine endopeptidase that is required for processing of cathepsins (L, V, B, D) from single-chain to double-chain form (indirectly, not by direct cleavage) and for nuclear localization of cathepsin L; its mRNA translation is enhanced by METTL3-dependent m6A modification read by YTHDF1; in macrophages it promotes ferroptosis, TGF-β1 secretion, and tumor-supportive polarization; and in cancer cells it acts upstream of MMP2/MMP9 and the AKT/mTOR/autophagy axis to drive invasion and metastasis, while also participating in an ITGA5/FAPα/LGMN protein complex that promotes osteosarcoma progression."},"narrative":{"mechanistic_narrative":"LGMN (legumain/asparagine endopeptidase) is a conserved lysosomal cysteine endopeptidase that controls lysosomal/autophagic proteolytic capacity and functions across macrophage immunobiology and tumor progression [PMID:8893817, PMID:38582932]. Within the endolysosomal system, LGMN is required for maturation of cathepsins L, V, B, and D from single-chain to two-chain form and for nuclear localization of cathepsin L; this processing is indirect, since recombinant legumain does not directly cleave these cathepsins [PMID:bio_10.1101_2025.08.17.670765]. Loss of LGMN impairs lysosomal/autophagic degradation and reduces the migratory, invasive, and metastatic capacity of cancer cells, where it acts upstream of MMP2/MMP9 and within an AKT/mTOR/autophagy axis [PMID:27656894, PMID:36464174, PMID:38582932]. LGMN translation is enhanced by METTL3-deposited m6A modification of its mRNA read by YTHDF1, and in macrophages elevated LGMN drives ox-LDL-induced ferroptosis, lipid deposition, and inflammation to promote atherosclerotic plaque formation [PMID:41506595]. In tumor-associated and M2 macrophages, LGMN supports a tumor-supportive, pro-fibrotic program: macrophage-specific deletion reprograms TAMs toward an anti-tumor phenotype, reduces Treg infiltration, increases CD8+ T cell infiltration, and lowers VEGF-A, while pharmacological LGMN inhibition reduces TGF-β1 secretion and macrophage-fibroblast crosstalk [PMID:42058204, PMID:42051490]. LGMN also assembles into an ITGA5/FAPα/LGMN complex that promotes osteosarcoma progression [PMID:41086694].","teleology":[{"year":1996,"claim":"Established LGMN as a distinct human cysteine protease, defining the gene product and placing it within a conserved protease family.","evidence":"cDNA cloning, sequence analysis, and FISH chromosomal mapping to 14q32.1","pmids":["8893817"],"confidence":"Medium","gaps":["No enzymatic activity validated in this study","Substrate repertoire and subcellular localization not defined"]},{"year":2016,"claim":"Placed LGMN upstream of matrix metalloproteinases in cancer cell invasion, linking the protease to an extracellular degradation program.","evidence":"shRNA knockdown in breast cancer cells with MMP2/MMP9 immunoblot and invasion assays","pmids":["27656894"],"confidence":"Medium","gaps":["Mechanism linking LGMN to MMP2/MMP9 expression not resolved","Direct substrates not identified"]},{"year":2022,"claim":"Positioned LGMN within the AKT/mTOR/autophagy axis by showing its suppression phenocopies metformin-induced inhibition of proliferation and invasion.","evidence":"siRNA knockdown, pharmacological autophagy modulation, and xenograft in choriocarcinoma cells","pmids":["36464174"],"confidence":"Medium","gaps":["Whether LGMN acts directly on AKT/mTOR components or downstream is unresolved","Causality vs. correlation in autophagy induction not fully dissected"]},{"year":2024,"claim":"Demonstrated that LGMN is genetically required for lysosomal/autophagic degradation and metastatic capacity, moving beyond expression correlations to loss-of-function.","evidence":"CRISPR/Cas9 editing via LNP delivery with invasion/migration and lung metastasis models in breast cancer cells","pmids":["38582932"],"confidence":"Medium","gaps":["Molecular substrates underlying degradation defect not identified","Single tumor type tested"]},{"year":2025,"claim":"Defined LGMN's lysosomal mechanism by showing it is required for cathepsin (L/V/B/D) maturation and cathepsin L nuclear localization, while establishing the action is indirect.","evidence":"LGMN-knockout cells, activity-based probes, negative recombinant cleavage assay, and N-terminomics (NICE)","pmids":["bio_10.1101_2025.08.17.670765"],"confidence":"Medium","gaps":["Preprint, not yet peer-reviewed","Intermediary linking LGMN to cathepsin processing unidentified","Putative nuclear substrates not validated"]},{"year":2025,"claim":"Identified an ITGA5/FAPα/LGMN protein complex driving osteosarcoma progression, defining LGMN's first characterized physical partners.","evidence":"Reciprocal Co-IP, immunofluorescence, and xenograft with individual inhibitor treatments","pmids":["41086694"],"confidence":"Medium","gaps":["Mechanism by which the complex drives progression not dissected","Stoichiometry and direct vs. bridged interactions unresolved"]},{"year":2025,"claim":"Proposed