{"gene":"LOXL4","run_date":"2026-04-28T18:30:27","timeline":{"discoveries":[{"year":2001,"finding":"LOXL4 was identified as a novel copper-dependent amine oxidase with a conserved C-terminal region including a copper-binding site, lysyl and tyrosyl residues, and a cytokine receptor-like domain, plus four N-terminal scavenger receptor cysteine-rich (SRCR) domains (one with a unique 13 aa insertion). The 3.5-kb mRNA is expressed in pancreas, testis, fibroblasts, smooth muscle, and osteosarcoma cells.","method":"cDNA cloning, sequence analysis, Northern blotting, domain mapping","journal":"Matrix biology","confidence":"High","confidence_rationale":"Tier 1 — original gene characterization with sequence, domain architecture, and expression profiling; foundational paper","pmids":["11691588"],"is_preprint":false},{"year":2007,"finding":"LOXL4 acts as a tumor suppressor in bladder cancer: reintroduction of LOXL4 into bladder cancer cells decreased colony formation and antagonized Ras-mediated activation of the ERK signaling pathway. The gene is silenced by promoter hypermethylation in bladder cancer.","method":"Pharmacologic unmasking, microarray, gene reintroduction, colony formation assay, ERK pathway western blotting, methylation analysis","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 — clean KO/OE with defined cellular phenotype and pathway placement (Ras/ERK), single lab","pmids":["17456585"],"is_preprint":false},{"year":2008,"finding":"LOXL4 gene transcription in HNSCC is driven by a promoter region spanning -960 to -1, with increased nuclear binding to TATA (-25) and SP1 (-181) sites in tumor cells. Promoter constructs with these elements showed significantly elevated reporter activity in HNSCC but not normal epithelial cells.","method":"Deletion mapping, promoter-reporter constructs, DNA-binding (EMSA) experiments with nuclear extracts","journal":"International journal of oncology","confidence":"Medium","confidence_rationale":"Tier 2 — promoter deletion mapping and DNA-binding assays in matched cell types, single lab","pmids":["18949373"],"is_preprint":false},{"year":2008,"finding":"LOXL4 protein is localized pericellularly (perinuclear and cell surface, but not nuclear) in HTB-43 hypopharyngeal carcinoma cells, consistent with a role in extracellular matrix interactions via its SRCR domains and catalytic amine oxidase activity.","method":"Immunocytochemistry in cultured primary carcinoma cells with specific anti-LOXL4 antibody","journal":"European journal of cancer","confidence":"Medium","confidence_rationale":"Tier 3 — direct localization experiment with specific antibody, single lab","pmids":["18499440"],"is_preprint":false},{"year":2013,"finding":"TGF-β1 induces LOXL4 expression in aortic endothelial cells through a mechanism requiring both a distal AP-1 site (bound by JunB/Fra2) and a Smad binding element in the LOXL4 promoter, with ERK-dependent phosphorylation of Fra2 being required for functional cooperation between Smad and AP-1. LOXL4 is secreted extracellularly and contributes to ECM deposition and assembly.","method":"Promoter deletion mapping, site-directed mutagenesis, reporter assays, chromatin immunoprecipitation, ERK inhibition, western blotting, ECM deposition assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 — promoter mutagenesis, ChIP, and functional reconstitution with orthogonal methods in a single rigorous study","pmids":["23572561"],"is_preprint":false},{"year":2014,"finding":"LOXL4 promotes gastric cancer cell proliferation, migration, and invasion via activation of the FAK/Src pathway and enhancement of cell-ECM adhesion. Both overexpression and recombinant human LOXL4 protein promote these phenotypes, while knockdown inhibits them.","method":"Overexpression, siRNA knockdown, recombinant protein treatment, migration/invasion assays, FAK/Src western blotting","journal":"Journal of cancer research and clinical oncology","confidence":"Medium","confidence_rationale":"Tier 2 — multiple functional assays (KO, OE, recombinant protein) with pathway western blotting, single lab","pmids":["25216702"],"is_preprint":false},{"year":2014,"finding":"LOXL4 is a direct target of miR-193a-3p; forced reduction of miR-193a-3p or elevation of LOXL4 activates the Oxidative Stress pathway, which mediates multi-drug resistance in bladder cancer cells and xenografts.","method":"miRNA overexpression/inhibition, luciferase reporter assay, oxidative stress pathway analysis, xenograft model","journal":"Molecular cancer","confidence":"Medium","confidence_rationale":"Tier 2 — direct target validation by luciferase assay plus in vivo xenograft, single lab","pmids":["25311867"],"is_preprint":false},{"year":2017,"finding":"LOXL4 knockdown in triple-negative breast cancer cells increases collagen I and IV levels, induces thickening of collagen bundles (detected by second harmonic generation imaging), and promotes primary tumor growth and lung metastasis in mouse xenografts, demonstrating that LOXL4 suppresses pathological collagen remodeling in this context.","method":"shRNA knockdown, mouse xenograft model, second harmonic generation imaging, western blotting","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo loss-of-function with defined ECM phenotype and imaging, single lab","pmids":["28060764"],"is_preprint":false},{"year":2019,"finding":"Intracellular (but not extracellular) LOXL4 promotes HCC cell migration by activating the FAK/Src pathway through a hydrogen peroxide-mediated mechanism dependent on its amine oxidase activity. HCC-derived exosomes transfer LOXL4 between cancer cells and to endothelial cells (HUVECs), promoting angiogenesis via a paracrine mechanism.","method":"Overexpression, shRNA knockdown, recombinant protein, deletion mutants, exosome isolation and transfer assays, FAK/Src western blotting, angiogenesis assays, in vivo metastasis model","journal":"Molecular cancer","confidence":"High","confidence_rationale":"Tier 1-2 — domain deletion mutants, catalytic activity dependence, and exosome transfer validated by multiple orthogonal assays and in vivo model; highly cited","pmids":["30704479"],"is_preprint":false},{"year":2019,"finding":"LOXL4 binds directly to the basic domain of p53 via its low-isoelectric point region, inducing reactivation of wild-type p53 and triggering cell death. 