{"gene":"DEFA1","run_date":"2026-04-28T17:46:02","timeline":{"discoveries":[{"year":1985,"finding":"HNP-1 (DEFA1 gene product) was isolated from human neutrophil azurophil granules and shown to be a small antimicrobial peptide (~3,500 Da) with broad-spectrum bactericidal, antifungal, and antiviral activity; immunogold electron microscopy confirmed its localization specifically to azurophil granules.","method":"Chromatographic/electrophoretic purification, antimicrobial killing assays, immunoperoxidase and immunogold electron microscopy","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 1-2 — original isolation with multiple orthogonal methods; foundational study replicated widely","pmids":["2997278"],"is_preprint":false},{"year":1985,"finding":"The primary amino acid sequences of HNP-1, HNP-2, and HNP-3 were determined; all three are 29-30 residues, rich in cystine and arginine, devoid of free sulfhydryls, and differ only at their amino-terminal residues, defining a multigene defensin family.","method":"Protein sequencing (Edman degradation), amino acid analysis","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 1 — direct protein sequencing of purified peptides","pmids":["4056036"],"is_preprint":false},{"year":1988,"finding":"Defensin cDNA clones encoding HNP-1 were isolated from an HL-60 library, establishing that defensins are synthesized as ~94 amino acid precursor proteins (preprodefensins) that require proteolytic processing to yield the mature 29-30 residue peptides; defensin mRNA was detected in bone marrow but not peripheral blood leukocytes.","method":"cDNA library screening, Northern blot, sequence analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1-2 — direct cDNA cloning and expression analysis establishing precursor architecture","pmids":["3174637"],"is_preprint":false},{"year":1991,"finding":"The crystal structure of defensin HNP-3 (a closely related paralog differing from HNP-1 only at position 1) was solved at 1.9 Å resolution, revealing a dimeric amphiphilic beta-sheet architecture; the dimer structure suggested a mechanism of membrane permeabilization in which defensins bind and intercalate into lipid bilayers to form channels.","method":"X-ray crystallography (1.9 Å resolution)","journal":"Science (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1 — high-resolution crystal structure with mechanistic interpretation; highly cited foundational study","pmids":["2006422"],"is_preprint":false},{"year":1992,"finding":"Metabolic labeling in HL-60 promyelocytes showed that preprodefensins are processed to mature HNP-1 (~29-30 aa) via two sequential intermediates: a 75 aa prodefensin (after signal sequence cleavage, found in cytoplasmic/microsomal fraction) and a 56 aa prodefensin (after preaspartate cleavage, found in granule-enriched fraction); neutralization of acidic compartments with monensin/chloroquine partially blocked conversion, implicating acidic vesicles in processing.","method":"Metabolic radiolabeling ([35S]-methionine), subcellular fractionation, SDS-PAGE, treatment with lysosomotropic agents","journal":"Blood","confidence":"High","confidence_rationale":"Tier 2 — pulse-chase labeling with fractionation and pharmacological intervention; clear mechanistic dissection","pmids":["1339298"],"is_preprint":false},{"year":1993,"finding":"Defensins (including HNP-1) kill microorganisms and mammalian cells through a common mechanism involving initial electrostatic interaction with negatively charged membrane lipid head groups, followed by membrane insertion and formation of voltage-regulated channels; defensins also act as opsonins, inhibit protein kinase C, and act as chemoattractants for monocytes.","method":"Review synthesizing lipid bilayer reconstitution, electrophysiology (voltage-regulated channels), and functional assays","journal":"Annual review of immunology","confidence":"High","confidence_rationale":"Tier 1-2 — synthesis of multiple orthogonal mechanistic studies; highly cited review","pmids":["8476558"],"is_preprint":false},{"year":1996,"finding":"The anionic propiece (residues 20-64) of HNP-1 acts as an intramolecular inhibitor of HNP-1 cytotoxicity: proHNP-1(20-94) is virtually inactive against bacteria and in permeabilizing cells, and the unlinked propiece inhibits bactericidal and cell-permeabilizing activity of mature HNP-1 in a dose-dependent manner by interfering with HNP-1 binding to target cells.","method":"Recombinant baculovirus expression of preproHNP-1, cyanogen bromide cleavage, microbicidal assays against Listeria monocytogenes, K562 cell permeabilization assay, HPLC, mass spectrometry, acid-urea PAGE","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 1-2 — reconstitution with purified components, multiple orthogonal assays, rigorous controls","pmids":["8601627"],"is_preprint":false},{"year":2000,"finding":"Human neutrophil defensins (including HNP-1) selectively chemoattract naive CD4+/CD45RA+ T cells, CD8+ T cells, and immature (but not mature) dendritic cells; the chemotactic effect is pertussis toxin-sensitive, indicating signaling through a Gαi protein-coupled receptor.","method":"Chemotaxis assays with human primary T cells and dendritic cell subsets, pertussis toxin inhibition","journal":"Journal of leukocyte biology","confidence":"High","confidence_rationale":"Tier 2 — functional assay with pharmacological receptor identification; replicated across cell types","pmids":["10914484"],"is_preprint":false},{"year":2001,"finding":"HNP-1 inhibits adenoviral infection of 293 cells with IC50 ~15 µg/ml and >95% inhibition at 50 µg/ml, suggesting that alpha-defensin-1 present in bronchoalveolar lavage can neutralize adenovirus infectivity.","method":"Adenovirus type-5 infection assay in 293 cells, dose-response analysis","journal":"Regulatory peptides","confidence":"Medium","confidence_rationale":"Tier 2 — clean in vitro infectivity assay but single lab, mechanism not fully resolved at molecular level","pmids":["11495691"],"is_preprint":false},{"year":2005,"finding":"Alpha-defensin-1 (HNP-1) inhibits HIV-1 at two levels: (1) a direct virucidal effect on HIV-1 virions at low MOI in the absence of serum, and (2) a cellular effect in which it inhibits PKC activity in primary CD4+ T cells, blocking HIV-1 nuclear import and transcription steps following reverse transcription and integration; bryostatin-1 (PKC activator) partially reversed this inhibition.","method":"HIV-1 replication kinetics assay, PKC phosphorylation analysis, pharmacological PKC inhibitors/activators, analysis of HIV-1 DNA intermediates in primary CD4+ T cells","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods, pharmacological epistasis, and mechanistic pathway placement","pmids":["15719067"],"is_preprint":false},{"year":2005,"finding":"Quantitative antimicrobial comparison showed that among human alpha-defensins, HNP-1 (DEFA1 product) has intermediate potency: against S. aureus the order is HNP2 > HNP1 > HNP3 > HNP4, while against gram-negative bacteria HNP4 > HNP2 > HNP1 = HNP3.","method":"Kinetic 96-well turbidimetric antimicrobial assay with synthetic peptides; virtual LD50/90/99 determination","journal":"Antimicrobial agents and chemotherapy","confidence":"High","confidence_rationale":"Tier 1 — quantitative reconstituted in vitro assay comparing all six human alpha-defensins simultaneously","pmids":["15616305"],"is_preprint":false},{"year":2007,"finding":"Truncated HNP-1 analogues modeled on the C-terminal beta-hairpin region but lacking disulfide bridges retained antimicrobial activity; the analogue 2Abz(23)S(29) displayed broad-spectrum antibacterial activity against all bacterial strains tested, suggesting the C-terminal beta-hairpin is a key antimicrobial pharmacophore.","method":"Solid-phase peptide synthesis, antimicrobial MIC assays against multiple bacterial strains including oral pathogens","journal":"Molecular immunology","confidence":"Medium","confidence_rationale":"Tier 2 — systematic structure-activity analysis with defined peptide analogues, single lab","pmids":["17548109"],"is_preprint":false},{"year":2008,"finding":"Human alpha-defensins (including HNP-1) inhibit adenovirus infection by directly binding the virus and blocking disassembly at the vertex region, thereby preventing release of the internal capsid protein pVI required for endosomal membrane penetration; this results in virion accumulation in early endosomes and lysosomes.","method":"Virus infectivity assays, confocal microscopy of endosomal trafficking, capsid disassembly assay, pVI release assay","journal":"Cell host & microbe","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods defining molecular mechanism of viral neutralization","pmids":["18191790"],"is_preprint":false},{"year":2009,"finding":"ART1 (ADP-ribosyltransferase 1) on airway epithelial cell surfaces ADP-ribosylates HNP-1 specifically on arginines 14 and 24; this modification decreases antimicrobial activity. Furthermore, ADP-ribosylation of arginine 14 undergoes nonenzymatic hydrolysis to yield the non-coded amino acid ornithine, and ADP-ribosyl-HNP-ornithine was detected in bronchoalveolar lavage fluid from IPF patients, indicating this conversion occurs in vivo.","method":"In vitro ADP-ribosylation assay with ART1, mass spectrometry, amino acid analysis, incubation at 37°C for nonenzymatic hydrolysis, analysis of patient BALF by MS","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro enzymatic assay with site-specific identification plus in vivo validation in patient samples","pmids":["19897717"],"is_preprint":false},{"year":2010,"finding":"HNP-1 binds to the bacterial cell wall precursor lipid II; reduction of lipid II levels in bacterial membranes significantly reduces HNP-1 killing, establishing inhibition of cell wall synthesis (via lipid II binding) as a novel antibacterial mechanism distinct from simple membrane disruption.","method":"Lipid II binding assay, bacterial killing assays with lipid II-depleted strains, membrane permeabilization assays (showing no correlation between membrane disruption and killing)","journal":"FEBS letters","confidence":"High","confidence_rationale":"Tier 1-2 — direct binding assay with functional validation using lipid II depletion; mechanistically separates killing from membrane disruption","pmids":["20214904"],"is_preprint":false},{"year":2010,"finding":"The three-dimensional structure of HNP-1 was determined in the microcrystalline state by solid-state NMR; the structure closely resembles the crystal structure of the HNP family but reveals flexibility in the loop region between the first and second beta-strands, suggesting this segment may regulate HNP-1 interaction with phospholipid membranes.","method":"Solid-state magic-angle spinning NMR (2D and 3D), 13C/15N chemical shift torsion angle constraints, inter-residue distance measurements","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 — high-resolution structure determination with direct torsion angle validation","pmids":["20097206"],"is_preprint":false},{"year":2010,"finding":"HNP-1 secretion by intestinal epithelial cells is induced specifically by NOD2 stimulation with MDP (muramyl dipeptide); HNP-1 is required for NOD2-dependent NF-κB activation and for NOD2-mediated antibacterial activity against S. typhimurium, as demonstrated by siRNA knockdown of HNP-1 abrogating both responses.","method":"qRT-PCR, Western blot, ELISA, NF-κB luciferase reporter assay, siRNA knockdown, gentamicin protection assay (bacterial killing), NOD2 site-directed mutagenesis","journal":"Inflammatory bowel diseases","confidence":"High","confidence_rationale":"Tier 2 — loss-of-function (siRNA) with multiple defined phenotypic readouts, epistasis with NOD2 pathway","pmids":["19856414"],"is_preprint":false},{"year":2013,"finding":"HNP-1 induces IL-1β release and pyroptotic pore formation in LPS-primed THP-1 macrophages through a P2X7 receptor → K+ efflux → caspase-1 activation pathway; GST pulldown and confocal microscopy demonstrated direct binding of HNP-1 to P2X7. NLRP3 knockdown decreased caspase-1 activation and pore formation but not IL-1β release, indicating NLRP3 plays different roles in these two HNP-1-induced outcomes.","method":"P2X7 inhibitor pharmacology, GST pulldown, confocal co-localization, caspase-1 activity assay, KCl efflux experiments, ethidium bromide uptake (pore formation), NLRP3 siRNA knockdown, ELISA","journal":"Innate immunity","confidence":"High","confidence_rationale":"Tier 2 — direct binding assay plus loss-of-function with multiple orthogonal mechanistic readouts","pmids":["23792296"],"is_preprint":false},{"year":2019,"finding":"In DEFA1/DEFA3 transgenic mice with neutrophil-specific expression, higher DEFA1/DEFA3 copy number caused more severe sepsis-related organ damage and mortality via endothelial barrier dysfunction and endothelial cell pyroptosis; mechanistically, HNP-1 induces endothelial pyroptosis via P2X7 receptor-mediated canonical caspase-1 activation in an NLRP3 inflammasome-dependent manner; a monoclonal antibody blocking HNP-1/P2X7 interaction protected high-copy-number mice from lethal sepsis.","method":"Transgenic mouse generation (neutrophil-specific DEFA1/DEFA3 expression), cecal ligation and puncture sepsis model, endothelial permeability assays, pyroptosis assays (caspase-1, NLRP3), P2X7 blocking antibody experiment","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — in vivo transgenic model with mechanistic pathway dissection and therapeutic intervention","pmids":["30718392"],"is_preprint":false}],"current_model":"DEFA1-encoded HNP-1 is synthesized as a preprodefensin precursor that undergoes sequential proteolytic processing (signal peptide removal, then anionic propiece cleavage in acidic granular compartments) to yield the mature 29-residue cationic peptide stored in neutrophil azurophil granules; the anionic propiece acts as an intramolecular inhibitor preventing autocytotoxicity during biosynthesis; mature HNP-1 kills bacteria primarily by binding the cell wall precursor lipid II (inhibiting cell wall synthesis) and by membrane permeabilization via amphiphilic dimer channel formation, while its arginines are critical for activity and can be post-translationally modified by ART1-mediated ADP-ribosylation (with subsequent nonenzymatic conversion to ornithine) to reduce antimicrobial potency; beyond direct antimicrobial functions, HNP-1 acts as an alarmin that chemoattracts naive T cells and immature dendritic cells via a Gαi-coupled receptor, neutralizes adenovirus by blocking endosomal escape, inhibits HIV-1 through both direct virucidal effects and PKC-mediated suppression of nuclear import/transcription, and triggers NLRP3 inflammasome-dependent caspase-1 activation and pyroptosis via P2X7 receptor engagement in macrophages and endothelial cells, with elevated DEFA1/DEFA3 gene copy number worsening sepsis severity in vivo."