{"gene":"NID1","run_date":"2026-04-29T11:37:56","timeline":{"discoveries":[{"year":1981,"finding":"Entactin (NID1) is a sulfated glycoprotein component of basement membranes, distinct from laminin (GP-2), with a molecular weight of ~158 kDa, localized at the surface of epithelial cells adjacent to basement membranes in rodent kidney and other tissues.","method":"Biochemical isolation, immunoelectron microscopy, antibody-based characterization","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1/2 — original isolation and immunolocalization, foundational paper with multiple orthogonal methods","pmids":["6262321"],"is_preprint":false},{"year":1988,"finding":"Mouse entactin is organized into two globular domains (70 kDa N-terminal and 36 kDa C-terminal) separated by a cysteine-rich 28 kDa stalk; the C-terminal domain shows homology to EGF precursor and LDL receptor; the molecule contains six EGF-type cysteine-rich repeats, one thyroglobulin repeat, and an RGD cell-recognition sequence in one EGF-type repeat; synthetic RGD-containing peptide promotes mammary tumor cell attachment.","method":"cDNA sequencing, sequence analysis, synthetic peptide cell attachment assay","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1 — complete cDNA sequence with functional validation of RGD peptide","pmids":["3264556"],"is_preprint":false},{"year":1988,"finding":"Entactin tyrosine sulfation occurs in the medial Golgi cisternae and is not the last modification before secretion; N-linked glycosylation and terminal glycosylation in the trans-Golgi occur after sulfation.","method":"Metabolic labeling with [35S]methionine and H2[35S]O4, tunicamycin and monensin inhibitor treatments, pulse-chase analysis","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 — multiple inhibitor conditions in a single study defining post-translational modification order","pmids":["3042455"],"is_preprint":false},{"year":1990,"finding":"Entactin promotes cell attachment through the integrin RGD recognition sequence; additionally, entactin directly binds calcium ions through sites in the N-terminal region, demonstrated with recombinant peptides containing the first 330 amino acids.","method":"Cell attachment assay with synthetic peptides and recombinant entactin, calcium binding assay with recombinant N-terminal fragment","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — reconstituted cell attachment and direct calcium-binding assay with recombinant proteins and mutagenic peptides","pmids":["2191952"],"is_preprint":false},{"year":1990,"finding":"Entactin forms a highly stable noncovalent complex with laminin intracellularly; transfection of entactin into JAR choriocarcinoma cells (which lack entactin but make laminin and collagen IV) stimulates incorporation of all three into extracellular matrix, indicating entactin bridges laminin and type IV collagen in basement membrane assembly.","method":"Cell transfection, immunofluorescence, extracellular matrix fractionation","journal":"American journal of respiratory cell and molecular biology","confidence":"High","confidence_rationale":"Tier 2 — reconstitution by transfection with functional readout of matrix assembly, replicated in multiple papers","pmids":["2119632"],"is_preprint":false},{"year":1991,"finding":"Entactin specifically binds fibrinogen through interactions with the Aα and Bβ chains of fibrinogen in a divalent cation-independent manner; entactin can be cross-linked to fibrinogen by transglutaminase.","method":"Solid phase binding assay with radiolabeled entactin, antibody inhibition, transglutaminase cross-linking","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — direct in vitro binding assay with saturability, antibody inhibition, and cross-linking","pmids":["1680863"],"is_preprint":false},{"year":1991,"finding":"Entactin forms a complex with fibronectin (independent of laminin) and co-localizes in the extracellular matrix of 4CQ embryonal carcinoma cells; direct binding between entactin and fibronectin was demonstrated by affinity chromatography and solid phase assay.","method":"Affinity column chromatography, solid phase binding assay, immunofluorescence","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — two orthogonal binding methods in a single lab","pmids":["1872841"],"is_preprint":false},{"year":1992,"finding":"The cell surface receptor for entactin on PC-3 prostate carcinoma cells is integrin α3β1; binding requires divalent cations (Ca2+, Mg2+, Mn2+) and is not inhibited by RGD-containing peptides; α3β1 purified from cells binds entactin-Sepharose, while α2β1 does not.","method":"Affinity chromatography on entactin-Sepharose, anti-integrin antibody identification, purified integrin binding assay, liposome reconstitution, antibody inhibition of cell attachment","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — receptor