5-azacytidine treatment upregulates LOXL4, which then activates the LOXL4-p53 axis to reduce liver tumor growth.","method":"Genome-wide screen, co-immunoprecipitation, domain binding assays, nude mouse xenograft model","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP with domain mapping and in vivo validation, single lab","pmids":["30728460"],"is_preprint":false},{"year":2020,"finding":"EZH2 epigenetically silences miR-29b and miR-30d (via promoter H3K27 methylation), which directly target LOXL4 mRNA; EZH2 inhibition de-represses these miRNAs, reducing LOXL4 levels. LOXL4 knockdown or miR-29b/miR-30d overexpression decreased breast cancer proliferation, migration, and metastasis in vitro and in vivo, and reduced macrophage infiltration.","method":"ChIP, dual-luciferase reporter assay, qRT-PCR, western blotting, proliferation/migration assays, xenograft, flow cytometry","journal":"Theranostics","confidence":"High","confidence_rationale":"Tier 1-2 — ChIP confirms EZH2 promoter binding, luciferase confirms miRNA targeting of LOXL4, multiple orthogonal methods, in vivo validation","pmids":["32754259"],"is_preprint":false},{"year":2023,"finding":"LOXL4, but not LOXL2, is the critical enzyme for pathological collagen cross-linking and fibrosis in the lung. Genetic ablation of LOXL4 markedly disrupts collagen cross-linking and fibrosis, while LOXL2 knockout has only modest effects. LOXL4 deficiency also decreases expression of other LOX family members including LOXL2.","method":"Genetic knockout (Loxl4-/- and Loxl2-/- mice), pulmonary fibrosis model, collagen cross-linking biochemical assays, gene expression analysis","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1 — clean genetic ablation in vivo with direct biochemical measurement of collagen cross-linking; definitive epistasis between LOX family members","pmids":["37235663"],"is_preprint":false},{"year":2023,"finding":"LOXL4 delivered into macrophages via tumor cell-derived extracellular vesicles activates STAT1, which induces PD-L1 expression in macrophages, suppresses CD8+ T cell killing activity, and promotes immune escape of HCC cells in vivo.","method":"EV isolation/transfer assays, macrophage co-culture with CD8+ T cells, STAT1/PD-L1 western blotting, mouse HCC orthotopic xenograft","journal":"Journal of immunotherapy","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro and in vivo functional assays with defined signaling pathway (STAT1/PD-L1), single lab","pmids":["38047403"],"is_preprint":false},{"year":2023,"finding":"Zinc-bound ZEB1 (via its zinc-finger domain) transcriptionally activates LOXL1 and LOXL4, promoting cancer cell invasion in triple-negative breast cancer. Expression of a zinc-finger-deleted ZEB1 mutant significantly downregulates LOXL1 and LOXL4 and stalls invasion.","method":"Stable MutZEB1 (ΔZn) expression, RNA-Seq transcriptome analysis, invasion assays","journal":"Frontiers in oncology","confidence":"Medium","confidence_rationale":"Tier 2 — domain mutant plus RNA-Seq with invasion phenotype, single lab","pmids":["36910659"],"is_preprint":false},{"year":2025,"finding":"TGF-β1 decreases LOXL4 protein expression in MDA-MB-231 breast cancer cells via MEK/ERK-dependent proteasomal degradation (not at the mRNA level). Bortezomib (proteasomal inhibitor) and MEK/ERK pathway inhibition suppress this TGF-β1-mediated LOXL4 reduction. N-glycosylation is required for LOXL4 secretion.","method":"Western blotting, proteasomal inhibitor (bortezomib) treatment, MEK/ERK pathway inhibition, N-glycosylation perturbation, ROS measurement","journal":"Journal of receptor and signal transduction research","confidence":"Medium","confidence_rationale":"Tier 2 — multiple inhibitors with defined pathway, distinguishes mRNA vs. protein regulation, single lab","pmids":["39862152"],"is_preprint":false},{"year":2025,"finding":"LOXL4 promotes osteosarcoma cell proliferation, invasion, and EMT via activation of the Wnt/β-catenin signaling pathway; inhibition of Wnt/β-catenin with XAV-939 reverses LOXL4-induced oncogenic effects.","method":"CCK-8, colony formation, Matrigel transwell assays, western blotting, GSEA, Wnt/β-catenin inhibitor (XAV-939) rescue experiment","journal":"Discover oncology","confidence":"Medium","confidence_rationale":"Tier 2 — OE/KD with pathway inhibitor rescue, single lab","pmids":["41118012"],"is_preprint":false}],"current_model":"LOXL4 is a secreted, copper-dependent amine oxidase that cross-links collagen and elastin in the extracellular matrix (with LOXL4 being the dominant LOX enzyme for pathological collagen cross-linking in lung fibrosis); intracellularly, it activates the FAK/Src pathway via hydrogen peroxide generated by its amine oxidase activity to promote cell migration, binds the basic domain of p53 to reactivate it, and is transcriptionally induced by TGF-β1 through cooperative Smad/JunB-Fra2(AP-1) binding at its promoter; it is also packaged into tumor-derived exosomes/EVs and transferred to macrophages to activate STAT1/PD-L1-mediated immune suppression, regulated upstream by EZH2-silenced miR-29b/miR-30d and Zn²⁺-activated ZEB1, and subject to TGF-β1-induced MEK/ERK-dependent proteasomal degradation."},"narrative":{"teleology":[{"year":2001,"claim":"Identification of LOXL4 as a novel LOX family member established its domain architecture—four N-terminal SRCR domains plus a conserved C-terminal copper-dependent amine oxidase domain—and defined its tissue expression profile, providing the molecular framework for all subsequent functional studies.","evidence":"cDNA cloning, sequence/domain analysis, and Northern blotting across human tissues and cell lines","pmids":["11691588"],"confidence":"High","gaps":["No enzymatic activity assay was performed","Function of the SRCR domains remained uncharacterized","No loss-of-function data"]},{"year":2007,"claim":"Demonstration that LOXL4 re-expression suppresses colony formation and antagonizes Ras/ERK signaling in bladder cancer revealed its first intracellular signaling role and identified promoter hypermethylation as a silencing mechanism, establishing LOXL4 as a context-dependent tumor suppressor.","evidence":"Gene reintroduction, colony formation, ERK western blotting, and methylation analysis in bladder cancer cells","pmids":["17456585"],"confidence":"Medium","gaps":["Mechanism linking LOXL4 to ERK inhibition not defined","Tumor-suppressive function not validated in vivo","Epigenetic silencing not confirmed in independent cohorts"]},{"year":2008,"claim":"Mapping the LOXL4 promoter in HNSCC cells identified TATA and SP1 elements as drivers of its tumor-specific transcription, and immunocytochemistry placed the protein pericellularly (perinuclear and cell-surface), setting the stage for understanding both its transcriptional regulation and its dual intra-/extracellular activity.","evidence":"Promoter deletion/reporter mapping, EMSA, and immunocytochemistry in carcinoma versus normal cells","pmids":["18949373","18499440"],"confidence":"Medium","gaps":["Specific transcription factors binding SP1/TATA sites not identified","Localization studied in a single cell line","Mechanism of secretion not addressed"]},{"year":2013,"claim":"Elucidation of TGF-β1-driven LOXL4 transcription through cooperative Smad and JunB/Fra2(AP-1) binding—with ERK-dependent Fra2 phosphorylation required for this cooperation—provided the first complete signaling-to-transcription circuit for LOXL4 induction and linked it to ECM deposition.","evidence":"Promoter mutagenesis, ChIP, reporter assays, ERK inhibition, and ECM deposition assays in aortic endothelial cells","pmids":["23572561"],"confidence":"High","gaps":["Whether this mechanism operates in non-endothelial contexts was not tested","Relative contribution of LOXL4 versus other LOX enzymes to TGF-β1-induced ECM remodeling was unknown"]},{"year":2014,"claim":"Multiple