CST6 as a regulatory interaction partner of LGMN in placental endothelial dysfunction.","evidence":"Recombinant CST6 treatment with expression analysis in TNFα-treated endothelial cells and trophoblast model","pmids":["40234537"],"confidence":"Low","gaps":["No direct binding assay performed; interaction inferred from expression changes","Functional consequence on LGMN enzymatic activity not measured"]},{"year":2026,"claim":"Traced an m6A regulatory circuit (METTL3 writer → YTHDF1 reader) that boosts LGMN translation in macrophages to drive ferroptosis and atherosclerosis.","evidence":"m6A analysis, YTHDF1 binding, METTL3 perturbation, macrophage-specific LGMN knockdown, and mouse atherosclerosis model","pmids":["41506595"],"confidence":"High","gaps":["Protease substrates mediating ferroptosis not identified","Link between LGMN catalytic activity and lipid peroxidation unresolved"]},{"year":2026,"claim":"Showed macrophage LGMN sustains a tumor-supportive and pro-fibrotic microenvironment via TAM polarization, T-cell modulation, VEGF-A, and TGF-β1.","evidence":"Macrophage-specific conditional knockout (gastric cancer) and RR-11a pharmacological inhibition (bleomycin lung fibrosis) with scRNA-seq, immunofluorescence, and secretion assays","pmids":["42058204","42051490"],"confidence":"Medium","gaps":["Direct LGMN substrates controlling VEGF-A and TGF-β1 not defined","Whether effects are cell-autonomous to macrophages or via cathepsin processing is unclear"]},{"year":null,"claim":"The direct proteolytic substrates of LGMN that link its asparagine endopeptidase activity to the diverse phenotypes (cathepsin maturation, MMP regulation, ferroptosis, immune reprogramming) remain unidentified.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No validated direct substrate connects catalytic activity to downstream effectors","Indirect mechanism of cathepsin processing not mechanistically resolved","Structural basis of partner interactions (ITGA5/FAPα) unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[4]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[3,4]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[2,3]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[4]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[6,7]}],"complexes":["ITGA5/FAPα/LGMN complex"],"partners":["ITGA5","FAPALPHA","CST6"],"other_free_text":[]}},"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":43,"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":35,"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":33,"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":"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":"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":"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":8,"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":5,"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":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":"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":1,"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":"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":"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":"42058204","id":"PMC_42058204","title":"LGMN+ macrophage promotes the formation of a tumor-supportive microenvironment in gastric cancer.","date":"2026","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/42058204","citation_count":0,"is_preprint":false},{"pmid":"42051490","id":"PMC_42051490","title":"LGMN promotes crosstalk between macrophages and fibroblasts in pulmonary fibrosis: a potential therapeutic target.","date":"2026","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/42051490","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":13930,"output_tokens":2859,"usd":0.042338,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10191,"output_tokens":3145,"usd":0.06479,"stage2_stop_reason":"end_turn"},"total_usd":0.107128,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1996,\n      \"finding\": \"LGMN (PRSC1) encodes a novel human cysteine protease of 433 amino acids with 40% sequence identity to Schistosoma japonicum hemoglobinase and 36% identity to a soybean vacuolar-processing cysteine protease, establishing it as a conserved cysteine protease family member; chromosomal location determined at 14q32.1 by fluorescence in situ hybridization.\",\n      \"method\": \"cDNA cloning, sequence analysis, northern blot, fluorescence in situ hybridization\",\n      \"journal\": \"Cytogenetics and cell genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — molecular cloning with sequence characterization and chromosomal mapping; single lab, multiple orthogonal methods but no enzymatic validation\",\n      \"pmids\": [\"8893817\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Knockdown of LGMN in breast cancer cells downregulates MMP2 and MMP9 expression and impairs colony formation, migration, and invasion, placing LGMN upstream of matrix metalloproteinases in breast cancer invasiveness.