isolated by affinity chromatography, identified by antibodies, confirmed with purified integrin and liposome reconstitution","pmids":["1527019"],"is_preprint":false},{"year":1992,"finding":"Entactin mediates neutrophil (PMN) adhesion and chemotaxis through its RGD domain and the leukocyte response integrin (LRI); a recombinant RGE-substituted entactin mutant (Asp674→Glu) lost both adhesive and chemotactic activities; anti-β1 and anti-β2 antibodies did not block the response whereas anti-LRI did.","method":"Adhesion assay, chemotaxis assay, RGD/RGE synthetic peptides, recombinant site-directed mutant entactin, monoclonal antibody blocking, leukocyte adhesion deficiency patient PMNs","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 1 — site-directed mutagenesis of RGD, multiple antibody blocking experiments, patient cell validation","pmids":["1469085"],"is_preprint":false},{"year":1992,"finding":"Entactin is required for long-term maintenance and adhesion of contractile skeletal myotubes; anti-entactin antibodies did not inhibit satellite cell attachment or fusion but caused myotube detachment after spontaneous contractions began, demonstrating a specific role for entactin in myotube maintenance.","method":"Anti-entactin antibody perturbation on Matrigel cultures of regenerated satellite cells, myotube adhesion assay","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 — specific antibody perturbation with defined cellular phenotype (myotube detachment)","pmids":["1734030"],"is_preprint":false},{"year":1993,"finding":"Entactin is specifically degraded by matrix metalloproteinases; matrilysin (MMP-7) is ~100-fold more effective than interstitial collagenase and ~600-fold more effective than 92 kDa gelatinase; matrilysin cleaves entactin at sites amino-terminal to leucine or isoleucine residues producing fragments of 29–115 kDa.","method":"In vitro protease digestion assay, kinetic analysis (Km, Vmax), Edman degradation for cleavage site identification","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — quantitative in vitro enzyme assay with precise cleavage site determination","pmids":["8380588"],"is_preprint":false},{"year":1993,"finding":"Entactin binds laminin, collagen IV, fibrinogen, and fibronectin; the laminin-entactin complex is formed intracellularly in M1536-B3 cells and transported in membrane-enclosed vesicles to the extracellular compartment.","method":"Co-immunoprecipitation, cell fractionation, transfection experiments, indirect immunofluorescence","journal":"Kidney international","confidence":"High","confidence_rationale":"Tier 2 — multiple binding partners confirmed by multiple orthogonal methods, intracellular complex formation demonstrated","pmids":["8433553"],"is_preprint":false},{"year":1993,"finding":"Recombinant entactin promotes primary trophoblast cell adhesion and migration through the RGD recognition sequence; a mutated entactin with Glu replacing Asp at the RGD site provided no trophoblast adhesive activity.","method":"Blastocyst outgrowth assay, RGD peptide inhibition, recombinant RGD→RGE mutant entactin, anti-entactin antibody","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1 — site-directed mutagenesis of RGD with loss-of-function confirmation in cell migration assay","pmids":["8491783"],"is_preprint":false},{"year":1994,"finding":"The binding of fibronectin to entactin is mediated through the 29 kDa amino-terminal fragment of fibronectin and the G2 domain of entactin (but not G1, E, or G3 domains); half-saturation for binding is ~5 nM.","method":"Solid phase binding assay with GST-domain fusion proteins of entactin and radiolabeled fibronectin fragment","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — domain-mapping by solid-phase assay with defined recombinant fragments","pmids":["8147897"],"is_preprint":false},{"year":1994,"finding":"A novel epitope of entactin at the neuromuscular junction is dependent on glycosylation; N-glycanase treatment reduces entactin molecular mass and eliminates the synaptic-specific 9H6 antibody epitope, indicating that synaptic entactin bears a distinct N-glycosylation pattern not found at extrasynaptic sites.","method":"Monoclonal antibody generation, Western blot, N-glycanase treatment, immunostaining of NMJ","journal":"The Journal of neuroscience","confidence":"Medium","confidence_rationale":"Tier 2 — glycosylation-dependent epitope demonstrated by N-glycanase treatment with specific antibody","pmids":["7514212"],"is_preprint":false},{"year":1995,"finding":"Entactin has two distinct cell attachment sites: (1) the RGD sequence in the EGF-like stalk (E domain) recognized by αvβ3 integrin, and (2) a second site in a 39-amino acid cysteine-rich EGF repeat of the G2 domain recognized by a β1 integrin family member; deletion/mutation of