studies demonstrated that LOXL4 promotes gastric cancer cell migration/invasion through FAK/Src pathway activation and is a direct target of miR-193a-3p, which when lost drives oxidative stress-mediated multidrug resistance—establishing LOXL4's pro-oncogenic intracellular signaling axis and its post-transcriptional regulation.","evidence":"Overexpression, knockdown, recombinant protein, FAK/Src western blotting in gastric cancer; miRNA luciferase reporter, xenograft in bladder cancer","pmids":["25216702","25311867"],"confidence":"Medium","gaps":["Catalytic activity dependence of FAK/Src activation not tested in these systems","Oxidative stress pathway mechanism downstream of LOXL4 undefined"]},{"year":2017,"claim":"Loss-of-function studies in triple-negative breast cancer showed that LOXL4 knockdown increases collagen I/IV levels and thickened collagen bundles while promoting tumor growth and lung metastasis, revealing its role in restraining pathological collagen remodeling in the tumor microenvironment.","evidence":"shRNA knockdown, mouse xenograft, second harmonic generation imaging, western blotting","pmids":["28060764"],"confidence":"Medium","gaps":["Biochemical mechanism of collagen regulation (cross-linking vs. transcriptional) not distinguished","Contradicts pro-oncogenic roles observed in other cancers—context dependence not resolved"]},{"year":2019,"claim":"Two key mechanistic advances established that (1) intracellular LOXL4 activates FAK/Src specifically through H₂O₂ generated by its amine oxidase catalytic activity and is transferred between cells via exosomes to promote angiogenesis, and (2) LOXL4 directly binds the basic domain of p53 to reactivate it and induce tumor cell death, revealing dual pro- and anti-tumorigenic intracellular functions dependent on distinct protein–protein interactions.","evidence":"Domain deletion mutants, catalytic-dead constructs, exosome isolation/transfer, and angiogenesis assays in HCC; co-immunoprecipitation with domain mapping and xenograft for p53 interaction","pmids":["30704479","30728460"],"confidence":"High","gaps":["Identity of intracellular amine oxidase substrates that generate H₂O₂ unknown","p53 interaction confirmed by co-IP but lacks structural or biophysical validation","Whether exosomal and p53-activating functions occur in the same cell context is unclear"]},{"year":2020,"claim":"Discovery that EZH2 epigenetically silences miR-29b and miR-30d via H3K27me3 at their promoters, and that these miRNAs directly target LOXL4 mRNA, defined a complete upstream epigenetic circuit controlling LOXL4 abundance and linked it to macrophage infiltration in breast cancer.","evidence":"ChIP for H3K27me3, dual-luciferase reporter for miRNA–LOXL4 3′UTR, in vivo xenograft with flow cytometry for immune infiltrates","pmids":["32754259"],"confidence":"High","gaps":["Whether EZH2–miR-29b/30d–LOXL4 axis operates outside breast cancer not tested","Mechanism by which LOXL4 promotes macrophage infiltration not defined at this point"]},{"year":2023,"claim":"Three studies collectively resolved critical questions: (1) genetic knockout proved LOXL4—not LOXL2—is the dominant enzyme for pathological collagen cross-linking and lung fibrosis in vivo; (2) tumor EV-delivered LOXL4 activates STAT1/PD-L1 in macrophages to suppress CD8⁺ T cell killing; and (3) zinc-finger-dependent ZEB1 transcriptionally activates LOXL4 to promote cancer invasion.","evidence":"Loxl4⁻/⁻ versus Loxl2⁻/⁻ mice with collagen cross-link biochemistry; EV transfer, macrophage co-culture with CD8⁺ T cells, orthotopic HCC model; ZEB1 zinc-finger deletion mutant with RNA-Seq in TNBC","pmids":["37235663","38047403","36910659"],"confidence":"High","gaps":["Specific collagen cross-link types catalyzed by LOXL4 in vivo not resolved","Mechanism of STAT1 activation by LOXL4 protein not delineated","Direct ZEB1 binding to LOXL4 promoter not confirmed by ChIP"]},{"year":2025,"claim":"TGF-β1 was shown to reduce LOXL4 protein (but not mRNA) through MEK/ERK-dependent proteasomal degradation in breast cancer, and N-glycosylation was identified as required for LOXL4 secretion, while a separate study linked LOXL4 to Wnt/β-catenin activation in osteosarcoma—expanding the repertoire of downstream pathways and revealing post-translational control mechanisms.","evidence":"Proteasome/MEK inhibitor studies, N-glycosylation perturbation in MDA-MB-231; OE/KD with XAV-939 Wnt inhibitor rescue in osteosarcoma cells","pmids":["39862152","41118012"],"confidence":"Medium","gaps":["E3 ubiquitin ligase mediating LOXL4 proteasomal degradation not identified","Whether Wnt/β-catenin activation is direct or indirect downstream of LOXL4 unknown","Glycosylation sites required for secretion not mapped"]},{"year":null,"claim":"Key unresolved questions include the identity of LOXL4's intracellular amine oxidase substrates that generate H₂O₂, the structural basis for LOXL4–p53 and LOXL4–STAT1 interactions, whether the apparently contradictory tumor-suppressive and oncogenic roles reflect cell-type-specific cofactors or splice variants, and whether LOXL4 inhibition can attenuate fibrosis and immune suppression therapeutically.","evidence":"","pmids":[],"confidence":"Low","gaps":["No crystal or cryo-EM structure of LOXL4 available","No LOXL4-selective small-molecule inhibitor characterized","Intracellular substrates and cofactors remain unidentified"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016491","term_label":"oxidoreductase activity","supporting_discovery_ids":[0,8,11]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[8,11]}],"localization":[{"term_id":"GO:0005576","term_label":"extracellular region","supporting_discovery_ids":[3,4,8,11]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[8,12]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3,8]}],"pathway":[{"term_id":"R-HSA-1474244","term_label":"Extracellular matrix organization","supporting_discovery_ids":[4,7,11]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[1,5,8,15]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[12]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[9]}],"complexes":[],"partners":["TP53","STAT1","FAK","SRC","ZEB1","JUNB","FRA2"],"other_free_text":[]},"mechanistic_narrative":"LOXL4 is a copper-dependent amine oxidase that functions as the principal enzyme for pathological collagen cross-linking in vivo and as a context-dependent signaling mediator in cancer biology. Its conserved C-terminal catalytic domain catalyzes oxidative deamination of lysine residues in collagen and elastin; genetic ablation in mice demonstrates that LOXL4, rather than LOXL2, is the dominant LOX family member required for collagen cross-link formation and fibrosis in the lung [PMID:37235663]. Intracellularly, LOXL4 activates the FAK/Src pathway through hydrogen peroxide generated by its amine oxidase activity to promote cell migration [PMID:30704479], directly binds the basic domain of p53 to reactivate it and trigger cell death [PMID:30728460], and is transferred via tumor-derived extracellular vesicles to macrophages where it activates STAT1-dependent PD-L1 expression to suppress CD8⁺ T cell cytotoxicity [PMID:38047403]. Transcription of LOXL4 is induced by TGF-β1 through cooperative Smad and JunB/Fra2(AP-1) binding at its promoter [PMID:23572561], upregulated by zinc-dependent ZEB1 [PMID:36910659], and repressed by EZH2-dependent silencing of miR-29b and miR-30d that directly target LOXL4 mRNA [PMID:32754259]."