\",\n      \"method\": \"shRNA-mediated knockdown, western blotting, colony formation assay, invasion assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — defined cellular phenotype (migration/invasion) with downstream molecular readout (MMP2/MMP9), single lab, multiple assays\",\n      \"pmids\": [\"27656894\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Metformin induces autophagy in choriocarcinoma cells by suppressing LGMN expression through the AKT/mTOR/LC3II signaling pathway; LGMN knockdown phenocopies metformin-induced inhibition of proliferation and invasion, placing LGMN within the AKT/mTOR autophagy axis.\",\n      \"method\": \"siRNA knockdown, western blotting, high-throughput sequencing, autophagy inhibitor/inducer pharmacological experiments, xenograft model\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — pathway placement via epistasis (KD phenocopies drug, overexpression rescues), single lab, in vitro and in vivo concordant results\",\n      \"pmids\": [\"36464174\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CRISPR/Cas9-mediated editing of LGMN impairs lysosomal/autophagic degradation and reduces migration, invasion, and experimental lung metastasis of breast cancer cells, demonstrating that LGMN is required for lysosomal/autophagic function and metastatic capacity.\",\n      \"method\": \"CRISPR/Cas9 gene editing via lipid nanoparticle delivery of Cas9 mRNA + gRNA, invasion/migration assays, experimental lung metastasis model\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined cellular and in vivo phenotype; single lab, in vitro and in vivo orthogonal methods\",\n      \"pmids\": [\"38582932\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"LGMN is required for processing of cathepsins L, V, B, and D from single-chain to two-chain form in cells; in LGMN-knockout cells this processing is abrogated. The mechanism is indirect since recombinant legumain does not directly cleave cathepsins in vitro. Loss of LGMN also reduces nuclear localization of cathepsin L (which preferentially exists in double-chain form in the nucleus). N-terminomics (NICE pipeline) identified putative nuclear substrates of LGMN and cathepsin L, suggesting roles in cell proliferation, cell cycle regulation, inflammation, and ribosomal biogenesis.\",\n      \"method\": \"LGMN-knockout cell lines, chemical activity-based probes, immunoblots, recombinant protein cleavage assay (negative for direct cleavage), chemical N-terminomics (NICE pipeline)\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — multiple orthogonal methods (activity probes, KO cells, in vitro reconstitution negative, N-terminomics), single lab preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.08.17.670765\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"METTL3-dependent N6-methyladenosine (m6A) modification of LGMN mRNA enhances its translation via YTHDF1 binding to m6A-methylated LGMN mRNA; elevated LGMN in macrophages promotes ox-LDL-induced ferroptosis, lipid deposition, and inflammatory responses, driving atherosclerosis plaque formation. Macrophage-specific LGMN knockdown reduces plaque formation and ferroptosis in vivo.\",\n      \"method\": \"RNA-sequencing, m6A modification analysis, YTHDF1 binding assay, macrophage-specific LGMN knockdown (in vivo and in vitro), METTL3 knockdown/overexpression, ferroptosis assays, lipid deposition assays, mouse atherosclerosis model\",\n      \"journal\": \"Journal of molecular and cellular cardiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (m6A assay, YTHDF1 binding, KD, rescue with LGMN overexpression, in vivo macrophage-specific KO), mechanistic pathway fully traced from writer (METTL3) to reader (YTHDF1) to effector (LGMN) to phenotype (ferroptosis/AS)\",\n      \"pmids\": [\"41506595\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Macrophage-specific conditional knockout of LGMN (LGMNflox/flox; Lyz2-Cre) inhibits gastric cancer tumor growth by reprogramming TAMs toward an anti-tumor phenotype, reducing Treg cell infiltration, enhancing CD8+ T cell infiltration, and inhibiting tumor angiogenesis by downregulating VEGF-A expression.\",\n      \"method\": \"Macrophage-specific conditional knockout mouse model, subcutaneous xenograft model, immunofluorescence, tube formation assay, scRNA-seq, bulk RNA-seq analysis\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cell-type-specific in vivo KO with defined mechanistic readouts (VEGF-A, Treg, CD8+ T cells); single lab, multiple orthogonal methods\",\n      \"pmids\": [\"42058204\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"LGMN is elevated in M2 macrophages and co-localizes with CD206 in fibrotic lung tissue; pharmacological inhibition of LGMN with RR-11a reduces TGF-β1 secretion from M2 macrophages, thereby diminishing macrophage-fibroblast crosstalk and alleviating bleomycin-induced pulmonary fibrosis in mice.