},"narrative":{"teleology":[{"year":1985,"claim":"Identification and sequencing of HNP-1 from azurophil granules established it as a small, cystine- and arginine-rich antimicrobial peptide and founding member of the defensin family.","evidence":"Chromatographic purification, immunogold EM localization to azurophil granules, Edman degradation sequencing of HNP-1/2/3","pmids":["2997278","4056036"],"confidence":"High","gaps":["Mechanism of microbial killing undefined","Gene structure and biosynthetic pathway unknown"]},{"year":1988,"claim":"Cloning of DEFA1 cDNA revealed that HNP-1 is synthesized as a ~94-residue preprodefensin precursor requiring proteolytic maturation, with expression restricted to bone marrow myeloid precursors.","evidence":"cDNA library screening from HL-60 cells, Northern blot of bone marrow vs. peripheral blood","pmids":["3174637"],"confidence":"High","gaps":["Identity of the processing protease(s) unknown","Subcellular site of each processing step undefined"]},{"year":1991,"claim":"The crystal structure of HNP-3 (differing from HNP-1 only at residue 1) at 1.9 Å resolution revealed a dimeric amphiphilic β-sheet fold, providing a structural basis for how defensins insert into and permeabilize lipid bilayers.","evidence":"X-ray crystallography of HNP-3 at 1.9 Å","pmids":["2006422"],"confidence":"High","gaps":["Structure solved for HNP-3, not HNP-1 directly","In-membrane conformation and channel stoichiometry unresolved"]},{"year":1992,"claim":"Pulse-chase metabolic labeling dissected the two-step precursor processing pathway—signal peptide removal yielding a 75-aa intermediate followed by propiece cleavage in acidic compartments yielding a 56-aa species en route to mature HNP-1.","evidence":"[35S]-methionine pulse-chase in HL-60 cells, subcellular fractionation, lysosomotropic agent blockade","pmids":["1339298"],"confidence":"High","gaps":["Specific protease responsible for propiece cleavage not identified","Whether processing differs across neutrophil lineage stages unclear"]},{"year":1996,"claim":"Reconstitution experiments demonstrated that the anionic propiece acts as an intramolecular chaperone-inhibitor, blocking HNP-1 binding to target membranes and preventing premature cytotoxicity during biosynthesis.","evidence":"Recombinant proHNP-1 expression in baculovirus, cyanogen bromide cleavage, bactericidal and cell-permeabilization assays with exogenous propiece","pmids":["8601627"],"confidence":"High","gaps":["Structural basis of propiece-mediated inhibition not defined","Whether propiece has independent biological function unknown"]},{"year":2000,"claim":"HNP-1 was shown to function as a chemoattractant for naive T cells and immature dendritic cells through a pertussis toxin-sensitive Gαi-coupled receptor, linking defensins to adaptive immune cell recruitment.","evidence":"Chemotaxis assays with primary human T cell subsets and dendritic cells, pertussis toxin inhibition","pmids":["10914484"],"confidence":"High","gaps":["Identity of the Gαi-coupled receptor not determined","In vivo relevance of defensin-mediated chemotaxis not established at this time"]},{"year":2005,"claim":"HNP-1 was found to inhibit HIV-1 through both direct virucidal effects and a cellular mechanism involving PKC suppression that blocks viral nuclear import and transcription after integration.","evidence":"HIV-1 replication kinetics, PKC phosphorylation analysis, pharmacological epistasis with bryostatin-1, analysis of HIV-1 DNA intermediates in primary CD4+ T cells","pmids":["15719067"],"confidence":"High","gaps":["Specific PKC isoform targeted not identified","In vivo relevance at physiological HNP-1 concentrations uncertain"]},{"year":2008,"claim":"The molecular mechanism of adenovirus neutralization was defined: HNP-1 binds the virion vertex and prevents capsid disassembly, blocking pVI release and endosomal escape, trapping virions in endosomes/lysosomes.","evidence":"Infectivity assays, confocal tracking of endosomal trafficking, capsid disassembly and pVI release assays","pmids":["18191790"],"confidence":"High","gaps":["Exact binding site on vertex proteins not resolved at atomic level","Breadth across other non-enveloped virus families untested"]},{"year":2009,"claim":"ART1-mediated ADP-ribosylation of HNP-1 at arginines 14 and 24 was identified as a post-translational modification that attenuates antimicrobial potency, with nonenzymatic conversion of ADP-ribosylarginine-14 to ornithine confirmed in patient bronchoalveolar lavage fluid.","evidence":"In vitro ADP-ribosylation with ART1, site identification by mass spectrometry, detection of ADP-ribosyl-HNP-ornithine in IPF patient BALF","pmids":["19897717"],"confidence":"High","gaps":["Physiological regulation of ART1-HNP-1 interaction not characterized","Whether ornithine conversion alters immunomodulatory functions unknown"]},{"year":2010,"claim":"Discovery that HNP-1 binds lipid II and that lipid II depletion abrogates bacterial killing established inhibition of cell wall biosynthesis as a primary antibacterial mechanism, distinct from membrane permeabilization alone.","evidence":"Direct lipid II binding assay, killing assays in lipid II-depleted bacteria, dissociation of killing from membrane permeabilization","pmids":["20214904"],"confidence":"High","gaps":["Structural basis of HNP-1–lipid II interaction unresolved","Relative contribution of lipid II binding vs. pore formation across different species not quantified"]},{"year":2010,"claim":"HNP-1 was positioned downstream of NOD2 in intestinal innate immunity: NOD2 stimulation with MDP induces HNP-1 secretion from epithelial cells, and HNP-1 is required for NOD2-dependent NF-κB activation and antibacterial activity against Salmonella.","evidence":"siRNA knockdown of HNP-1 in epithelial cells, NF-κB reporter assays, gentamicin protection assay, NOD2 mutagenesis","pmids":["19856414"],"confidence":"High","gaps":["How HNP-1 feeds back to activate NF-κB mechanistically is unclear","Relevance to Crohn's disease-associated NOD2 mutations not directly tested"]},{"year":2013,"claim":"The inflammasome-activating mechanism of HNP-1 was delineated: direct binding to P2X7 receptor triggers K+ efflux, NLRP3/caspase-1 activation, pyroptotic pore formation, and IL-1β release in macrophages.","evidence":"P2X7 pharmacological inhibition, GST pulldown, confocal co-localization, NLRP3 siRNA, caspase-1 and ethidium bromide uptake assays in THP-1 cells","pmids":["23792296"],"confidence":"High","gaps":["Binding interface between HNP-1 and P2X7 not structurally defined","Whether other defensins share this pathway untested"]},{"year":2019,"claim":"In vivo validation in transgenic mice demonstrated that DEFA1/DEFA3 copy number drives sepsis severity through HNP-1-induced endothelial pyroptosis via P2X7/NLRP3/caspase-1, and a P2X7-blocking antibody rescued high-copy-number animals from lethal sepsis.","evidence":"Neutrophil-specific DEFA1/DEFA3 transgenic mice, CLP sepsis model, endothelial permeability and pyroptosis assays, therapeutic anti-P2X7 antibody","pmids":["30718392"],"confidence":"High","gaps":["Translational relevance of DEFA1 copy number variation to human sepsis outcomes requires clinical validation","Whether anti-P2X7 blockade impairs necessary defensin antimicrobial functions in vivo unknown"]},{"year":null,"claim":"Key unresolved questions include the identity of the Gαi-coupled chemotactic receptor for HNP-1, the structural basis of HNP-1–lipid II and HNP-1–P2X7 interactions, and the protease(s) responsible for propiece cleavage during biosynthetic maturation.","evidence":"","pmids":[],"confidence":"High","gaps":["Chemotactic receptor identity unknown","HNP-1–lipid II co-crystal structure lacking","Propiece-processing protease not identified"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0090729","term_label":"toxin activity","supporting_discovery_ids":[0,10,14]},{"term_id":"GO:0048018","term_label":"receptor ligand activity","supporting_discovery_ids":[7,17]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[9,16]}],"localization":[{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[0,4]},{"term_id":"GO:0005576","term_label":"extracellular region","supporting_discovery_ids":[7,13,18]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,7,12,16,17,18]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[17,18]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[9,16,17]}],"complexes":[],"partners":["P2RX7","ART1","NOD2","NLRP3"],"other_free_text":[]},"mechanistic_narrative":"DEFA1 encodes neutrophil defensin 1 (HNP-1), a cationic antimicrobial peptide of the innate immune system that is synthesized as a preprodefensin precursor, sequentially processed via signal peptide removal and anionic propiece cleavage in acidic granular compartments, and stored as a mature 29-residue peptide in neutrophil azurophil granules [PMID:2997278, PMID:3174637, PMID:1339298]. The anionic propiece functions as an intramolecular inhibitor that prevents autocytotoxicity during biosynthesis, while the mature peptide kills bacteria through dual mechanisms: binding the cell wall precursor lipid II to inhibit cell wall synthesis and forming amphiphilic dimeric channels that permeabilize membranes [PMID:8601627, PMID:20214904, PMID:2006422]. Beyond direct microbicidal activity, HNP-1 chemoattracts naive T cells and immature dendritic cells via a Gαi-coupled receptor, neutralizes adenovirus by blocking endosomal capsid disassembly, inhibits HIV-1 replication through PKC-dependent suppression of nuclear import, and triggers P2X7/NLRP3-dependent caspase-1 activation and pyroptosis in macrophages and endothelial cells—with elevated DEFA1/DEFA3 gene copy number worsening sepsis severity in vivo [PMID:10914484, PMID:18191790, PMID:15719067, PMID:30718392]."},"prefetch_data":{"uniprot":{"accession":"P59665","full_name":"Neutrophil defensin 1","aliases":["Defensin, alpha 1","HNP-1","HP-1","HP1"],"length_aa":94,"mass_kda":10.2,"function":"Effector molecule of the innate immune system that acts via antibiotic-like properties against a broad array of infectious agents including bacteria, fungi, and viruses or by promoting the activation and maturation of some APCs (PubMed:15616305, PubMed:17142766, PubMed:20220136, PubMed:24236072). Interacts with the essential precursor of cell wall synthesis lipid II to inhibit bacterial cell wall synthesis (PubMed:20214904). Inhibits adenovirus infection via inhibition of viral disassembly at the vertex region, thereby restricting the release of internal capsid protein pVI, which is required for endosomal membrane penetration during cell entry (PubMed:18191790). In addition, interaction with adenovirus capsid leads to the redirection of viral particles to TLR4 thereby promoting a NLRP3-mediated inflammasome response and interleukin 1-beta (IL-1beta) release (PubMed:35080426). Induces the production of proinflammatory cytokines including type I interferon (IFN) in plasmacytoid dendritic cells (pDCs) by triggering the degradation of NFKBIA and nuclear translocation of IRF1, both of which are required for activation of pDCs (PubMed:27031443)","subcellular_location":"Secreted","url":"https://www.uniprot.org/uniprotkb/P59665/entry"},"depmap":{"release":"DepMap","has_data":false,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DEFA1"},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/DEFA1","total_profiled":1310},"omim":[{"mim_id":"606611","title":"DEFENSIN, BETA, 103A; DEFB103A","url":"https://www.omim.org/entry/606611"},{"mim_id":"606464","title":"HEPCIDIN ANTIMICROBIAL PEPTIDE; HAMP","url":"https://www.omim.org/entry/606464"},{"mim_id":"604522","title":"DEFENSIN, ALPHA, 3; DEFA3","url":"https://www.omim.org/entry/604522"},{"mim_id":"602215","title":"DEFENSIN, BETA, 4A; DEFB4A","url":"https://www.omim.org/entry/602215"},{"mim_id":"600472","title":"DEFENSIN, ALPHA, 5; DEFA5","url":"https://www.omim.org/entry/600472"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"bone marrow","ntpm":59493.5}],"url":"https://www.proteinatlas.org/search/DEFA1"},"hgnc":{"alias_symbol":["HNP-1"],"prev_symbol":["DEF1","MRS","DEFA2"]},"alphafold":{"accession":"P59665","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P59665","model_url":"https://alphafold.ebi.ac.uk/files/AF-P59665-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P59665-F1-predicted_aligned_error_v6.png","plddt_mean":73.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DEFA1","jax_strain_url":"https://www.jax.org/strain/search?query=DEFA1"},"sequence":{"accession":"P59665","fasta_url":"https://rest.uniprot.org/uniprotkb/P59665.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P59665/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P59665"}},"corpus_meta":[{"pmid":"8856684","id":"PMC_8856684","title":"Inhibition of N-acetylaspartate production: implications for 1H MRS studies in vivo.","date":"1996","source":"Neuroreport","url":"https://pubmed.ncbi.nlm.nih.gov/8856684","citation_count":356,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"21746807","id":"PMC_21746807","title":"Glutamate in schizophrenia: a focused review and meta-analysis of ¹H-MRS studies.","date":"2011","source":"Schizophrenia bulletin","url":"https://pubmed.ncbi.nlm.nih.gov/21746807","citation_count":356,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"20842758","id":"PMC_20842758","title":"Fluorine (19F) MRS and MRI in biomedicine.","date":"2010","source":"NMR in biomedicine","url":"https://pubmed.ncbi.nlm.nih.gov/20842758","citation_count":350,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17628042","id":"PMC_17628042","title":"Absolute quantification of phosphorus metabolite concentrations in human muscle in vivo by 31P MRS: a quantitative review.","date":"2007","source":"NMR in biomedicine","url":"https://pubmed.ncbi.nlm.nih.gov/17628042","citation_count":251,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"21882281","id":"PMC_21882281","title":"13C MRS studies of neuroenergetics and neurotransmitter cycling in humans.","date":"2011","source":"NMR in biomedicine","url":"https://pubmed.ncbi.nlm.nih.gov/21882281","citation_count":216,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23284644","id":"PMC_23284644","title":"Characterization of neurophysiological and behavioral changes, MRI brain volumetry and 1H MRS in zQ175 knock-in mouse model of Huntington's disease.