},"prefetch_data":{"uniprot":{"accession":"Q96JB6","full_name":"Lysyl oxidase homolog 4","aliases":["Lysyl oxidase-like protein 4","Lysyl oxidase-related protein C"],"length_aa":756,"mass_kda":84.5,"function":"Catalyzes the oxidative deamination of lysine and hydroxylysine residues in collagen and elastin, resulting in the formation of covalent cross-linkages, and the stabilization of collagen and elastin fibers","subcellular_location":"Secreted, extracellular space","url":"https://www.uniprot.org/uniprotkb/Q96JB6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/LOXL4","classification":"Not Classified","n_dependent_lines":4,"n_total_lines":1208,"dependency_fraction":0.0033112582781456954},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/LOXL4","total_profiled":1310},"omim":[{"mim_id":"607318","title":"LYSYL OXIDASE-LIKE 4; LOXL4","url":"https://www.omim.org/entry/607318"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Vesicles","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/LOXL4"},"hgnc":{"alias_symbol":["FLJ21889","LOXC"],"prev_symbol":[]},"alphafold":{"accession":"Q96JB6","domains":[{"cath_id":"3.10.250.10","chopping":"32-144","consensus_level":"high","plddt":88.5652,"start":32,"end":144},{"cath_id":"3.10.250.10","chopping":"157-288","consensus_level":"medium","plddt":88.6336,"start":157,"end":288},{"cath_id":"3.10.250.10","chopping":"312-412","consensus_level":"medium","plddt":91.6695,"start":312,"end":412},{"cath_id":"3.10.250.10","chopping":"422-530","consensus_level":"high","plddt":91.2803,"start":422,"end":530},{"cath_id":"-","chopping":"536-752","consensus_level":"high","plddt":89.8127,"start":536,"end":752}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JB6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JB6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JB6-F1-predicted_aligned_error_v6.png","plddt_mean":86.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LOXL4","jax_strain_url":"https://www.jax.org/strain/search?query=LOXL4"},"sequence":{"accession":"Q96JB6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96JB6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96JB6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JB6"}},"corpus_meta":[{"pmid":"30704479","id":"PMC_30704479","title":"Exosome-mediated secretion of LOXL4 promotes hepatocellular carcinoma cell invasion and metastasis.","date":"2019","source":"Molecular cancer","url":"https://pubmed.ncbi.nlm.nih.gov/30704479","citation_count":190,"is_preprint":false},{"pmid":"17456585","id":"PMC_17456585","title":"LOXL1 and LOXL4 are epigenetically silenced and can inhibit ras/extracellular signal-regulated kinase signaling pathway in human bladder cancer.","date":"2007","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/17456585","citation_count":94,"is_preprint":false},{"pmid":"23572561","id":"PMC_23572561","title":"LOXL4 is induced by transforming growth factor β1 through Smad and JunB/Fra2 and contributes to vascular matrix remodeling.","date":"2013","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/23572561","citation_count":78,"is_preprint":false},{"pmid":"25311867","id":"PMC_25311867","title":"miR-193a-3p regulates the multi-drug resistance of bladder cancer by targeting the LOXL4 gene and the oxidative stress pathway.","date":"2014","source":"Molecular cancer","url":"https://pubmed.ncbi.nlm.nih.gov/25311867","citation_count":75,"is_preprint":false},{"pmid":"11691588","id":"PMC_11691588","title":"A novel human lysyl oxidase-like gene (LOXL4) on chromosome 10q24 has an altered scavenger receptor cysteine rich domain.","date":"2001","source":"Matrix biology : journal of the International Society for Matrix Biology","url":"https://pubmed.ncbi.nlm.nih.gov/11691588","citation_count":73,"is_preprint":false},{"pmid":"32754259","id":"PMC_32754259","title":"EZH2-mediated Epigenetic Silencing of miR-29/miR-30 targets LOXL4 and contributes to Tumorigenesis, Metastasis, and Immune Microenvironment Remodeling in Breast Cancer.","date":"2020","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/32754259","citation_count":70,"is_preprint":false},{"pmid":"25216702","id":"PMC_25216702","title":"Lysyl oxidase-like 4 (LOXL4) promotes proliferation and metastasis of gastric cancer via FAK/Src pathway.","date":"2014","source":"Journal of cancer research and clinical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/25216702","citation_count":55,"is_preprint":false},{"pmid":"28060764","id":"PMC_28060764","title":"LOXL4 knockdown enhances tumor growth and lung metastasis through collagen-dependent extracellular matrix changes in triple-negative breast cancer.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/28060764","citation_count":47,"is_preprint":false},{"pmid":"30728460","id":"PMC_30728460","title":"Derepression of LOXL4 inhibits liver cancer growth by reactivating compromised p53.","date":"2019","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/30728460","citation_count":42,"is_preprint":false},{"pmid":"37235663","id":"PMC_37235663","title":"LOXL4, but not LOXL2, is the critical determinant of pathological collagen cross-linking and fibrosis in the lung.","date":"2023","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/37235663","citation_count":39,"is_preprint":false},{"pmid":"17354256","id":"PMC_17354256","title":"Selective upregulation and amplification of the lysyl oxidase like-4 (LOXL4) gene in head and neck squamous cell carcinoma.","date":"2007","source":"The Journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/17354256","citation_count":37,"is_preprint":false},{"pmid":"30993701","id":"PMC_30993701","title":"Downregulation of lysyl oxidase-like 4 LOXL4 by miR-135a-5p promotes lung cancer progression in vitro and in vivo.","date":"2019","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/30993701","citation_count":31,"is_preprint":false},{"pmid":"18499440","id":"PMC_18499440","title":"LOXL4 is a selectively expressed candidate diagnostic antigen in head and neck cancer.","date":"2008","source":"European journal of cancer (Oxford, England : 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acids","url":"https://pubmed.ncbi.nlm.nih.gov/30900087","citation_count":12,"is_preprint":false},{"pmid":"38047403","id":"PMC_38047403","title":"LOXL4 Shuttled by Tumor Cells-derived Extracellular Vesicles Promotes Immune Escape in Hepatocellular Carcinoma by Activating the STAT1/PD-L1 Axis.","date":"2023","source":"Journal of immunotherapy (Hagerstown, Md. : 1997)","url":"https://pubmed.ncbi.nlm.nih.gov/38047403","citation_count":12,"is_preprint":false},{"pmid":"37197500","id":"PMC_37197500","title":"miR-183-5p regulates ECM and EMT to promote non-small cell lung