\",\n      \"method\": \"LGMN inhibitor (RR-11a) treatment, immunofluorescence co-localization, TGF-β1 secretion assay, bleomycin pulmonary fibrosis mouse model, in vitro M2 macrophage culture\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pharmacological inhibition with defined downstream molecular readout (TGF-β1) and in vivo disease model; single lab, in vitro and in vivo concordant\",\n      \"pmids\": [\"42051490\"],\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; polyethylene microplastic exposure upregulates ITGA5, which promotes assembly of this complex and drives cancer progression in a dose-dependent manner. Inhibitors targeting ITGA5, FAPα, or LGMN individually partially alleviate tumor growth in vivo.\",\n      \"method\": \"Co-immunoprecipitation (Co-IP), immunofluorescence staining, high-throughput sequencing, subcutaneous xenograft mouse model, pharmacological inhibition\",\n      \"journal\": \"Ecotoxicology and environmental safety\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — reciprocal Co-IP confirms complex formation, but mechanistic dissection of how the complex drives progression is limited; single lab\",\n      \"pmids\": [\"41086694\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CST6 (Cystatin 6), a cysteine protease inhibitor, is a high-affinity target interaction partner of LGMN in the placenta; administration of recombinant CST6 to endothelial cells enhances endothelial dysfunction markers and LGMN expression in the presence of TNFα, suggesting a regulatory relationship between CST6 and LGMN activity.\",\n      \"method\": \"mRNA expression analysis, recombinant protein treatment, endothelial cell dysfunction assays (TNFα model), human trophoblast stem cell differentiation model\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — indirect evidence of interaction via expression changes after recombinant protein treatment; no direct binding assay performed; single lab\",\n      \"pmids\": [\"40234537\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LGMN (legumain/asparagine endopeptidase) is a lysosomal cysteine endopeptidase that is required for processing of cathepsins (L, V, B, D) from single-chain to double-chain form (indirectly, not by direct cleavage) and for nuclear localization of cathepsin L; its mRNA translation is enhanced by METTL3-dependent m6A modification read by YTHDF1; in macrophages it promotes ferroptosis, TGF-β1 secretion, and tumor-supportive polarization; and in cancer cells it acts upstream of MMP2/MMP9 and the AKT/mTOR/autophagy axis to drive invasion and metastasis, while also participating in an ITGA5/FAPα/LGMN protein complex that promotes osteosarcoma progression.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LGMN (legumain/asparagine endopeptidase) is a conserved lysosomal cysteine endopeptidase that controls lysosomal/autophagic proteolytic capacity and functions across macrophage immunobiology and tumor progression [#0, #3]. Within the endolysosomal system, LGMN is required for maturation of cathepsins L, V, B, and D from single-chain to two-chain form and for nuclear localization of cathepsin L; this processing is indirect, since recombinant legumain does not directly cleave these cathepsins [#4]. Loss of LGMN impairs lysosomal/autophagic degradation and reduces the migratory, invasive, and metastatic capacity of cancer cells, where it acts upstream of MMP2/MMP9 and within an AKT/mTOR/autophagy axis [#1, #2, #3]. LGMN translation is enhanced by METTL3-deposited m6A modification of its mRNA read by YTHDF1, and in macrophages elevated LGMN drives ox-LDL-induced ferroptosis, lipid deposition, and inflammation to promote atherosclerotic plaque formation [#5]. In tumor-associated and M2 macrophages, LGMN supports a tumor-supportive, pro-fibrotic program: macrophage-specific deletion reprograms TAMs toward an anti-tumor phenotype, reduces Treg infiltration, increases CD8+ T cell infiltration, and lowers VEGF-A, while pharmacological LGMN inhibition reduces TGF-\\u03b21 secretion and macrophage-fibroblast crosstalk [#6, #7]. LGMN also assembles into an ITGA5/FAP\\u03b1/LGMN complex that promotes osteosarcoma progression [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Established LGMN as a distinct human cysteine protease, defining the gene product and placing it within a conserved protease family.\",\n      \"evidence\": \"cDNA cloning, sequence analysis, and FISH chromosomal mapping to 14q32.1\",\n      \"pmids\": [\"8893817\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No enzymatic activity validated in this study\", \"Substrate repertoire and subcellular localization not defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Placed LGMN upstream of matrix metalloproteinases in cancer cell invasion, linking the protease to an extracellular degradation program.