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23284644","citation_count":207,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11859374","id":"PMC_11859374","title":"A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage.","date":"2002","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/11859374","citation_count":188,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11495691","id":"PMC_11495691","title":"Human alpha-defensin 1 (HNP-1) inhibits adenoviral infection in vitro.","date":"2001","source":"Regulatory peptides","url":"https://pubmed.ncbi.nlm.nih.gov/11495691","citation_count":132,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25379453","id":"PMC_25379453","title":"GABA and glutamate in schizophrenia: a 7 T ¹H-MRS study.","date":"2014","source":"NeuroImage. Clinical","url":"https://pubmed.ncbi.nlm.nih.gov/25379453","citation_count":131,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"8584606","id":"PMC_8584606","title":"Corticosterone, brain mineralocorticoid receptors (MRs) and the activity of the hypothalamic-pituitary-adrenal (HPA) axis: the Lewis rat as an example of increased central MR capacity and a hyporesponsive HPA axis.","date":"1995","source":"Psychoneuroendocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/8584606","citation_count":130,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"8601627","id":"PMC_8601627","title":"Intramolecular inhibition of human defensin HNP-1 by its propiece.","date":"1996","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/8601627","citation_count":111,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"15880397","id":"PMC_15880397","title":"A review of the possible relevance of inositol and the phosphatidylinositol second messenger system (PI-cycle) to psychiatric disorders--focus on magnetic resonance spectroscopy (MRS) studies.","date":"2005","source":"Human psychopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/15880397","citation_count":107,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11279290","id":"PMC_11279290","title":"Direct determination of the N-acetyl-L-aspartate synthesis rate in the human brain by (13)C MRS and [1-(13)C]glucose infusion.","date":"2001","source":"Journal of neurochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11279290","citation_count":95,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"22892723","id":"PMC_22892723","title":"Altered neurochemical profile after traumatic brain injury: (1)H-MRS biomarkers of pathological mechanisms.","date":"2012","source":"Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/22892723","citation_count":95,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"19398702","id":"PMC_19398702","title":"Changes in MRS neuronal markers and T cell phenotypes observed during early HIV infection.","date":"2009","source":"Neurology","url":"https://pubmed.ncbi.nlm.nih.gov/19398702","citation_count":77,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23993092","id":"PMC_23993092","title":"Proteasome-mediated processing of Def1, a critical step in the cellular response to transcription stress.","date":"2013","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/23993092","citation_count":71,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"30833588","id":"PMC_30833588","title":"Dynamic Imaging of Glucose and Lactate Metabolism by 13C-MRS without Hyperpolarization.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/30833588","citation_count":68,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26705534","id":"PMC_26705534","title":"MRI/MRS in neuroinflammation: methodology and applications.","date":"2015","source":"Clinical and translational imaging","url":"https://pubmed.ncbi.nlm.nih.gov/26705534","citation_count":63,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"30718392","id":"PMC_30718392","title":"Increased gene copy number of DEFA1/DEFA3 worsens sepsis by inducing endothelial pyroptosis.","date":"2019","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/30718392","citation_count":63,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"34093845","id":"PMC_34093845","title":"Prodromal neuroinflammatory, cholinergic and metabolite dysfunction detected by PET and MRS in the TgF344-AD transgenic rat model of AD: a collaborative multi-modal study.","date":"2021","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/34093845","citation_count":60,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"15621015","id":"PMC_15621015","title":"Heterogeneity in 1H-MRS profiles of presymptomatic and early manifest Huntington's disease.","date":"2005","source":"Brain research","url":"https://pubmed.ncbi.nlm.nih.gov/15621015","citation_count":60,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"29155183","id":"PMC_29155183","title":"Insights into brain microstructure from in vivo DW-MRS.","date":"2017","source":"NeuroImage","url":"https://pubmed.ncbi.nlm.nih.gov/29155183","citation_count":58,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"22383901","id":"PMC_22383901","title":"Gamma-aminobutyric acid and glutamic acid levels in the auditory pathway of rats with chronic tinnitus: a direct determination using high resolution point-resolved proton magnetic resonance spectroscopy (H-MRS).","date":"2012","source":"Frontiers in systems neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/22383901","citation_count":57,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"9264153","id":"PMC_9264153","title":"Behavioral and neuroendocrine responses controlled by the concerted action of central mineralocorticoid (MRS) and glucocorticoid receptors (GRS).","date":"1997","source":"Psychoneuroendocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/9264153","citation_count":55,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"35775808","id":"PMC_35775808","title":"MRSCloud: A cloud-based MRS tool for basis set simulation.","date":"2022","source":"Magnetic resonance in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35775808","citation_count":52,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"1449969","id":"PMC_1449969","title":"The contribution made by cell death and oxygenation to 31P MRS observations of tumour energy metabolism.","date":"1992","source":"NMR in biomedicine","url":"https://pubmed.ncbi.nlm.nih.gov/1449969","citation_count":51,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26550544","id":"PMC_26550544","title":"The use of dynamic nuclear polarization (13)C-pyruvate MRS in cancer.","date":"2015","source":"American journal of nuclear medicine and molecular imaging","url":"https://pubmed.ncbi.nlm.nih.gov/26550544","citation_count":51,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"16157902","id":"PMC_16157902","title":"Quantitative proton MRS of Pelizaeus-Merzbacher disease: evidence of dys- and hypomyelination.","date":"2005","source":"Neurology","url":"https://pubmed.ncbi.nlm.nih.gov/16157902","citation_count":51,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"22366441","id":"PMC_22366441","title":"Correlation of a priori DCE-MRI and (1)H-MRS data with molecular markers in neck nodal metastases: Initial analysis.","date":"2012","source":"Oral oncology","url":"https://pubmed.ncbi.nlm.nih.gov/22366441","citation_count":50,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"10227616","id":"PMC_10227616","title":"Sjögren-Larsson syndrome: clinical and MRI/MRS findings in FALDH-deficient patients.","date":"1999","source":"Neurology","url":"https://pubmed.ncbi.nlm.nih.gov/10227616","citation_count":49,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17375322","id":"PMC_17375322","title":"Ha-DEF1, a sunflower defensin, induces cell death in Orobanche parasitic plants.","date":"2007","source":"Planta","url":"https://pubmed.ncbi.nlm.nih.gov/17375322","citation_count":47,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"30112276","id":"PMC_30112276","title":"Integrated imaging of [11C]-PBR28 PET, MR diffusion and magnetic resonance spectroscopy 1H-MRS in amyotrophic lateral sclerosis.","date":"2018","source":"NeuroImage. Clinical","url":"https://pubmed.ncbi.nlm.nih.gov/30112276","citation_count":47,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"15166235","id":"PMC_15166235","title":"DNA damage-induced Def1-RNA polymerase II interaction and Def1 requirement for polymerase ubiquitylation in vitro.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15166235","citation_count":47,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28549111","id":"PMC_28549111","title":"Diabetic db/db mice do not develop heart failure upon pressure overload: a longitudinal in vivo PET, MRI, and MRS study on cardiac metabolic, structural, and functional adaptations.","date":"2017","source":"Cardiovascular research","url":"https://pubmed.ncbi.nlm.nih.gov/28549111","citation_count":46,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27532027","id":"PMC_27532027","title":"Activation of Phosphatidylcholine-Specific Phospholipase C in Breast and Ovarian Cancer: Impact on MRS-Detected Choline Metabolic Profile and Perspectives for Targeted Therapy.","date":"2016","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/27532027","citation_count":46,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"15140601","id":"PMC_15140601","title":"Time course of NAA T2 and ADC(w) in ischaemic stroke patients: 1H MRS imaging and diffusion-weighted MRI.","date":"2004","source":"Journal of the neurological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/15140601","citation_count":44,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"19897717","id":"PMC_19897717","title":"ADP-ribosylation of human defensin HNP-1 results in the replacement of the modified arginine with the noncoded amino acid ornithine.","date":"2009","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/19897717","citation_count":44,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17548109","id":"PMC_17548109","title":"Antimicrobial activity of truncated alpha-defensin (human neutrophil peptide (HNP)-1) analogues without disulphide bridges.","date":"2007","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/17548109","citation_count":44,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"33581932","id":"PMC_33581932","title":"Anterior cingulate cortex neurometabolites in bipolar disorder are influenced by mood state and medication: A meta-analysis of 1H-MRS studies.","date":"2021","source":"European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/33581932","citation_count":43,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23792296","id":"PMC_23792296","title":"Alarmin HNP-1 promotes pyroptosis and IL-1β release through different roles of NLRP3 inflammasome via P2X7 in LPS-primed macrophages.","date":"2013","source":"Innate immunity","url":"https://pubmed.ncbi.nlm.nih.gov/23792296","citation_count":41,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17654590","id":"PMC_17654590","title":"Response of choline metabolites to docetaxel therapy is quantified in vivo by localized (31)P MRS of human breast cancer xenografts and in vitro by high-resolution (31)P NMR spectroscopy of cell extracts.","date":"2007","source":"Magnetic resonance in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/17654590","citation_count":41,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"30580380","id":"PMC_30580380","title":"Imaging features (CT, MRI, MRS, and PET/CT) of primary central nervous system lymphoma in immunocompetent patients.","date":"2018","source":"Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology","url":"https://pubmed.ncbi.nlm.nih.gov/30580380","citation_count":41,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"9588530","id":"PMC_9588530","title":"An MRI and MRS study of Pelizaeus-Merzbacher disease.","date":"1998","source":"Pediatric neurology","url":"https://pubmed.ncbi.nlm.nih.gov/9588530","citation_count":40,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"32488963","id":"PMC_32488963","title":"Functions of lactate in the brain of rat with intracerebral hemorrhage evaluated with MRI/MRS and in vitro approaches.","date":"2020","source":"CNS neuroscience & therapeutics","url":"https://pubmed.ncbi.nlm.nih.gov/32488963","citation_count":40,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"12217878","id":"PMC_12217878","title":"Glycolysis as a metabolic marker in orthotopic breast cancer, monitored by in vivo (13)C MRS.","date":"2002","source":"American journal of physiology. Endocrinology and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/12217878","citation_count":39,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27618908","id":"PMC_27618908","title":"Associations between Dietary Nutrient Intakes and Hepatic Lipid Contents in NAFLD Patients Quantified by ¹H-MRS and Dual-Echo MRI.","date":"2016","source":"Nutrients","url":"https://pubmed.ncbi.nlm.nih.gov/27618908","citation_count":39,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"20805522","id":"PMC_20805522","title":"MRS in presymptomatic MAPT mutation carriers: a potential biomarker for tau-mediated pathology.","date":"2010","source":"Neurology","url":"https://pubmed.ncbi.nlm.nih.gov/20805522","citation_count":38,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"15508174","id":"PMC_15508174","title":"In vivo cardiac 1H-MRS in the mouse.","date":"2004","source":"Magnetic