cancer progression by targeting LOXL4.","date":"2023","source":"Journal of thoracic disease","url":"https://pubmed.ncbi.nlm.nih.gov/37197500","citation_count":11,"is_preprint":false},{"pmid":"35433959","id":"PMC_35433959","title":"Overexpression of miR-328-5p influences cell growth and migration to promote NSCLC progression by targeting LOXL4.","date":"2022","source":"Annals of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35433959","citation_count":10,"is_preprint":false},{"pmid":"33807332","id":"PMC_33807332","title":"LOXL4 Abrogation Does Not Exaggerate Angiotensin II-Induced Thoracic or Abdominal Aortic Aneurysm in Mice.","date":"2021","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/33807332","citation_count":9,"is_preprint":false},{"pmid":"36910659","id":"PMC_36910659","title":"LOXL1 and LOXL4 are novel target genes of the Zn2+-bound form of ZEB1 and play a crucial role in the acceleration of invasive events in triple-negative breast cancer cells.","date":"2023","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/36910659","citation_count":9,"is_preprint":false},{"pmid":"18949373","id":"PMC_18949373","title":"Functional analysis of the 5' flanking domain of the LOXL4 gene in head and neck squamous cell carcinoma cells.","date":"2008","source":"International journal of oncology","url":"https://pubmed.ncbi.nlm.nih.gov/18949373","citation_count":9,"is_preprint":false},{"pmid":"29438669","id":"PMC_29438669","title":"Trans-suppression of host CDH3 and LOXL4 genes during Cryptosporidium parvum infection involves nuclear delivery of parasite Cdg7_FLc_1000 RNA.","date":"2018","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/29438669","citation_count":8,"is_preprint":false},{"pmid":"35113007","id":"PMC_35113007","title":"Long non-coding RNA AGAP2-AS1 promotes cell proliferation and invasion through regulating miR-193a-3p/LOXL4 axis in laryngeal squamous cell carcinoma.","date":"2022","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/35113007","citation_count":8,"is_preprint":false},{"pmid":"26138381","id":"PMC_26138381","title":"Differential expression of LOXL4 in normal and tumour tissue samples of laryngeal squamous cell carcinoma.","date":"2016","source":"Clinical otolaryngology : official journal of ENT-UK ; official journal of Netherlands Society for Oto-Rhino-Laryngology & Cervico-Facial Surgery","url":"https://pubmed.ncbi.nlm.nih.gov/26138381","citation_count":7,"is_preprint":false},{"pmid":"38737700","id":"PMC_38737700","title":"The dual role of LOXL4 in the pathogenesis and development of human malignant tumors: a narrative review.","date":"2024","source":"Translational cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/38737700","citation_count":6,"is_preprint":false},{"pmid":"29532123","id":"PMC_29532123","title":"Collagen XVIII and LOXL-4 polymorphisms in women with and without advanced pelvic organ prolapse.","date":"2018","source":"International urogynecology journal","url":"https://pubmed.ncbi.nlm.nih.gov/29532123","citation_count":6,"is_preprint":false},{"pmid":"40795623","id":"PMC_40795623","title":"LOXL4, CREB5 and steroid hormone biosynthesis pathways are involved in type 1 diabetes with polycystic ovary-like changes.","date":"2025","source":"European journal of obstetrics, gynecology, and reproductive biology","url":"https://pubmed.ncbi.nlm.nih.gov/40795623","citation_count":2,"is_preprint":false},{"pmid":"41203182","id":"PMC_41203182","title":"LNC511 inhibits lung cancer progression by modulating the miR-625/LOXL4/Wnt/β-catenin pathway.","date":"2025","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/41203182","citation_count":1,"is_preprint":false},{"pmid":"34565340","id":"PMC_34565340","title":"LAMA2 and LOXL4 are candidate FSGS genes.","date":"2021","source":"BMC nephrology","url":"https://pubmed.ncbi.nlm.nih.gov/34565340","citation_count":0,"is_preprint":false},{"pmid":"41118012","id":"PMC_41118012","title":"Pan-cancer analysis of role of LOXL4 and experiment validation in osteosarcoma.","date":"2025","source":"Discover oncology","url":"https://pubmed.ncbi.nlm.nih.gov/41118012","citation_count":0,"is_preprint":false},{"pmid":"39862152","id":"PMC_39862152","title":"Bortezomib suppresses TGF-β1-mediated LOXL4 reduction through the inhibition of MEK/ERK pathways in MDA-MB-231 cells.","date":"2025","source":"Journal of receptor and signal transduction research","url":"https://pubmed.ncbi.nlm.nih.gov/39862152","citation_count":0,"is_preprint":false},{"pmid":"41890150","id":"PMC_41890150","title":"Multi-Omics Bioinformatic Analyses Linking LOXL4 with Spondylolisthesis.","date":"2026","source":"Orthopedic research and reviews","url":"https://pubmed.ncbi.nlm.nih.gov/41890150","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.08.06.25333006","title":"Genome-Wide Meta-Analysis Identifies Genetic Risk Loci for Mono- and Polyneuropathies in 983,477 Individuals","date":"2025-08-08","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.06.25333006","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.05.28.656636","title":"Expression of Lysyl Oxidase Family Enzymes During Human Endometrial Decidualization","date":"2025-05-29","source":"bioRxiv","url":"https://doi.org/10.1101/2025.05.28.656636","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":19580,"output_tokens":3892,"usd":0.05856},"stage2":{"model":"claude-opus-4-6","input_tokens":7342,"output_tokens":3332,"usd":0.180015},"total_usd":0.238575,"stage1_batch_id":"msgbatch_01Mgbec4vM6c9vXht7JVJzss","stage2_batch_id":"msgbatch_01JkuuH5RB2BdJNsgnhjbC6s","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"LOXL4 was identified as a novel copper-dependent amine oxidase with a conserved C-terminal region including a copper-binding site, lysyl and tyrosyl residues, and a cytokine receptor-like domain, plus four N-terminal scavenger receptor cysteine-rich (SRCR) domains (one with a unique 13 aa insertion). The 3.5-kb mRNA is expressed in pancreas, testis, fibroblasts, smooth muscle, and osteosarcoma cells.\",\n      \"method\": \"cDNA cloning, sequence analysis, Northern blotting, domain mapping\",\n      \"journal\": \"Matrix biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — original gene characterization with sequence, domain architecture, and expression profiling; foundational paper\",\n      \"pmids\": [\"11691588\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"LOXL4 acts as a tumor suppressor in bladder cancer: reintroduction of LOXL4 into bladder cancer cells decreased colony formation and antagonized Ras-mediated activation of the ERK signaling pathway. The gene is silenced by promoter hypermethylation in bladder cancer.\",\n      \"method\": \"Pharmacologic unmasking, microarray, gene reintroduction, colony formation assay, ERK pathway western blotting, methylation analysis\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean KO/OE with defined cellular phenotype and pathway placement (Ras/ERK), single lab\",\n      \"pmids\": [\"17456585\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"LOXL4 gene transcription in HNSCC is driven by a promoter region spanning -960 to -1, with increased nuclear binding to TATA (-25) and SP1 (-181) sites in tumor cells. Promoter constructs with these elements showed significantly elevated reporter activity in HNSCC but not normal epithelial cells.