\",\n      \"evidence\": \"shRNA knockdown in breast cancer cells with MMP2/MMP9 immunoblot and invasion assays\",\n      \"pmids\": [\"27656894\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking LGMN to MMP2/MMP9 expression not resolved\", \"Direct substrates not identified\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Positioned LGMN within the AKT/mTOR/autophagy axis by showing its suppression phenocopies metformin-induced inhibition of proliferation and invasion.\",\n      \"evidence\": \"siRNA knockdown, pharmacological autophagy modulation, and xenograft in choriocarcinoma cells\",\n      \"pmids\": [\"36464174\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether LGMN acts directly on AKT/mTOR components or downstream is unresolved\", \"Causality vs. correlation in autophagy induction not fully dissected\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated that LGMN is genetically required for lysosomal/autophagic degradation and metastatic capacity, moving beyond expression correlations to loss-of-function.\",\n      \"evidence\": \"CRISPR/Cas9 editing via LNP delivery with invasion/migration and lung metastasis models in breast cancer cells\",\n      \"pmids\": [\"38582932\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular substrates underlying degradation defect not identified\", \"Single tumor type tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined LGMN's lysosomal mechanism by showing it is required for cathepsin (L/V/B/D) maturation and cathepsin L nuclear localization, while establishing the action is indirect.\",\n      \"evidence\": \"LGMN-knockout cells, activity-based probes, negative recombinant cleavage assay, and N-terminomics (NICE)\",\n      \"pmids\": [\"bio_10.1101_2025.08.17.670765\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not yet peer-reviewed\", \"Intermediary linking LGMN to cathepsin processing unidentified\", \"Putative nuclear substrates not validated\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified an ITGA5/FAP\\u03b1/LGMN protein complex driving osteosarcoma progression, defining LGMN's first characterized physical partners.\",\n      \"evidence\": \"Reciprocal Co-IP, immunofluorescence, and xenograft with individual inhibitor treatments\",\n      \"pmids\": [\"41086694\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which the complex drives progression not dissected\", \"Stoichiometry and direct vs. bridged interactions unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Proposed CST6 as a regulatory interaction partner of LGMN in placental endothelial dysfunction.\",\n      \"evidence\": \"Recombinant CST6 treatment with expression analysis in TNF\\u03b1-treated endothelial cells and trophoblast model\",\n      \"pmids\": [\"40234537\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct binding assay performed; interaction inferred from expression changes\", \"Functional consequence on LGMN enzymatic activity not measured\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Traced an m6A regulatory circuit (METTL3 writer \\u2192 YTHDF1 reader) that boosts LGMN translation in macrophages to drive ferroptosis and atherosclerosis.\",\n      \"evidence\": \"m6A analysis, YTHDF1 binding, METTL3 perturbation, macrophage-specific LGMN knockdown, and mouse atherosclerosis model\",\n      \"pmids\": [\"41506595\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Protease substrates mediating ferroptosis not identified\", \"Link between LGMN catalytic activity and lipid peroxidation unresolved\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Showed macrophage LGMN sustains a tumor-supportive and pro-fibrotic microenvironment via TAM polarization, T-cell modulation, VEGF-A, and TGF-\\u03b21.\",\n      \"evidence\": \"Macrophage-specific conditional knockout (gastric cancer) and RR-11a pharmacological inhibition (bleomycin lung fibrosis) with scRNA-seq, immunofluorescence, and secretion assays\",\n      \"pmids\": [\"42058204\", \"42051490\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct LGMN substrates controlling VEGF-A and TGF-\\u03b21 not defined\", \"Whether effects are cell-autonomous to macrophages or via cathepsin processing is unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct proteolytic substrates of LGMN that link its asparagine endopeptidase activity to the diverse phenotypes (cathepsin maturation, MMP regulation, ferroptosis, immune reprogramming) remain unidentified.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No validated direct substrate connects catalytic activity to downstream effectors\", \"Indirect mechanism of cathepsin processing not mechanistically resolved\", \"Structural basis of partner interactions (ITGA5/FAP\\u03b1) unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0008234\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [6, 7]}\n    ],\n    \"complexes\": [\n      \"ITGA5/FAP\\u03b1/LGMN complex\"\n    ],\n    \"partners\": [\n      \"ITGA5\",\n      \"FAPalpha\",\n      \"CST6\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":5,"faith_total":5,"faith_pct":100.0}}