resonance in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/15508174","citation_count":37,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"20097206","id":"PMC_20097206","title":"Resonance assignment and three-dimensional structure determination of a human alpha-defensin, HNP-1, by solid-state NMR.","date":"2010","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/20097206","citation_count":36,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31863914","id":"PMC_31863914","title":"Task-related measures of short-interval intracortical inhibition and GABA levels in healthy young and older adults: A multimodal TMS-MRS study.","date":"2019","source":"NeuroImage","url":"https://pubmed.ncbi.nlm.nih.gov/31863914","citation_count":36,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"10022919","id":"PMC_10022919","title":"DEF-1, a novel Src SH3 binding protein that promotes adipogenesis in fibroblastic cell lines.","date":"1999","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10022919","citation_count":35,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"15002049","id":"PMC_15002049","title":"Neuroradiological findings (MRS, MRI, SPECT) in infantile neuronal ceroid-lipofuscinosis (infantile CLN1) at different stages of the disease.","date":"2004","source":"Neuropediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/15002049","citation_count":35,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"24465179","id":"PMC_24465179","title":"Def1 promotes the degradation of Pol3 for polymerase exchange to occur during DNA-damage--induced mutagenesis in Saccharomyces cerevisiae.","date":"2014","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/24465179","citation_count":32,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"20842423","id":"PMC_20842423","title":"Pyruvate carboxylation in different model systems studied by (13)C MRS.","date":"2010","source":"Neurochemical research","url":"https://pubmed.ncbi.nlm.nih.gov/20842423","citation_count":32,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"18060716","id":"PMC_18060716","title":"Quantitative correlation between (1)H MRS and dynamic contrast-enhanced MRI of human breast cancer.","date":"2007","source":"Magnetic resonance imaging","url":"https://pubmed.ncbi.nlm.nih.gov/18060716","citation_count":31,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"35394776","id":"PMC_35394776","title":"Selenium-Enriched Pediococcus acidilactici MRS-7 Alleviates Patulin-Induced Jejunum Injuries in Mice and Its Possible Mechanisms.","date":"2022","source":"Journal of agricultural and food chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/35394776","citation_count":31,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"18035849","id":"PMC_18035849","title":"Non-invasive detection of hippocampal sclerosis: correlation between metabolite alterations detected by (1)H-MRS and neuropathology.","date":"2008","source":"NMR in biomedicine","url":"https://pubmed.ncbi.nlm.nih.gov/18035849","citation_count":30,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27283029","id":"PMC_27283029","title":"The recovery trajectory of adolescent social defeat stress-induced behavioral, (1)H-MRS metabolites and myelin changes in Balb/c mice.","date":"2016","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/27283029","citation_count":30,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"19856414","id":"PMC_19856414","title":"MDP-NOD2 stimulation induces HNP-1 secretion, which contributes to NOD2 antibacterial function.","date":"2010","source":"Inflammatory bowel diseases","url":"https://pubmed.ncbi.nlm.nih.gov/19856414","citation_count":28,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"29531533","id":"PMC_29531533","title":"Metabolic Heterogeneity Evidenced by MRS among Patient-Derived Glioblastoma Multiforme Stem-Like Cells Accounts for Cell Clustering and Different Responses to Drugs.","date":"2018","source":"Stem cells international","url":"https://pubmed.ncbi.nlm.nih.gov/29531533","citation_count":28,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28420383","id":"PMC_28420383","title":"PPBP and DEFA1/DEFA3 genes in hyperlipidaemia as feasible synergistic inflammatory biomarkers for coronary heart disease.","date":"2017","source":"Lipids in health and disease","url":"https://pubmed.ncbi.nlm.nih.gov/28420383","citation_count":26,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"20925526","id":"PMC_20925526","title":"Trypanosoma cruzi infection modulates the expression of Triatoma brasiliensis def1 in the midgut.","date":"2010","source":"Vector borne and zoonotic diseases (Larchmont, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/20925526","citation_count":26,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"24009739","id":"PMC_24009739","title":"Proton magnetic resonance spectroscopy ((1)H-MRS) reveals geniculocalcarine and striate area degeneration in primary glaucoma.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24009739","citation_count":26,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17704911","id":"PMC_17704911","title":"Fucosidosis: MRI and MRS findings.","date":"2007","source":"Pediatric radiology","url":"https://pubmed.ncbi.nlm.nih.gov/17704911","citation_count":26,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"24638096","id":"PMC_24638096","title":"Evaluation of dietary effects on hepatic lipids in high fat and placebo diet fed rats by in vivo MRS and LC-MS techniques.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24638096","citation_count":26,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"24651393","id":"PMC_24651393","title":"Biochemical changes in the brain of hemiplegic migraine patients measured with 7 tesla 1H-MRS.","date":"2014","source":"Cephalalgia : an international journal of headache","url":"https://pubmed.ncbi.nlm.nih.gov/24651393","citation_count":26,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28301071","id":"PMC_28301071","title":"Applications of high-resolution magic angle spinning MRS in biomedical studies I-cell line and animal models.","date":"2017","source":"NMR in biomedicine","url":"https://pubmed.ncbi.nlm.nih.gov/28301071","citation_count":25,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27379200","id":"PMC_27379200","title":"(13)C MRS and LC-MS Flux Analysis of Tumor Intermediary Metabolism.","date":"2016","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/27379200","citation_count":25,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"34673176","id":"PMC_34673176","title":"Diffusion-weighted MR spectroscopy (DW-MRS) is sensitive to LPS-induced changes in human glial morphometry: A preliminary study.","date":"2021","source":"Brain, behavior, and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/34673176","citation_count":25,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"21550593","id":"PMC_21550593","title":"The respective and interaction effects of spinal GRs and MRs on radicular pain induced by chronic compression of the dorsal root ganglion in the rat.","date":"2011","source":"Brain research","url":"https://pubmed.ncbi.nlm.nih.gov/21550593","citation_count":25,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"24239247","id":"PMC_24239247","title":"An 1H-MRS framework predicts the onset of Alzheimer's disease symptoms in PSEN1 mutation carriers.","date":"2013","source":"Alzheimer's & dementia : the journal of the Alzheimer's Association","url":"https://pubmed.ncbi.nlm.nih.gov/24239247","citation_count":25,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"33186716","id":"PMC_33186716","title":"Age-related GABAergic differences in the primary sensorimotor cortex: A multimodal approach combining PET, MRS and TMS.","date":"2020","source":"NeuroImage","url":"https://pubmed.ncbi.nlm.nih.gov/33186716","citation_count":24,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"15588883","id":"PMC_15588883","title":"Utility of 19F MRS detection of the hypoxic cell marker EF5 to assess cellular hypoxia in solid tumors.","date":"2004","source":"Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology","url":"https://pubmed.ncbi.nlm.nih.gov/15588883","citation_count":23,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"24331847","id":"PMC_24331847","title":"Clinical protocols for ³¹P MRS of the brain and their use in evaluating optic pathway gliomas in children.","date":"2013","source":"European journal of radiology","url":"https://pubmed.ncbi.nlm.nih.gov/24331847","citation_count":23,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"9055230","id":"PMC_9055230","title":"Differentiation between cortical atrophy and hydrocephalus using 1H MRS.","date":"1997","source":"Magnetic resonance in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/9055230","citation_count":23,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"12203763","id":"PMC_12203763","title":"Proton MRS in Kennedy disease: absolute metabolite and macromolecular concentrations.","date":"2002","source":"Journal of magnetic resonance imaging : JMRI","url":"https://pubmed.ncbi.nlm.nih.gov/12203763","citation_count":22,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"10589584","id":"PMC_10589584","title":"Short TE proton MRS and neurofibromatosis type 1 intracranial lesions.","date":"1999","source":"Journal of computer assisted tomography","url":"https://pubmed.ncbi.nlm.nih.gov/10589584","citation_count":22,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"20144147","id":"PMC_20144147","title":"Correlation between lactate and neuronal cell damage in the rat brain after focal ischemia: An in vivo 1H magnetic resonance spectroscopic (1H-MRS) study.","date":"2010","source":"Acta radiologica (Stockholm, Sweden : 1987)","url":"https://pubmed.ncbi.nlm.nih.gov/20144147","citation_count":21,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"34482366","id":"PMC_34482366","title":"Kynurenines increase MRS metabolites in basal ganglia and decrease resting-state connectivity in frontostriatal reward circuitry in depression.","date":"2021","source":"Translational psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/34482366","citation_count":21,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17506115","id":"PMC_17506115","title":"1H MRS identifies specific metabolite profiles associated with MYCN-amplified and non-amplified tumour subtypes of neuroblastoma cell lines.","date":"2007","source":"NMR in biomedicine","url":"https://pubmed.ncbi.nlm.nih.gov/17506115","citation_count":21,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17163172","id":"PMC_17163172","title":"MRS as endogenous molecular imaging for brain and prostate tumors: FP6 project \"eTUMOR\".","date":"2006","source":"Advances in experimental medicine and biology","url":"https://pubmed.ncbi.nlm.nih.gov/17163172","citation_count":19,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28928899","id":"PMC_28928899","title":"Hyperpolarized 13C Diffusion MRS of Co-Polarized Pyruvate and Fumarate to Measure Lactate Export and Necrosis.","date":"2017","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/28928899","citation_count":19,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"29165704","id":"PMC_29165704","title":"Involvement of the def-1 Mutation in the Response of Tomato Plants to Arbuscular Mycorrhizal Symbiosis Under Well-Watered and Drought Conditions.","date":"2018","source":"Plant & cell physiology","url":"https://pubmed.ncbi.nlm.nih.gov/29165704","citation_count":19,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"18035282","id":"PMC_18035282","title":"In vivo monitoring response to chemotherapy of human diffuse large B-cell lymphoma xenografts in SCID mice by 1H and 31P MRS.","date":"2007","source":"Academic radiology","url":"https://pubmed.ncbi.nlm.nih.gov/18035282","citation_count":19,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"8694519","id":"PMC_8694519","title":"Introduction to in vivo MRS of cancer: new perspectives and open problems.","date":"1996","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/8694519","citation_count":19,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"35633597","id":"PMC_35633597","title":"UBAP2/UBAP2L regulate UV-induced ubiquitylation of RNA polymerase II and are the human orthologues of yeast Def1.","date":"2022","source":"DNA repair","url":"https://pubmed.ncbi.nlm.nih.gov/35633597","citation_count":18,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"19885604","id":"PMC_19885604","title":"Identification of mobile lipids in human cancer tissues by ex vivo diffusion edited HR-MAS MRS.","date":"2009","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/19885604","citation_count":18,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28017739","id":"PMC_28017739","title":"MRS studies of neuroenergetics and glutamate/glutamine exchange in rats: Extensions to hyperammonemic models.","date":"2016","source":"Analytical biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/28017739","citation_count":18,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"30077647","id":"PMC_30077647","title":"Multifaceted assessment of the APP/PS1 mouse model for Alzheimer's disease: Applying MRS, DTI, and ASL.","date":"2018","source":"Brain research","url":"https://pubmed.ncbi.nlm.nih.gov/30077647","citation_count":18,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23794521","id":"PMC_23794521","title":"Enhancing the [13C]bicarbonate signal in cardiac hyperpolarized [1-13C]pyruvate MRS studies by infusion of glucose, insulin and potassium.","date":"2013","source":"NMR in biomedicine","url":"https://pubmed.ncbi.nlm.nih.gov/23794521","citation_count":18,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"21955813","id":"PMC_21955813","title":"(1)H-MRS evaluation of therapeutic effect of neural stem cell transplantation on Alzheimer's disease in AβPP/PS1 double transgenic mice.","date":"2012","source":"Journal of Alzheimer's disease : JAD","url":"https://pubmed.ncbi.nlm.nih.gov/21955813","citation_count":17,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23613869","id":"PMC_23613869","title":"Combined MRI and ³¹P-MRS investigations of the ACTA1(H40Y) mouse model of nemaline myopathy show impaired muscle function and altered energy metabolism.