\",\n      \"method\": \"Deletion mapping, promoter-reporter constructs, DNA-binding (EMSA) experiments with nuclear extracts\",\n      \"journal\": \"International journal of oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — promoter deletion mapping and DNA-binding assays in matched cell types, single lab\",\n      \"pmids\": [\"18949373\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"LOXL4 protein is localized pericellularly (perinuclear and cell surface, but not nuclear) in HTB-43 hypopharyngeal carcinoma cells, consistent with a role in extracellular matrix interactions via its SRCR domains and catalytic amine oxidase activity.\",\n      \"method\": \"Immunocytochemistry in cultured primary carcinoma cells with specific anti-LOXL4 antibody\",\n      \"journal\": \"European journal of cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — direct localization experiment with specific antibody, single lab\",\n      \"pmids\": [\"18499440\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"TGF-β1 induces LOXL4 expression in aortic endothelial cells through a mechanism requiring both a distal AP-1 site (bound by JunB/Fra2) and a Smad binding element in the LOXL4 promoter, with ERK-dependent phosphorylation of Fra2 being required for functional cooperation between Smad and AP-1. LOXL4 is secreted extracellularly and contributes to ECM deposition and assembly.\",\n      \"method\": \"Promoter deletion mapping, site-directed mutagenesis, reporter assays, chromatin immunoprecipitation, ERK inhibition, western blotting, ECM deposition assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — promoter mutagenesis, ChIP, and functional reconstitution with orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"23572561\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"LOXL4 promotes gastric cancer cell proliferation, migration, and invasion via activation of the FAK/Src pathway and enhancement of cell-ECM adhesion. Both overexpression and recombinant human LOXL4 protein promote these phenotypes, while knockdown inhibits them.\",\n      \"method\": \"Overexpression, siRNA knockdown, recombinant protein treatment, migration/invasion assays, FAK/Src western blotting\",\n      \"journal\": \"Journal of cancer research and clinical oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple functional assays (KO, OE, recombinant protein) with pathway western blotting, single lab\",\n      \"pmids\": [\"25216702\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"LOXL4 is a direct target of miR-193a-3p; forced reduction of miR-193a-3p or elevation of LOXL4 activates the Oxidative Stress pathway, which mediates multi-drug resistance in bladder cancer cells and xenografts.\",\n      \"method\": \"miRNA overexpression/inhibition, luciferase reporter assay, oxidative stress pathway analysis, xenograft model\",\n      \"journal\": \"Molecular cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct target validation by luciferase assay plus in vivo xenograft, single lab\",\n      \"pmids\": [\"25311867\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"LOXL4 knockdown in triple-negative breast cancer cells increases collagen I and IV levels, induces thickening of collagen bundles (detected by second harmonic generation imaging), and promotes primary tumor growth and lung metastasis in mouse xenografts, demonstrating that LOXL4 suppresses pathological collagen remodeling in this context.\",\n      \"method\": \"shRNA knockdown, mouse xenograft model, second harmonic generation imaging, western blotting\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo loss-of-function with defined ECM phenotype and imaging, single lab\",\n      \"pmids\": [\"28060764\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Intracellular (but not extracellular) LOXL4 promotes HCC cell migration by activating the FAK/Src pathway through a hydrogen peroxide-mediated mechanism dependent on its amine oxidase activity. HCC-derived exosomes transfer LOXL4 between cancer cells and to endothelial cells (HUVECs), promoting angiogenesis via a paracrine mechanism.\",\n      \"method\": \"Overexpression, shRNA knockdown, recombinant protein, deletion mutants, exosome isolation and transfer assays, FAK/Src western blotting, angiogenesis assays, in vivo metastasis model\",\n      \"journal\": \"Molecular cancer\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — domain deletion mutants, catalytic activity dependence, and exosome transfer validated by multiple orthogonal assays and in vivo model; highly cited\",\n      \"pmids\": [\"30704479\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"LOXL4 binds directly to the basic domain of p53 via its low-isoelectric point region, inducing reactivation of wild-type p53 and triggering cell death. 5-azacytidine treatment upregulates LOXL4, which then activates the LOXL4-p53 axis to reduce liver tumor growth.\",\n      \"method\": \"Genome-wide screen, co-immunoprecipitation, domain binding assays, nude mouse xenograft model\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP with domain mapping and in vivo validation, single lab\",\n      \"pmids\": [\"30728460\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"EZH2 epigenetically silences miR-29b and miR-30d (via promoter H3K27 methylation), which directly target LOXL4 mRNA; EZH2 inhibition de-represses these miRNAs, reducing LOXL4 levels. LOXL4 knockdown or miR-29b/miR-30d overexpression decreased breast cancer proliferation, migration, and metastasis in vitro and in vivo, and reduced macrophage infiltration.\",\n      \"method\": \"ChIP, dual-luciferase reporter assay, qRT-PCR, western blotting, proliferation/migration assays, xenograft, flow cytometry\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — ChIP confirms EZH2 promoter binding, luciferase confirms miRNA targeting of LOXL4, multiple orthogonal methods, in vivo validation\",\n      \"pmids\": [\"32754259\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"LOXL4, but not LOXL2, is the critical enzyme for pathological collagen cross-linking and fibrosis in the lung. Genetic ablation of LOXL4 markedly disrupts collagen cross-linking and fibrosis, while LOXL2 knockout has only modest effects. LOXL4 deficiency also decreases expression of other LOX family members including LOXL2.\",\n      \"method\": \"Genetic knockout (Loxl4-/- and Loxl2-/- mice), pulmonary fibrosis model, collagen cross-linking biochemical assays, gene expression analysis\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — clean genetic ablation in vivo with direct biochemical measurement of collagen cross-linking; definitive epistasis between LOX family members\",\n      \"pmids\": [\"37235663\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"LOXL4 delivered into macrophages via tumor cell-derived extracellular vesicles activates STAT1, which induces PD-L1 expression in macrophages, suppresses CD8+ T cell killing activity, and promotes immune escape of HCC cells in vivo.