RGD reveals the second site.","method":"GST-domain fusion protein cell attachment assay, baculovirus-expressed full-length RGD deletion mutant, anti-integrin antibody inhibition","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — domain dissection with mutagenesis, antibody blocking, and reconstitution in baculovirus system","pmids":["7797588"],"is_preprint":false},{"year":1996,"finding":"Entactin E domain (containing RGD) ligates the leukocyte response integrin (LRI/β3-like) and signals for neutrophil chemotaxis, while the G2 domain ligates α3β1 and signals for enhancement of Fc receptor-mediated phagocytosis; matrilysin cleavage of entactin liberates fragments retaining both activities.","method":"GST-domain fusion protein neutrophil activation assays (chemotaxis, phagocytosis), matrilysin cleavage, anti-integrin antibody blocking","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — domain-specific functional dissection with defined receptor identification and protease cleavage experiments","pmids":["8940031"],"is_preprint":false},{"year":1996,"finding":"Stromelysin-1 (MMP-3) cleaves entactin in mammary gland basement membrane in vivo; enhanced cleavage of entactin correlates directly with apoptosis of overlying mammary epithelial cells; TIMP-1 overexpression blocks both entactin cleavage and apoptosis.","method":"Transgenic mouse cross (stromelysin-1 × TIMP-1 overexpressing mice), apoptosis assay, in vivo entactin protein quantification","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 — in vivo genetic evidence with dose-response across multiple genotypes linking entactin cleavage to apoptosis","pmids":["8978831"],"is_preprint":false},{"year":1998,"finding":"Human mesangial cells adhere to native entactin via both αvβ3 (binding to the RGD sequence on the E domain) and a β1 integrin receptor (binding to a non-RGD site); cation dependence was demonstrated and tertiary molecular structure of entactin contributes to binding.","method":"Anti-integrin antibody inhibition of adhesion, wild-type and mutant recombinant entactin fragments, immunoprecipitation of integrin receptors","journal":"Cell adhesion and communication","confidence":"Medium","confidence_rationale":"Tier 2 — domain-specific adhesion mapped with mutant entactin and antibody blocking","pmids":["9686320"],"is_preprint":false},{"year":2000,"finding":"Nidogen-1/entactin-1 is exclusively produced and secreted by mesenchymal peritubular cells (not Sertoli cells) in the testis; monoclonal antibody perturbation against entactin-1 caused loss of peritubular cell adhesion (autocrine function) while Sertoli cells remained adherent.","method":"DD-RT-PCR, Western blotting of cell fractions and supernatants, monoclonal antibody perturbation of cell adhesion","journal":"European journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2 — cell-type-specific expression confirmed and function demonstrated by antibody perturbation","pmids":["10727019"],"is_preprint":false},{"year":2001,"finding":"Entactin inhibits amyloid β-protein (Aβ1-40) fibril formation in vitro in a dose-dependent manner at a molar ratio of 50:1 (Aβ:entactin); entactin induces a random coil structure in Aβ40 as shown by circular dichroism spectroscopy.","method":"Thioflavin T fluorometric assay, electron microscopy, circular dichroism spectroscopy","journal":"Neuroscience letters","confidence":"Medium","confidence_rationale":"Tier 1 — in vitro assay with multiple orthogonal methods confirming mechanism","pmids":["11376898"],"is_preprint":false},{"year":2002,"finding":"Targeted disruption of entactin-1/nidogen-1 in mice results in neurological deficits (seizure-like symptoms, loss of hind-leg muscle control) and selective structural alterations in basement membranes of brain capillaries and lens capsule, while other basement membranes appear morphologically normal.","method":"Gene targeting/knockout mouse, behavioral phenotyping, immunohistochemistry, electron microscopy","journal":"Laboratory investigation","confidence":"High","confidence_rationale":"Tier 2 — in vivo knockout with defined neurological and tissue-specific phenotypes","pmids":["12480912"],"is_preprint":false},{"year":2003,"finding":"In entactin-1-null mice, the glomerular basement membrane is thickened; distribution of anionic charges is significantly altered; αv-integrin density on glomerular cells is increased; glomerular filtration permselectivity (albumin distribution) is altered; type IV collagen and laminin distributions remain unchanged.","method":"Immunocytochemistry in knockout mice, morphometry, glomerular filtration analysis with endogenous albumin","journal":"The journal of histochemistry and cytochemistry","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo knockout with multiple functional readouts of glomerular