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23613869","citation_count":17,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23977274","id":"PMC_23977274","title":"Multimodal MRI and (31)P-MRS investigations of the ACTA1(Asp286Gly) mouse model of nemaline myopathy provide evidence of impaired in vivo muscle function, altered muscle structure and disturbed energy metabolism.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23977274","citation_count":16,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27279278","id":"PMC_27279278","title":"The intergenic region of the maize defensin-like protein genes Def1 and Def2 functions as an embryo-specific asymmetric bidirectional promoter.","date":"2016","source":"Journal of experimental botany","url":"https://pubmed.ncbi.nlm.nih.gov/27279278","citation_count":15,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"16246421","id":"PMC_16246421","title":"Parkinson's disease, chronic hydrocarbon exposure and striatal neuronal damage: a 1-H MRS study.","date":"2005","source":"Neurotoxicology","url":"https://pubmed.ncbi.nlm.nih.gov/16246421","citation_count":15,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26515723","id":"PMC_26515723","title":"MRI and MRS findings in fucosidosis; a rare lysosomal storage disease.","date":"2015","source":"Brain & development","url":"https://pubmed.ncbi.nlm.nih.gov/26515723","citation_count":15,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"20578027","id":"PMC_20578027","title":"Pretreatment and early intratreatment prediction of clinicopathologic response of head and neck cancer to chemoradiotherapy using 1H-MRS.","date":"2010","source":"Journal of magnetic resonance imaging : JMRI","url":"https://pubmed.ncbi.nlm.nih.gov/20578027","citation_count":15,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"29180430","id":"PMC_29180430","title":"Def1 interacts with TFIIH and modulates RNA polymerase II transcription.","date":"2017","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/29180430","citation_count":14,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"19780165","id":"PMC_19780165","title":"Proton MRS detects metabolic changes in hormone sensitive and resistant human prostate cancer models CWR22 and CWR22r.","date":"2009","source":"Magnetic resonance in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/19780165","citation_count":14,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"1614307","id":"PMC_1614307","title":"Correlations between in vivo 31P MRS measurements, tumor size, cell survival, and hypoxic fraction in the murine EMT6 tumor.","date":"1992","source":"Magnetic resonance in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/1614307","citation_count":13,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"16169070","id":"PMC_16169070","title":"A human protein-protein interaction network: a resource for annotating the proteome.","date":"2005","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/16169070","citation_count":1704,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"12477932","id":"PMC_12477932","title":"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.","date":"2002","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/12477932","citation_count":1479,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"2997278","id":"PMC_2997278","title":"Defensins. Natural peptide antibiotics of human neutrophils.","date":"1985","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/2997278","citation_count":1192,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"28514442","id":"PMC_28514442","title":"Architecture of the human interactome defines protein communities and disease networks.","date":"2017","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/28514442","citation_count":1085,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"32296183","id":"PMC_32296183","title":"A reference map of the human binary protein interactome.","date":"2020","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/32296183","citation_count":849,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"8476558","id":"PMC_8476558","title":"Defensins: antimicrobial and cytotoxic peptides of mammalian cells.","date":"1993","source":"Annual review of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/8476558","citation_count":820,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"33961781","id":"PMC_33961781","title":"Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.","date":"2021","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/33961781","citation_count":705,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21873635","id":"PMC_21873635","title":"Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.","date":"2011","source":"Briefings in bioinformatics","url":"https://pubmed.ncbi.nlm.nih.gov/21873635","citation_count":656,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"8915011","id":"PMC_8915011","title":"Widespread expression of beta-defensin hBD-1 in human secretory glands and epithelial cells.","date":"1996","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/8915011","citation_count":468,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"2006422","id":"PMC_2006422","title":"Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization.","date":"1991","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/2006422","citation_count":444,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"15489334","id":"PMC_15489334","title":"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).","date":"2004","source":"Genome research","url":"https://pubmed.ncbi.nlm.nih.gov/15489334","citation_count":438,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"4056036","id":"PMC_4056036","title":"Primary structures of three human neutrophil defensins.","date":"1985","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/4056036","citation_count":434,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"20360068","id":"PMC_20360068","title":"Systematic analysis of human protein complexes identifies chromosome segregation proteins.","date":"2010","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/20360068","citation_count":421,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"9030614","id":"PMC_9030614","title":"Fragile X mental retardation protein: nucleocytoplasmic shuttling and association with somatodendritic ribosomes.","date":"1997","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/9030614","citation_count":413,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"10914484","id":"PMC_10914484","title":"Human neutrophil defensins selectively chemoattract naive T and immature dendritic cells.","date":"2000","source":"Journal of leukocyte biology","url":"https://pubmed.ncbi.nlm.nih.gov/10914484","citation_count":385,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"15616305","id":"PMC_15616305","title":"Antibacterial activity and specificity of the six human {alpha}-defensins.","date":"2005","source":"Antimicrobial agents and chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/15616305","citation_count":263,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21900206","id":"PMC_21900206","title":"A directed protein interaction network for investigating intracellular signal transduction.","date":"2011","source":"Science signaling","url":"https://pubmed.ncbi.nlm.nih.gov/21900206","citation_count":258,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"19199708","id":"PMC_19199708","title":"Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT).","date":"2009","source":"Journal of proteome research","url":"https://pubmed.ncbi.nlm.nih.gov/19199708","citation_count":237,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"20551380","id":"PMC_20551380","title":"Proteomics characterization of extracellular space components in the human aorta.","date":"2010","source":"Molecular & cellular proteomics : MCP","url":"https://pubmed.ncbi.nlm.nih.gov/20551380","citation_count":231,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"17207965","id":"PMC_17207965","title":"hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.","date":"2007","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/17207965","citation_count":222,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"15719067","id":"PMC_15719067","title":"Dual role of alpha-defensin-1 in anti-HIV-1 innate immunity.","date":"2005","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/15719067","citation_count":191,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"20214904","id":"PMC_20214904","title":"Functional interaction of human neutrophil peptide-1 with the cell wall precursor lipid II.","date":"2010","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/20214904","citation_count":185,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"17088326","id":"PMC_17088326","title":"Crystal structures of human alpha-defensins HNP4, HD5, and HD6.","date":"2006","source":"Protein science : a publication of the Protein Society","url":"https://pubmed.ncbi.nlm.nih.gov/17088326","citation_count":174,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"1339298","id":"PMC_1339298","title":"Posttranslational processing of defensins in immature human myeloid cells.","date":"1992","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/1339298","citation_count":161,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"25256621","id":"PMC_25256621","title":"The alpha defensin-1 biomarker assay can be used to evaluate the potentially infected total joint arthroplasty.","date":"2014","source":"Clinical orthopaedics and related research","url":"https://pubmed.ncbi.nlm.nih.gov/25256621","citation_count":158,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"18191790","id":"PMC_18191790","title":"Mechanism of adenovirus neutralization by Human alpha-defensins.","date":"2008","source":"Cell host & microbe","url":"https://pubmed.ncbi.nlm.nih.gov/18191790","citation_count":155,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"15944200","id":"PMC_15944200","title":"Copy number polymorphism and expression level variation of the human alpha-defensin genes DEFA1 and DEFA3.","date":"2005","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/15944200","citation_count":152,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"12710851","id":"PMC_12710851","title":"Antimicrobial peptides in amniotic fluid: defensins, calprotectin and bacterial/permeability-increasing protein in patients with microbial invasion of the amniotic cavity, intra-amniotic inflammation, preterm labor and premature rupture of membranes.","date":"2003","source":"The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians","url":"https://pubmed.ncbi.nlm.nih.gov/12710851","citation_count":150,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"3174637","id":"PMC_3174637","title":"Isolation and characterization of human defensin cDNA clones.","date":"1988","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/3174637","citation_count":140,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"23533145","id":"PMC_23533145","title":"In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine.","date":"2013","source":"Proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/23533145","citation_count":138,"is_preprint":false,"source_track":"gene2pubmed"}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":51631,"output_tokens":2327,"usd":0.094899},"stage2":{"model":"claude-opus-4-6","input_tokens":5639,"output_tokens":2675,"usd":0.142605},"total_usd":0.570023,"stage1_batch_id":"msgbatch_0118RScg3WGaGkaZRtWZbtce","stage2_batch_id":"msgbatch_01Cpfzvtbj42aqp5oYZ5Te2s","note":"batch pricing = 50% of standard","round2_stage1":{"model":"claude-sonnet-4-6","input_tokens":64885,"output_tokens":6066,"usd":0.142822},"round2_rules_fired":"R3","round2_stage2":{"model":"claude-opus-4-6","input_tokens":8648,"output_tokens":3329,"usd":0.189697}},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1996,\n      \"finding\": \"The anionic propiece of preproHNP-1 acts as an intramolecular inhibitor of mature HNP-1 (DEFA1) cytotoxicity: linked propiece (and to a lesser extent unlinked propiece) interferes with binding of HNP-1 to target cells, blocking both its bactericidal activity against Listeria monocytogenes and its ability to permeabilize K562 cells in a dose-dependent manner.\",\n      \"method\": \"Recombinant baculovirus expression of preproHNP-1, cyanogen bromide cleavage to generate mature HNP-1 and propiece, microbicidal assay, cell permeabilization assay, mass spectrometry, HPLC, acid-urea PAGE, conformation-specific antibody\",\n      \"journal\": \"The Journal of Clinical Investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with multiple orthogonal assays and rigorous controls\",\n      \"pmids\": [\"8601627\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"HNP-1 (DEFA1) inhibits adenoviral infection in vitro, reducing adenoviral infectivity of 293 cells by >95% at 50 µg/ml with an IC50 of ~15 µg/ml, whereas HBD-2 had little effect, indicating a peptide-specific antiviral mechanism.\",\n      \"method\": \"In vitro adenoviral infection assay of 293 cells with HNP-1 or HBD-2 treatment; dose-response analysis\",\n      \"journal\": \"Regulatory Peptides\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean in vitro functional assay, single lab, single method\",\n      \"pmids\": [\"11495691\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Truncated C-terminal analogues of HNP-1 (DEFA1) lacking disulfide bridges retain broad-spectrum antibacterial activity, demonstrating that the C-terminal beta-hairpin region is sufficient for antimicrobial function and that the disulfide bonds are not strictly required for activity.\",\n      \"method\": \"Chemical synthesis of truncated HNP-1 analogues; antimicrobial activity assays against multiple bacterial strains including oral pathogens\",\n      \"journal\": \"Molecular Immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with synthesized peptides, single lab\",\n      \"pmids\": [\"17548109\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"ADP-ribosyltransferase ART1 on airway epithelial cell surfaces ADP-ribosylates HNP-1 (DEFA1) specifically on arginines 14 and 24, altering its biological activity; ADP-ribosylation at arginine 14 undergoes subsequent nonenzymatic hydrolysis to replace the modified arginine with ornithine, providing a post-translational modification pathway that reduces HNP-1 function.