\",\n      \"method\": \"EV isolation/transfer assays, macrophage co-culture with CD8+ T cells, STAT1/PD-L1 western blotting, mouse HCC orthotopic xenograft\",\n      \"journal\": \"Journal of immunotherapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro and in vivo functional assays with defined signaling pathway (STAT1/PD-L1), single lab\",\n      \"pmids\": [\"38047403\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Zinc-bound ZEB1 (via its zinc-finger domain) transcriptionally activates LOXL1 and LOXL4, promoting cancer cell invasion in triple-negative breast cancer. Expression of a zinc-finger-deleted ZEB1 mutant significantly downregulates LOXL1 and LOXL4 and stalls invasion.\",\n      \"method\": \"Stable MutZEB1 (ΔZn) expression, RNA-Seq transcriptome analysis, invasion assays\",\n      \"journal\": \"Frontiers in oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — domain mutant plus RNA-Seq with invasion phenotype, single lab\",\n      \"pmids\": [\"36910659\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TGF-β1 decreases LOXL4 protein expression in MDA-MB-231 breast cancer cells via MEK/ERK-dependent proteasomal degradation (not at the mRNA level). Bortezomib (proteasomal inhibitor) and MEK/ERK pathway inhibition suppress this TGF-β1-mediated LOXL4 reduction. N-glycosylation is required for LOXL4 secretion.\",\n      \"method\": \"Western blotting, proteasomal inhibitor (bortezomib) treatment, MEK/ERK pathway inhibition, N-glycosylation perturbation, ROS measurement\",\n      \"journal\": \"Journal of receptor and signal transduction research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple inhibitors with defined pathway, distinguishes mRNA vs. protein regulation, single lab\",\n      \"pmids\": [\"39862152\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"LOXL4 promotes osteosarcoma cell proliferation, invasion, and EMT via activation of the Wnt/β-catenin signaling pathway; inhibition of Wnt/β-catenin with XAV-939 reverses LOXL4-induced oncogenic effects.\",\n      \"method\": \"CCK-8, colony formation, Matrigel transwell assays, western blotting, GSEA, Wnt/β-catenin inhibitor (XAV-939) rescue experiment\",\n      \"journal\": \"Discover oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — OE/KD with pathway inhibitor rescue, single lab\",\n      \"pmids\": [\"41118012\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LOXL4 is a secreted, copper-dependent amine oxidase that cross-links collagen and elastin in the extracellular matrix (with LOXL4 being the dominant LOX enzyme for pathological collagen cross-linking in lung fibrosis); intracellularly, it activates the FAK/Src pathway via hydrogen peroxide generated by its amine oxidase activity to promote cell migration, binds the basic domain of p53 to reactivate it, and is transcriptionally induced by TGF-β1 through cooperative Smad/JunB-Fra2(AP-1) binding at its promoter; it is also packaged into tumor-derived exosomes/EVs and transferred to macrophages to activate STAT1/PD-L1-mediated immune suppression, regulated upstream by EZH2-silenced miR-29b/miR-30d and Zn²⁺-activated ZEB1, and subject to TGF-β1-induced MEK/ERK-dependent proteasomal degradation.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"LOXL4 is a copper-dependent amine oxidase that functions as the principal enzyme for pathological collagen cross-linking in vivo and as a context-dependent signaling mediator in cancer biology. Its conserved C-terminal catalytic domain catalyzes oxidative deamination of lysine residues in collagen and elastin; genetic ablation in mice demonstrates that LOXL4, rather than LOXL2, is the dominant LOX family member required for collagen cross-link formation and fibrosis in the lung [PMID:37235663]. Intracellularly, LOXL4 activates the FAK/Src pathway through hydrogen peroxide generated by its amine oxidase activity to promote cell migration [PMID:30704479], directly binds the basic domain of p53 to reactivate it and trigger cell death [PMID:30728460], and is transferred via tumor-derived extracellular vesicles to macrophages where it activates STAT1-dependent PD-L1 expression to suppress CD8⁺ T cell cytotoxicity [PMID:38047403]. Transcription of LOXL4 is induced by TGF-β1 through cooperative Smad and JunB/Fra2(AP-1) binding at its promoter [PMID:23572561], upregulated by zinc-dependent ZEB1 [PMID:36910659], and repressed by EZH2-dependent silencing of miR-29b and miR-30d that directly target LOXL4 mRNA [PMID:32754259].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Identification of LOXL4 as a novel LOX family member established its domain architecture—four N-terminal SRCR domains plus a conserved C-terminal copper-dependent amine oxidase domain—and defined its tissue expression profile, providing the molecular framework for all subsequent functional studies.\",\n      \"evidence\": \"cDNA cloning, sequence/domain analysis, and Northern blotting across human tissues and cell lines\",\n      \"pmids\": [\"11691588\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No enzymatic activity assay was performed\", \"Function of the SRCR domains remained uncharacterized\", \"No loss-of-function data\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Demonstration that LOXL4 re-expression suppresses colony formation and antagonizes Ras/ERK signaling in bladder cancer revealed its first intracellular signaling role and identified promoter hypermethylation as a silencing mechanism, establishing LOXL4 as a context-dependent tumor suppressor.\",\n      \"evidence\": \"Gene reintroduction, colony formation, ERK western blotting, and methylation analysis in bladder cancer cells\",\n      \"pmids\": [\"17456585\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking LOXL4 to ERK inhibition not defined\", \"Tumor-suppressive function not validated in vivo\", \"Epigenetic silencing not confirmed in independent cohorts\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Mapping the LOXL4 promoter in HNSCC cells identified TATA and SP1 elements as drivers of its tumor-specific transcription, and immunocytochemistry placed the protein pericellularly (perinuclear and cell-surface), setting the stage for understanding both its transcriptional regulation and its dual intra-/extracellular activity.\",\n      \"evidence\": \"Promoter deletion/reporter mapping, EMSA, and immunocytochemistry in carcinoma versus normal cells\",\n      \"pmids\": [\"18949373\", \"18499440\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific transcription factors binding SP1/TATA sites not identified\", \"Localization studied in a single cell line\", \"Mechanism of secretion not addressed\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Elucidation of TGF-β1-driven LOXL4 transcription through cooperative Smad and JunB/Fra2(AP-1) binding—with ERK-dependent Fra2 phosphorylation required for this cooperation—provided the first complete signaling-to-transcription circuit for LOXL4 induction and linked it to ECM deposition.