\",\n      \"method\": \"In vitro ART1-catalyzed ADP-ribosylation assay, mass spectrometry, amino acid analysis, isolation of ADP-ribosylated HNP-1 from bronchoalveolar lavage fluid (BALF) of patients\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro enzymatic assay with MS characterization, validated in patient-derived BALF samples\",\n      \"pmids\": [\"19897717\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Solid-state NMR determined the three-dimensional structure of HNP-1 (DEFA1) in a microcrystalline state, revealing close similarity to crystal structures of the HNP family but with conformational flexibility in the loop region between the first and second beta-strands, which may regulate HNP-1 interaction with phospholipid membranes of microbial cells.\",\n      \"method\": \"Solid-state NMR (SSNMR) magic-angle spinning experiments; 2D and 3D 13C/15N chemical shift and inter-residue distance constraints\",\n      \"journal\": \"Journal of Molecular Biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — first high-resolution SSNMR structure of human defensin with torsion angle validation\",\n      \"pmids\": [\"20097206\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"HNP-1 (DEFA1) secretion in intestinal epithelial cells is induced by NOD2 stimulation with muramyl dipeptide (MDP-LD), and HNP-1 is required for NOD2-dependent NF-κB activation and antibacterial function against Salmonella typhimurium; siRNA knockdown of HNP-1 abrogated both NF-κB activation and NOD2-mediated bacterial clearance.\",\n      \"method\": \"RT-PCR, Western blot, ELISA, NF-κB luciferase reporter assay, siRNA knockdown, gentamicin protection assay, site-directed mutagenesis of NOD2\",\n      \"journal\": \"Inflammatory Bowel Diseases\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (siRNA, reporter assay, bacterial killing assay) in a single study\",\n      \"pmids\": [\"19856414\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"HNP-1 (DEFA1) acts as an alarmin that promotes pyroptosis and IL-1β release in LPS-primed macrophages via direct binding to P2X7 receptor (demonstrated by GST pull-down and confocal microscopy), activating P2X7-K+ efflux-caspase-1 signaling; NLRP3 inflammasome knockdown reduced caspase-1 activation and pore formation but not IL-1β release, indicating distinct roles for NLRP3 in pore formation versus cytokine secretion.\",\n      \"method\": \"GST pull-down assay, confocal microscopy, caspase-1 activity assay, ethidium bromide uptake assay, NLRP3 siRNA knockdown, pharmacological inhibition of P2X7 and caspase-1\",\n      \"journal\": \"Innate Immunity\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct binding demonstrated by pull-down; multiple orthogonal methods including siRNA, pharmacological inhibitors, and pore-formation assay\",\n      \"pmids\": [\"23792296\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"DEFA1/DEFA3 gene copy number variation modulates sepsis severity in vivo: transgenic mice with high copy number show more severe endothelial barrier dysfunction and endothelial cell pyroptosis via HNP-1–P2X7 receptor interaction activating canonical caspase-1 in an NLRP3 inflammasome-dependent manner; a monoclonal antibody blocking HNP-1–P2X7 interaction protected high-copy-number mice from lethal sepsis.\",\n      \"method\": \"DEFA1/DEFA3 transgenic mouse generation with neutrophil-specific expression, cecal ligation and puncture sepsis model, endothelial permeability assay, pyroptosis assay, monoclonal antibody blockade, NLRP3/caspase-1 pathway analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo transgenic model with mechanistic pathway elucidation and therapeutic antibody validation; multiple orthogonal methods\",\n      \"pmids\": [\"30718392\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DEFA1-encoded HNP-1 is an alpha-defensin antimicrobial peptide whose activity is regulated by intramolecular inhibition via its anionic propiece during biosynthesis, and extracellularly by ART1-mediated ADP-ribosylation on key arginines (which can further convert to ornithine nonenzymatically); its C-terminal beta-hairpin confers membrane-disrupting antimicrobial and antiviral activity, it signals through direct binding to the P2X7 receptor to activate NLRP3/caspase-1-dependent pyroptosis and IL-1β release in macrophages and endothelial cells, and its expression in epithelial cells is induced downstream of NOD2-MDP signaling to mediate NF-κB activation and bacterial clearance.\"\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\nLooking through the corpus, I need to identify papers about the canonical human protein DEFA1 (alpha-defensin 1, HNP-1).\n\n**Classification:**\n- Papers [1]-[6], [9]-[15], [17]-[18], [20]-[30], [32], [34]-[36], [39], [41]-[48], [50], [52], [54]-[58], [60], [63]-[69], [71]-[82], [84]-[85], [87]-[93], [95]-[100] from the retrieved set are about MRS/MRI techniques, neuroscience, or unrelated topics → EXCLUDE\n- Paper [7] (Rad26-Def1 complex, yeast): describes yeast Def1, a different protein family (RNAPII degradation factor) → EXCLUDE (symbol collision with different function)\n- Paper [16] (Wilson 2013, yeast Def1): same yeast Def1 → EXCLUDE\n- Paper [31] (Ha-DEF1, sunflower): plant defensin → EXCLUDE (symbol collision, plant)\n- Paper [33] (Reid 2004, yeast Def1): yeast Def1 → EXCLUDE\n- Paper [37] (Stevens 2009, HNP-1 ADP-ribosylation): KEEP\n- Paper [38] (Lundy 2007, HNP-1 analogues): KEEP\n- Paper [40] (Chen 2013, HNP-1/P2X7/NLRP3): KEEP\n- Paper [49] (Zhang 2010, HNP-1 solid-state NMR structure): KEEP\n- Paper [51] (King 1999, DEF-1 Src SH3): different protein (bovine brain DEF-1/differentiation-enhancing factor) → EXCLUDE\n- Paper [53] (Daraba 2014, yeast Def1): yeast Def1 → EXCLUDE\n- Paper [59] (Yamamoto-Furusho 2010, HNP-1/NOD2): KEEP\n- Paper [61] (Maneerat 2017, DEFA1/DEFA3): expression correlation only → EXCLUDE\n- Paper [62] (Waniek 2010, Triatoma def1): insect defensin → EXCLUDE (symbol collision)\n- Paper [83] (Sánchez-Romera 2018, tomato def-1): plant → EXCLUDE\n- Paper [86] (Herlihy 2022, UBAP2/yeast Def1): yeast Def1 orthologues → EXCLUDE\n- Paper [94] (Liu 2016, maize Def1/Def2): plant → EXCLUDE\n- Paper [98] (Damodaren 2017, yeast Def1/TFIIH): yeast Def1 → EXCLUDE\n- Paper [8] (Bastian 2001, HNP-1 inhibits adenovirus): KEEP\n- Paper [19] (Chen 2019, DEFA1/DEFA3 transgenic mice, sepsis): KEEP\n\n**Gene2pubmed curated papers:**\n- [3] Ganz 1985: KEEP (original defensin discovery, HNP-1 antimicrobial, azurophil granule localization)\n- [6] Lehrer 1993: KEEP (mechanism of membrane permeabilization, channel formation)\n- [10] Hill 1991: KEEP (crystal structure HNP-3, dimer, membrane permeabilization mechanism)\n- [11] Valore 1996: KEEP (propiece inhibition of HNP-1)\n- [12] Selsted 1985: KEEP (primary structure)\n- [15] Yang 2000: KEEP (chemotaxis via Gi-coupled receptor)\n- [16] Ericksen 2005: KEEP (antimicrobial activity comparison)\n- [21] Chang 2005: KEEP (alpha-defensin-1 inhibits HIV via PKC)\n- [22] de Leeuw 2010: KEEP (HNP-1 binds lipid II)\n- [23] Szyk 2006: KEEP (crystal structures)\n- [24] Valore 1992: KEEP (posttranslational processing)\n- [26] Smith 2008: KEEP (mechanism of adenovirus neutralization)\n- [27] Aldred 2005: KEEP (copy number variation, expression)\n- [29] Daher 1988: KEEP (cDNA clones, precursor structure)\n- [1],[2],[4],[5],[7],[8],[9],[13],[14],[17],[18],[19],[20],[25],[28],[30] from gene2pubmed: mostly proteomics/interaction networks/general resources or clinical biomarker → EXCLUDE from mechanistic discoveries\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1985,\n      \"finding\": \"HNP-1 (DEFA1 gene product) was isolated from human neutrophil azurophil granules and shown to be a small antimicrobial peptide (~3,500 Da) with broad-spectrum bactericidal, antifungal, and antiviral activity; immunogold electron microscopy confirmed its localization specifically to azurophil granules.\",\n      \"method\": \"Chromatographic/electrophoretic purification, antimicrobial killing assays, immunoperoxidase and immunogold electron microscopy\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — original isolation with multiple orthogonal methods; foundational study replicated widely\",\n      \"pmids\": [\"2997278\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1985,\n      \"finding\": \"The primary amino acid sequences of HNP-1, HNP-2, and HNP-3 were determined; all three are 29-30 residues, rich in cystine and arginine, devoid of free sulfhydryls, and differ only at their amino-terminal residues, defining a multigene defensin family.\",\n      \"method\": \"Protein sequencing (Edman degradation), amino acid analysis\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct protein sequencing of purified peptides\",\n      \"pmids\": [\"4056036\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1988,\n      \"finding\": \"Defensin cDNA clones encoding HNP-1 were isolated from an HL-60 library, establishing that defensins are synthesized as ~94 amino acid precursor proteins (preprodefensins) that require proteolytic processing to yield the mature 29-30 residue peptides; defensin mRNA was detected in bone marrow but not peripheral blood leukocytes.\",\n      \"method\": \"cDNA library screening, Northern blot, sequence analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — direct cDNA cloning and expression analysis establishing precursor architecture\",\n      \"pmids\": [\"3174637\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1991,\n      \"finding\": \"The crystal structure of defensin HNP-3 (a closely related paralog differing from HNP-1 only at position 1) was solved at 1.9 Å resolution, revealing a dimeric amphiphilic beta-sheet architecture; the dimer structure suggested a mechanism of membrane permeabilization in which defensins bind and intercalate into lipid bilayers to form channels.\",\n      \"method\": \"X-ray crystallography (1.9 Å resolution)\",\n      \"journal\": \"Science (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution crystal structure with mechanistic interpretation; highly cited foundational study\",\n      \"pmids\": [\"2006422\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"Metabolic labeling in HL-60 promyelocytes showed that preprodefensins are processed to mature HNP-1 (~29-30 aa) via two sequential intermediates: a 75 aa prodefensin (after signal sequence cleavage, found in cytoplasmic/microsomal fraction) and a 56 aa prodefensin (after preaspartate cleavage, found in granule-enriched fraction); neutralization of acidic compartments with monensin/chloroquine partially blocked conversion, implicating acidic vesicles in processing.\",\n      \"method\": \"Metabolic radiolabeling ([35S]-methionine), subcellular fractionation, SDS-PAGE, treatment with lysosomotropic agents\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — pulse-chase labeling with fractionation and pharmacological intervention; clear mechanistic dissection\",\n      \"pmids\": [\"1339298\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Defensins (including HNP-1) kill microorganisms and mammalian cells through a common mechanism involving initial electrostatic interaction with negatively charged membrane lipid head groups, followed by membrane insertion and formation of voltage-regulated channels; defensins also act as opsonins, inhibit protein kinase C, and act as chemoattractants for monocytes.\",\n      \"method\": \"Review synthesizing lipid bilayer reconstitution, electrophysiology (voltage-regulated channels), and functional assays\",\n      \"journal\": \"Annual review of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — synthesis of multiple orthogonal mechanistic studies; highly cited review\",\n      \"pmids\": [\"8476558\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"The anionic propiece (residues 20-64) of HNP-1 acts as an intramolecular inhibitor of HNP-1 cytotoxicity: proHNP-1(20-94) is virtually inactive against bacteria and in permeabilizing cells, and the unlinked propiece inhibits bactericidal and cell-permeabilizing activity of mature HNP-1 in a dose-dependent manner by interfering with HNP-1 binding to target cells.\",\n      \"method\": \"Recombinant baculovirus expression of preproHNP-1, cyanogen bromide cleavage, microbicidal assays against Listeria monocytogenes, K562 cell permeabilization assay, HPLC, mass spectrometry, acid-urea PAGE\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — reconstitution with purified components, multiple orthogonal assays, rigorous controls\",\n      \"pmids\": [\"8601627\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Human neutrophil defensins (including HNP-1) selectively chemoattract naive CD4+/CD45RA+ T cells, CD8+ T cells, and immature (but not mature) dendritic cells; the chemotactic effect is pertussis toxin-sensitive, indicating signaling through a Gαi protein-coupled receptor.\",\n      \"method\": \"Chemotaxis assays with human primary T cells and dendritic cell subsets, pertussis toxin inhibition\",\n      \"journal\": \"Journal of leukocyte biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — functional assay with pharmacological receptor identification; replicated across cell types\",\n      \"pmids\": [\"10914484\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"HNP-1 inhibits adenoviral infection of 293 cells with IC50 ~15 µg/ml and >95% inhibition at 50 µg/ml, suggesting that alpha-defensin-1 present in bronchoalveolar lavage can neutralize adenovirus infectivity.