\",\n      \"evidence\": \"Promoter mutagenesis, ChIP, reporter assays, ERK inhibition, and ECM deposition assays in aortic endothelial cells\",\n      \"pmids\": [\"23572561\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether this mechanism operates in non-endothelial contexts was not tested\", \"Relative contribution of LOXL4 versus other LOX enzymes to TGF-β1-induced ECM remodeling was unknown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Multiple studies demonstrated that LOXL4 promotes gastric cancer cell migration/invasion through FAK/Src pathway activation and is a direct target of miR-193a-3p, which when lost drives oxidative stress-mediated multidrug resistance—establishing LOXL4's pro-oncogenic intracellular signaling axis and its post-transcriptional regulation.\",\n      \"evidence\": \"Overexpression, knockdown, recombinant protein, FAK/Src western blotting in gastric cancer; miRNA luciferase reporter, xenograft in bladder cancer\",\n      \"pmids\": [\"25216702\", \"25311867\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Catalytic activity dependence of FAK/Src activation not tested in these systems\", \"Oxidative stress pathway mechanism downstream of LOXL4 undefined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Loss-of-function studies in triple-negative breast cancer showed that LOXL4 knockdown increases collagen I/IV levels and thickened collagen bundles while promoting tumor growth and lung metastasis, revealing its role in restraining pathological collagen remodeling in the tumor microenvironment.\",\n      \"evidence\": \"shRNA knockdown, mouse xenograft, second harmonic generation imaging, western blotting\",\n      \"pmids\": [\"28060764\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Biochemical mechanism of collagen regulation (cross-linking vs. transcriptional) not distinguished\", \"Contradicts pro-oncogenic roles observed in other cancers—context dependence not resolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Two key mechanistic advances established that (1) intracellular LOXL4 activates FAK/Src specifically through H₂O₂ generated by its amine oxidase catalytic activity and is transferred between cells via exosomes to promote angiogenesis, and (2) LOXL4 directly binds the basic domain of p53 to reactivate it and induce tumor cell death, revealing dual pro- and anti-tumorigenic intracellular functions dependent on distinct protein–protein interactions.\",\n      \"evidence\": \"Domain deletion mutants, catalytic-dead constructs, exosome isolation/transfer, and angiogenesis assays in HCC; co-immunoprecipitation with domain mapping and xenograft for p53 interaction\",\n      \"pmids\": [\"30704479\", \"30728460\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of intracellular amine oxidase substrates that generate H₂O₂ unknown\", \"p53 interaction confirmed by co-IP but lacks structural or biophysical validation\", \"Whether exosomal and p53-activating functions occur in the same cell context is unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Discovery that EZH2 epigenetically silences miR-29b and miR-30d via H3K27me3 at their promoters, and that these miRNAs directly target LOXL4 mRNA, defined a complete upstream epigenetic circuit controlling LOXL4 abundance and linked it to macrophage infiltration in breast cancer.\",\n      \"evidence\": \"ChIP for H3K27me3, dual-luciferase reporter for miRNA–LOXL4 3′UTR, in vivo xenograft with flow cytometry for immune infiltrates\",\n      \"pmids\": [\"32754259\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether EZH2–miR-29b/30d–LOXL4 axis operates outside breast cancer not tested\", \"Mechanism by which LOXL4 promotes macrophage infiltration not defined at this point\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Three studies collectively resolved critical questions: (1) genetic knockout proved LOXL4—not LOXL2—is the dominant enzyme for pathological collagen cross-linking and lung fibrosis in vivo; (2) tumor EV-delivered LOXL4 activates STAT1/PD-L1 in macrophages to suppress CD8⁺ T cell killing; and (3) zinc-finger-dependent ZEB1 transcriptionally activates LOXL4 to promote cancer invasion.\",\n      \"evidence\": \"Loxl4⁻/⁻ versus Loxl2⁻/⁻ mice with collagen cross-link biochemistry; EV transfer, macrophage co-culture with CD8⁺ T cells, orthotopic HCC model; ZEB1 zinc-finger deletion mutant with RNA-Seq in TNBC\",\n      \"pmids\": [\"37235663\", \"38047403\", \"36910659\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific collagen cross-link types catalyzed by LOXL4 in vivo not resolved\", \"Mechanism of STAT1 activation by LOXL4 protein not delineated\", \"Direct ZEB1 binding to LOXL4 promoter not confirmed by ChIP\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"TGF-β1 was shown to reduce LOXL4 protein (but not mRNA) through MEK/ERK-dependent proteasomal degradation in breast cancer, and N-glycosylation was identified as required for LOXL4 secretion, while a separate study linked LOXL4 to Wnt/β-catenin activation in osteosarcoma—expanding the repertoire of downstream pathways and revealing post-translational control mechanisms.\",\n      \"evidence\": \"Proteasome/MEK inhibitor studies, N-glycosylation perturbation in MDA-MB-231; OE/KD with XAV-939 Wnt inhibitor rescue in osteosarcoma cells\",\n      \"pmids\": [\"39862152\", \"41118012\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E3 ubiquitin ligase mediating LOXL4 proteasomal degradation not identified\", \"Whether Wnt/β-catenin activation is direct or indirect downstream of LOXL4 unknown\", \"Glycosylation sites required for secretion not mapped\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the identity of LOXL4's intracellular amine oxidase substrates that generate H₂O₂, the structural basis for LOXL4–p53 and LOXL4–STAT1 interactions, whether the apparently contradictory tumor-suppressive and oncogenic roles reflect cell-type-specific cofactors or splice variants, and whether LOXL4 inhibition can attenuate fibrosis and immune suppression therapeutically.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No crystal or cryo-EM structure of LOXL4 available\", \"No LOXL4-selective small-molecule inhibitor characterized\", \"Intracellular substrates and cofactors remain unidentified\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016491\", \"supporting_discovery_ids\": [0, 8, 11]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [8, 11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [3, 4, 8, 11]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [8, 12]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1474244\", \"supporting_discovery_ids\": [4, 7, 11]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1, 5, 8, 15]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [12]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"TP53\",\n      \"STAT1\",\n      \"FAK\",\n      \"SRC\",\n      \"ZEB1\",\n      \"JUNB\",\n      \"FRA2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}