\",\n      \"method\": \"Adenovirus type-5 infection assay in 293 cells, dose-response analysis\",\n      \"journal\": \"Regulatory peptides\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean in vitro infectivity assay but single lab, mechanism not fully resolved at molecular level\",\n      \"pmids\": [\"11495691\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Alpha-defensin-1 (HNP-1) inhibits HIV-1 at two levels: (1) a direct virucidal effect on HIV-1 virions at low MOI in the absence of serum, and (2) a cellular effect in which it inhibits PKC activity in primary CD4+ T cells, blocking HIV-1 nuclear import and transcription steps following reverse transcription and integration; bryostatin-1 (PKC activator) partially reversed this inhibition.\",\n      \"method\": \"HIV-1 replication kinetics assay, PKC phosphorylation analysis, pharmacological PKC inhibitors/activators, analysis of HIV-1 DNA intermediates in primary CD4+ T cells\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods, pharmacological epistasis, and mechanistic pathway placement\",\n      \"pmids\": [\"15719067\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Quantitative antimicrobial comparison showed that among human alpha-defensins, HNP-1 (DEFA1 product) has intermediate potency: against S. aureus the order is HNP2 > HNP1 > HNP3 > HNP4, while against gram-negative bacteria HNP4 > HNP2 > HNP1 = HNP3.\",\n      \"method\": \"Kinetic 96-well turbidimetric antimicrobial assay with synthetic peptides; virtual LD50/90/99 determination\",\n      \"journal\": \"Antimicrobial agents and chemotherapy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — quantitative reconstituted in vitro assay comparing all six human alpha-defensins simultaneously\",\n      \"pmids\": [\"15616305\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Truncated HNP-1 analogues modeled on the C-terminal beta-hairpin region but lacking disulfide bridges retained antimicrobial activity; the analogue 2Abz(23)S(29) displayed broad-spectrum antibacterial activity against all bacterial strains tested, suggesting the C-terminal beta-hairpin is a key antimicrobial pharmacophore.\",\n      \"method\": \"Solid-phase peptide synthesis, antimicrobial MIC assays against multiple bacterial strains including oral pathogens\",\n      \"journal\": \"Molecular immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — systematic structure-activity analysis with defined peptide analogues, single lab\",\n      \"pmids\": [\"17548109\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Human alpha-defensins (including HNP-1) inhibit adenovirus infection by directly binding the virus and blocking disassembly at the vertex region, thereby preventing release of the internal capsid protein pVI required for endosomal membrane penetration; this results in virion accumulation in early endosomes and lysosomes.\",\n      \"method\": \"Virus infectivity assays, confocal microscopy of endosomal trafficking, capsid disassembly assay, pVI release assay\",\n      \"journal\": \"Cell host & microbe\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods defining molecular mechanism of viral neutralization\",\n      \"pmids\": [\"18191790\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"ART1 (ADP-ribosyltransferase 1) on airway epithelial cell surfaces ADP-ribosylates HNP-1 specifically on arginines 14 and 24; this modification decreases antimicrobial activity. Furthermore, ADP-ribosylation of arginine 14 undergoes nonenzymatic hydrolysis to yield the non-coded amino acid ornithine, and ADP-ribosyl-HNP-ornithine was detected in bronchoalveolar lavage fluid from IPF patients, indicating this conversion occurs in vivo.\",\n      \"method\": \"In vitro ADP-ribosylation assay with ART1, mass spectrometry, amino acid analysis, incubation at 37°C for nonenzymatic hydrolysis, analysis of patient BALF by MS\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro enzymatic assay with site-specific identification plus in vivo validation in patient samples\",\n      \"pmids\": [\"19897717\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"HNP-1 binds to the bacterial cell wall precursor lipid II; reduction of lipid II levels in bacterial membranes significantly reduces HNP-1 killing, establishing inhibition of cell wall synthesis (via lipid II binding) as a novel antibacterial mechanism distinct from simple membrane disruption.\",\n      \"method\": \"Lipid II binding assay, bacterial killing assays with lipid II-depleted strains, membrane permeabilization assays (showing no correlation between membrane disruption and killing)\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — direct binding assay with functional validation using lipid II depletion; mechanistically separates killing from membrane disruption\",\n      \"pmids\": [\"20214904\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The three-dimensional structure of HNP-1 was determined in the microcrystalline state by solid-state NMR; the structure closely resembles the crystal structure of the HNP family but reveals flexibility in the loop region between the first and second beta-strands, suggesting this segment may regulate HNP-1 interaction with phospholipid membranes.\",\n      \"method\": \"Solid-state magic-angle spinning NMR (2D and 3D), 13C/15N chemical shift torsion angle constraints, inter-residue distance measurements\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution structure determination with direct torsion angle validation\",\n      \"pmids\": [\"20097206\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"HNP-1 secretion by intestinal epithelial cells is induced specifically by NOD2 stimulation with MDP (muramyl dipeptide); HNP-1 is required for NOD2-dependent NF-κB activation and for NOD2-mediated antibacterial activity against S. typhimurium, as demonstrated by siRNA knockdown of HNP-1 abrogating both responses.\",\n      \"method\": \"qRT-PCR, Western blot, ELISA, NF-κB luciferase reporter assay, siRNA knockdown, gentamicin protection assay (bacterial killing), NOD2 site-directed mutagenesis\",\n      \"journal\": \"Inflammatory bowel diseases\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function (siRNA) with multiple defined phenotypic readouts, epistasis with NOD2 pathway\",\n      \"pmids\": [\"19856414\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"HNP-1 induces IL-1β release and pyroptotic pore formation in LPS-primed THP-1 macrophages through a P2X7 receptor → K+ efflux → caspase-1 activation pathway; GST pulldown and confocal microscopy demonstrated direct binding of HNP-1 to P2X7. NLRP3 knockdown decreased caspase-1 activation and pore formation but not IL-1β release, indicating NLRP3 plays different roles in these two HNP-1-induced outcomes.\",\n      \"method\": \"P2X7 inhibitor pharmacology, GST pulldown, confocal co-localization, caspase-1 activity assay, KCl efflux experiments, ethidium bromide uptake (pore formation), NLRP3 siRNA knockdown, ELISA\",\n      \"journal\": \"Innate immunity\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct binding assay plus loss-of-function with multiple orthogonal mechanistic readouts\",\n      \"pmids\": [\"23792296\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In DEFA1/DEFA3 transgenic mice with neutrophil-specific expression, higher DEFA1/DEFA3 copy number caused more severe sepsis-related organ damage and mortality via endothelial barrier dysfunction and endothelial cell pyroptosis; mechanistically, HNP-1 induces endothelial pyroptosis via P2X7 receptor-mediated canonical caspase-1 activation in an NLRP3 inflammasome-dependent manner; a monoclonal antibody blocking HNP-1/P2X7 interaction protected high-copy-number mice from lethal sepsis.\",\n      \"method\": \"Transgenic mouse generation (neutrophil-specific DEFA1/DEFA3 expression), cecal ligation and puncture sepsis model, endothelial permeability assays, pyroptosis assays (caspase-1, NLRP3), P2X7 blocking antibody experiment\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo transgenic model with mechanistic pathway dissection and therapeutic intervention\",\n      \"pmids\": [\"30718392\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DEFA1-encoded HNP-1 is synthesized as a preprodefensin precursor that undergoes sequential proteolytic processing (signal peptide removal, then anionic propiece cleavage in acidic granular compartments) to yield the mature 29-residue cationic peptide stored in neutrophil azurophil granules; the anionic propiece acts as an intramolecular inhibitor preventing autocytotoxicity during biosynthesis; mature HNP-1 kills bacteria primarily by binding the cell wall precursor lipid II (inhibiting cell wall synthesis) and by membrane permeabilization via amphiphilic dimer channel formation, while its arginines are critical for activity and can be post-translationally modified by ART1-mediated ADP-ribosylation (with subsequent nonenzymatic conversion to ornithine) to reduce antimicrobial potency; beyond direct antimicrobial functions, HNP-1 acts as an alarmin that chemoattracts naive T cells and immature dendritic cells via a Gαi-coupled receptor, neutralizes adenovirus by blocking endosomal escape, inhibits HIV-1 through both direct virucidal effects and PKC-mediated suppression of nuclear import/transcription, and triggers NLRP3 inflammasome-dependent caspase-1 activation and pyroptosis via P2X7 receptor engagement in macrophages and endothelial cells, with elevated DEFA1/DEFA3 gene copy number worsening sepsis severity in vivo.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"DEFA1 encodes human neutrophil peptide-1 (HNP-1), an alpha-defensin with dual roles as a membrane-disrupting antimicrobial/antiviral effector and an innate immune alarmin that activates inflammatory signaling. During biosynthesis, the anionic propiece of preproHNP-1 acts as an intramolecular inhibitor that blocks mature HNP-1 binding to target cells, preventing premature cytotoxicity and bactericidal activity [PMID:8601627]; extracellularly, ART1-mediated ADP-ribosylation of arginines 14 and 24 attenuates HNP-1 function, with Arg14 modification undergoing nonenzymatic hydrolysis to ornithine [PMID:19897717]. The C-terminal beta-hairpin region is sufficient for broad-spectrum antibacterial activity independent of disulfide bonds [PMID:17548109], and HNP-1 inhibits adenoviral infection [PMID:11495691]. HNP-1 also functions as an alarmin by directly binding the P2X7 receptor to activate NLRP3/caspase-1-dependent pyroptosis and IL-1β release in macrophages and endothelial cells, a pathway whose pathological activation during sepsis is modulated by DEFA1/DEFA3 gene copy number and can be blocked by anti-HNP-1 monoclonal antibody [PMID:23792296, PMID:30718392]; in intestinal epithelial cells, HNP-1 expression is induced by NOD2-MDP signaling and is required for NOD2-dependent NF-κB activation and Salmonella clearance [PMID:19856414].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"The mechanism preventing premature cytotoxicity during HNP-1 biosynthesis was unknown; this work showed the anionic propiece functions as an intramolecular inhibitor that blocks HNP-1 binding to target cells, establishing a built-in safety mechanism in defensin maturation.\",\n      \"evidence\": \"Recombinant baculovirus expression of preproHNP-1, cyanogen bromide cleavage, microbicidal and cell permeabilization assays with propiece co-incubation\",\n      \"pmids\": [\"8601627\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Mechanism of propiece removal during neutrophil granule maturation not defined\",\n        \"Whether propiece regulation applies equally to DEFA3 and DEFA4 not tested\",\n        \"No structural model of propiece–HNP-1 interaction\"\n      ]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Whether alpha-defensins possess antiviral activity beyond antibacterial function was unclear; HNP-1 was shown to inhibit adenoviral infection with >95% reduction at 50 µg/ml, establishing a peptide-specific antiviral role distinct from beta-defensins.\",\n      \"evidence\": \"In vitro adenoviral infection assay in 293 cells with dose-response analysis comparing HNP-1 and HBD-2\",\n      \"pmids\": [\"11495691\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism of antiviral action (viral entry block vs. post-entry inhibition) not determined\",\n        \"In vivo antiviral relevance not established\",\n        \"Activity against other virus families not tested\"\n      ]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"The minimal structural determinant for HNP-1 antimicrobial activity was undefined; truncated C-terminal analogues lacking disulfide bridges retained broad-spectrum antibacterial activity, establishing the C-terminal beta-hairpin as the core antimicrobial module.\",\n      \"evidence\": \"Chemical synthesis of truncated HNP-1 analogues and antimicrobial activity assays against multiple bacterial strains\",\n      \"pmids\": [\"17548109\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"How the beta-hairpin interacts with and disrupts microbial membranes at atomic resolution not resolved\",\n        \"Whether disulfide-independent activity extends to antiviral function not tested\"\n      ]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"How extracellular HNP-1 activity is regulated post-secretion was unknown; ART1-mediated ADP-ribosylation at Arg14 and Arg24 was identified as a post-translational modification that attenuates HNP-1 function, with Arg14 modification further converting to ornithine nonenzymatically, revealing an airway-specific activity dampening mechanism.\",\n      \"evidence\": \"In vitro ART1 enzymatic assay with mass spectrometry characterization, validated in bronchoalveolar lavage fluid from patients\",\n      \"pmids\": [\"19897717\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Quantitative impact of ADP-ribosylation on antimicrobial potency not fully characterized\",\n        \"Whether ADP-ribosylation also modulates HNP-1 alarmin/P2X7 signaling not tested\",\n        \"Reversibility and regulation of ART1 activity toward HNP-1 in vivo not established\"\n      ]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Two key advances established HNP-1 structural dynamics and its role as an effector downstream of NOD2: solid-state NMR revealed conformational flexibility in the loop between the first and second beta-strands that may regulate membrane interaction, and independently, HNP-1 was shown to be required for NOD2-MDP-dependent NF-κB activation and Salmonella clearance in intestinal epithelial cells.\",\n      \"evidence\": \"Solid-state NMR structure determination of microcrystalline HNP-1 (SSNMR); separately, siRNA knockdown, NF-κB reporter assay, and gentamicin protection assay in intestinal epithelial cells\",\n      \"pmids\": [\"20097206\", \"19856414\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis for HNP-1 membrane disruption not determined at lipid-bilayer interface\",\n        \"How NOD2 signaling transcriptionally or post-transcriptionally upregulates HNP-1 not defined\",\n        \"Whether NOD2-HNP-1 axis operates in vivo in intestinal defense not confirmed\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"The receptor and signaling pathway mediating HNP-1 alarmin activity in macrophages were unknown; direct binding of HNP-1 to the P2X7 receptor was demonstrated, activating K+ efflux, caspase-1, and NLRP3-dependent pyroptosis with IL-1β release, establishing HNP-1 as an endogenous danger signal.\",\n      \"evidence\": \"GST pull-down, confocal microscopy, caspase-1 activity assay, ethidium bromide uptake, NLRP3 siRNA knockdown, and pharmacological P2X7/caspase-1 inhibition in LPS-primed macrophages\",\n      \"pmids\": [\"23792296\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Binding site on P2X7 receptor for HNP-1 not mapped\",\n        \"Whether HNP-1 activates P2X7 as a full agonist or via a distinct mechanism from ATP not resolved\",\n        \"NLRP3 appeared dispensable for IL-1β release, raising questions about alternative secretion pathways\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Whether the HNP-1–P2X7 pathway has pathological relevance in vivo was untested; DEFA1/DEFA3 copy number variation was shown to modulate sepsis severity in transgenic mice through HNP-1–P2X7–NLRP3/caspase-1-dependent endothelial pyroptosis, and a blocking monoclonal antibody rescued lethal sepsis, validating the pathway as a therapeutic target.\",\n      \"evidence\": \"DEFA1/DEFA3 transgenic mice with neutrophil-specific expression, cecal ligation and puncture model, endothelial permeability/pyroptosis assays, anti-HNP-1 monoclonal antibody blockade\",\n      \"pmids\": [\"30718392\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Translation of monoclonal antibody efficacy to human sepsis not tested\",\n        \"Whether copy number variation affects antimicrobial defense as well as inflammation not assessed\",\n        \"Relative contribution of DEFA1 versus DEFA3 to the sepsis phenotype not deconvoluted\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis for HNP-1 binding to P2X7, the mechanism by which HNP-1 disrupts microbial versus mammalian membranes selectively, and whether the NOD2–HNP-1 axis operates in vivo remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No co-crystal or cryo-EM structure of HNP-1–P2X7 complex\",\n        \"Selectivity mechanism for microbial versus host membrane disruption not defined\",\n        \"In vivo validation of NOD2-dependent HNP-1 induction in intestinal epithelium lacking\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0090729\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0048018\", \"supporting_discovery_ids\": [6, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [3, 6, 7]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [5, 6, 7]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"P2RX7\",\n      \"ART1\",\n      \"NOD2\",\n      \"NLRP3\",\n      \"CASP1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"mechanistic_narrative\": \"DEFA1 encodes neutrophil defensin 1 (HNP-1), a cationic antimicrobial peptide of the innate immune system that is synthesized as a preprodefensin precursor, sequentially processed via signal peptide removal and anionic propiece cleavage in acidic granular compartments, and stored as a mature 29-residue peptide in neutrophil azurophil granules [PMID:2997278, PMID:3174637, PMID:1339298]. The anionic propiece functions as an intramolecular inhibitor that prevents autocytotoxicity during biosynthesis, while the mature peptide kills bacteria through dual mechanisms: binding the cell wall precursor lipid II to inhibit cell wall synthesis and forming amphiphilic dimeric channels that permeabilize membranes [PMID:8601627, PMID:20214904, PMID:2006422]. Beyond direct microbicidal activity, HNP-1 chemoattracts naive T cells and immature dendritic cells via a Gαi-coupled receptor, neutralizes adenovirus by blocking endosomal capsid disassembly, inhibits HIV-1 replication through PKC-dependent suppression of nuclear import, and triggers P2X7/NLRP3-dependent caspase-1 activation and pyroptosis in macrophages and endothelial cells—with elevated DEFA1/DEFA3 gene copy number worsening sepsis severity in vivo [PMID:10914484, PMID:18191790, PMID:15719067, PMID:30718392].\",\n  \"teleology\": [\n    {\n      \"year\": 1985,\n      \"claim\": \"Identification and sequencing of HNP-1 from azurophil granules established it as a small, cystine- and arginine-rich antimicrobial peptide and founding member of the defensin family.\",\n      \"evidence\": \"Chromatographic purification, immunogold EM localization to azurophil granules, Edman degradation sequencing of HNP-1/2/3\",\n      \"pmids\": [\"2997278\", \"4056036\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of microbial killing undefined\", \"Gene structure and biosynthetic pathway unknown\"]\n    },\n    {\n      \"year\": 1988,\n      \"claim\": \"Cloning of DEFA1 cDNA revealed that HNP-1 is synthesized as a ~94-residue preprodefensin precursor requiring proteolytic maturation, with expression restricted to bone marrow myeloid precursors.\",\n      \"evidence\": \"cDNA library screening from HL-60 cells, Northern blot of bone marrow vs. peripheral blood\",\n      \"pmids\": [\"3174637\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the processing protease(s) unknown\", \"Subcellular site of each processing step undefined\"]\n    },\n    {\n      \"year\": 1991,\n      \"claim\": \"The crystal structure of HNP-3 (differing from HNP-1 only at residue 1) at 1.9 Å resolution revealed a dimeric amphiphilic β-sheet fold, providing a structural basis for how defensins insert into and permeabilize lipid bilayers.\",\n      \"evidence\": \"X-ray crystallography of HNP-3 at 1.9 Å\",\n      \"pmids\": [\"2006422\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure solved for HNP-3, not HNP-1 directly\", \"In-membrane conformation and channel stoichiometry unresolved\"]\n    },\n    {\n      \"year\": 1992,\n      \"claim\": \"Pulse-chase metabolic labeling dissected the two-step precursor processing pathway—signal peptide removal yielding a 75-aa intermediate followed by propiece cleavage in acidic compartments yielding a 56-aa species en route to mature HNP-1.\",\n      \"evidence\": \"[35S]-methionine pulse-chase in HL-60 cells, subcellular fractionation, lysosomotropic agent blockade\",\n      \"pmids\": [\"1339298\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific protease responsible for propiece cleavage not identified\", \"Whether processing differs across neutrophil lineage stages unclear\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Reconstitution experiments demonstrated that the anionic propiece acts as an intramolecular chaperone-inhibitor, blocking HNP-1 binding to target membranes and preventing premature cytotoxicity during biosynthesis.\",\n      \"evidence\": \"Recombinant proHNP-1 expression in baculovirus, cyanogen bromide cleavage, bactericidal and cell-permeabilization assays with exogenous propiece\",\n      \"pmids\": [\"8601627\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of propiece-mediated inhibition not defined\", \"Whether propiece has independent biological function unknown\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"HNP-1 was shown to function as a chemoattractant for naive T cells and immature dendritic cells through a pertussis toxin-sensitive Gαi-coupled receptor, linking defensins to adaptive immune cell recruitment.\",\n      \"evidence\": \"Chemotaxis assays with primary human T cell subsets and dendritic cells, pertussis toxin inhibition\",\n      \"pmids\": [\"10914484\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the Gαi-coupled receptor not determined\", \"In vivo relevance of defensin-mediated chemotaxis not established at this time\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"HNP-1 was found to inhibit HIV-1 through both direct virucidal effects and a cellular mechanism involving PKC suppression that blocks viral nuclear import and transcription after integration.\",\n      \"evidence\": \"HIV-1 replication kinetics, PKC phosphorylation analysis, pharmacological epistasis with bryostatin-1, analysis of HIV-1 DNA intermediates in primary CD4+ T cells\",\n      \"pmids\": [\"15719067\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific PKC isoform targeted not identified\", \"In vivo relevance at physiological HNP-1 concentrations uncertain\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"The molecular mechanism of adenovirus neutralization was defined: HNP-1 binds the virion vertex and prevents capsid disassembly, blocking pVI release and endosomal escape, trapping virions in endosomes/lysosomes.\",\n      \"evidence\": \"Infectivity assays, confocal tracking of endosomal trafficking, capsid disassembly and pVI release assays\",\n      \"pmids\": [\"18191790\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Exact binding site on vertex proteins not resolved at atomic level\", \"Breadth across other non-enveloped virus families untested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"ART1-mediated ADP-ribosylation of HNP-1 at arginines 14 and 24 was identified as a post-translational modification that attenuates antimicrobial potency, with nonenzymatic conversion of ADP-ribosylarginine-14 to ornithine confirmed in patient bronchoalveolar lavage fluid.\",\n      \"evidence\": \"In vitro ADP-ribosylation with ART1, site identification by mass spectrometry, detection of ADP-ribosyl-HNP-ornithine in IPF patient BALF\",\n      \"pmids\": [\"19897717\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological regulation of ART1-HNP-1 interaction not characterized\", \"Whether ornithine conversion alters immunomodulatory functions unknown\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Discovery that HNP-1 binds lipid II and that lipid II depletion abrogates bacterial killing established inhibition of cell wall biosynthesis as a primary antibacterial mechanism, distinct from membrane permeabilization alone.\",\n      \"evidence\": \"Direct lipid II binding assay, killing assays in lipid II-depleted bacteria, dissociation of killing from membrane permeabilization\",\n      \"pmids\": [\"20214904\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of HNP-1–lipid II interaction unresolved\", \"Relative contribution of lipid II binding vs. pore formation across different species not quantified\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"HNP-1 was positioned downstream of NOD2 in intestinal innate immunity: NOD2 stimulation with MDP induces HNP-1 secretion from epithelial cells, and HNP-1 is required for NOD2-dependent NF-κB activation and antibacterial activity against Salmonella.\",\n      \"evidence\": \"siRNA knockdown of HNP-1 in epithelial cells, NF-κB reporter assays, gentamicin protection assay, NOD2 mutagenesis\",\n      \"pmids\": [\"19856414\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How HNP-1 feeds back to activate NF-κB mechanistically is unclear\", \"Relevance to Crohn's disease-associated NOD2 mutations not directly tested\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"The inflammasome-activating mechanism of HNP-1 was delineated: direct binding to P2X7 receptor triggers K+ efflux, NLRP3/caspase-1 activation, pyroptotic pore formation, and IL-1β release in macrophages.\",\n      \"evidence\": \"P2X7 pharmacological inhibition, GST pulldown, confocal co-localization, NLRP3 siRNA, caspase-1 and ethidium bromide uptake assays in THP-1 cells\",\n      \"pmids\": [\"23792296\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Binding interface between HNP-1 and P2X7 not structurally defined\", \"Whether other defensins share this pathway untested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"In vivo validation in transgenic mice demonstrated that DEFA1/DEFA3 copy number drives sepsis severity through HNP-1-induced endothelial pyroptosis via P2X7/NLRP3/caspase-1, and a P2X7-blocking antibody rescued high-copy-number animals from lethal sepsis.\",\n      \"evidence\": \"Neutrophil-specific DEFA1/DEFA3 transgenic mice, CLP sepsis model, endothelial permeability and pyroptosis assays, therapeutic anti-P2X7 antibody\",\n      \"pmids\": [\"30718392\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Translational relevance of DEFA1 copy number variation to human sepsis outcomes requires clinical validation\", \"Whether anti-P2X7 blockade impairs necessary defensin antimicrobial functions in vivo unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the identity of the Gαi-coupled chemotactic receptor for HNP-1, the structural basis of HNP-1–lipid II and HNP-1–P2X7 interactions, and the protease(s) responsible for propiece cleavage during biosynthetic maturation.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Chemotactic receptor identity unknown\", \"HNP-1–lipid II co-crystal structure lacking\", \"Propiece-processing protease not identified\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0090729\", \"supporting_discovery_ids\": [0, 10, 14]},\n      {\"term_id\": \"GO:0048018\", \"supporting_discovery_ids\": [7, 17]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [9, 16]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [7, 13, 18]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 7, 12, 16, 17, 18]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [17, 18]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [9, 16, 17]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"P2RX7\",\n      \"ART1\",\n      \"NOD2\",\n      \"NLRP3\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}