function","pmids":["14566019"],"is_preprint":false},{"year":2013,"finding":"Mutations in NID1 and its binding partner LAMC1 cause autosomal dominant Dandy-Walker malformation; structural modeling of the NID1-LAMC1 complex shows each mutation disrupts the protein-protein interaction.","method":"Whole-exome sequencing, protein interaction network analysis, structural modeling of NID1-LAMC1 complex","journal":"Human mutation","confidence":"Medium","confidence_rationale":"Tier 2 — human genetics combined with structural modeling showing disruption of defined interaction","pmids":["23674478"],"is_preprint":false},{"year":2017,"finding":"NID1 activates ERK/MAPK signaling to promote epithelial-mesenchymal transition (EMT) in ovarian cancer cells; ectopic NID1 expression induces EMT with enhanced motility, invasiveness, and cisplatin resistance, while NID1 knockdown reverses these effects.","method":"Ectopic overexpression and siRNA knockdown, EMT marker analysis, migration/invasion assays, ERK/MAPK pathway analysis","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 — bidirectional manipulation (overexpression and knockdown) with pathway identification","pmids":["28416770"],"is_preprint":false},{"year":2019,"finding":"NID1 is secreted by mesenchymal-like colorectal cancer cells and induces EMT in neighboring epithelial-like CRC cells via paracrine signaling; p53 suppresses NID1 expression by inducing miR-192 and miR-215, which directly target the NID1 mRNA; NID1 is required and sufficient for inducing EMT in recipient cells.","method":"Conditioned medium transfer, cytokine array, miRNA target validation, p53 activation experiments, rescue assays","journal":"Cellular and molecular gastroenterology and hepatology","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods identifying p53/miR-192/215/NID1 regulatory axis with functional EMT readout","pmids":["30831320"],"is_preprint":false},{"year":2019,"finding":"Drosophila Nidogen/entactin (NDG) is not essential for basement membrane assembly but mediates BM stability and ECM-dependent neural plasticity; loss of Laminin strongly affects BM localization of NDG; Ndg-null mutants have ultrastructural BM defects compromising barrier function, impaired larval crawling, and defects in chordotonal organs and neuromuscular junction.","method":"Drosophila Ndg-null mutants, TEM ultrastructure, in vivo barrier function assay, behavioral assays, confocal immunostaining","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 — comprehensive in vivo loss-of-function in Drosophila ortholog with multiple phenotypic readouts","pmids":["30567930"],"is_preprint":false},{"year":2020,"finding":"BRD4 inhibitor JQ1 reduces NID1 expression in gastric cancer cells via RUNX2; RUNX2 directly binds the NID1 promoter region (demonstrated by ChIP), and RUNX2/NID1 axis mediates JQ1-inhibited metastasis; NID1 knockdown inhibits migration and invasion by inducing MET.","method":"ATAC-seq, RNA-seq, ChIP, luciferase reporter assay, rescue experiments, in vivo tumor models","journal":"Oncogenesis","confidence":"High","confidence_rationale":"Tier 1–2 — ChIP demonstrating direct RUNX2 occupancy at NID1 promoter, luciferase reporter, and rescue experiments","pmids":["32157097"],"is_preprint":false},{"year":2021,"finding":"Enteric neuron-derived Nidogen-1 (NID1) is secreted by enteric neurons and promotes colorectal cancer cell migration; the NID1-enriched secretome of Ndrg4-/- ENS cells boosts intestinal organoid growth; NID1 is enriched in human CRC secretomes.","method":"Ndrg4 knockout mouse models, indirect co-culture, quantitative proteomics, in vitro migration assay, immunostaining","journal":"EMBO reports","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo and in vitro models with proteomics identifying NID1 as functional secreted factor","pmids":["33890711"],"is_preprint":false},{"year":2022,"finding":"NID1 overexpression promotes salivary gland adenoid cystic carcinoma (SACC) metastasis via PI3K/AKT pathway activation and subsequent EMT; HIF-1α directly binds the NID1 promoter and drives NID1 transcription under hypoxia, as confirmed by ChIP and dual-luciferase reporter assay.","method":"ChIP, dual-luciferase reporter assay, NID1 overexpression, PI3K/AKT pathway analysis, in vivo lung metastasis mouse model","journal":"Oral oncology","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP and reporter assay confirming HIF-1α binding; PI3K/AKT pathway mechanistically linked","pmids":["35689951"],"is_preprint":false},{"year":2022,"finding":"Skeletal muscle fibro-adipogenic progenitors (FAPs) are the primary source of elevated NID1 during obesity; increased NID1 impairs muscle stem cell proliferation and primes FAPs toward fibrogenic differentiation, causing excessive ECM deposition.","method":"High-fat diet mouse model, cell fractionation, in vitro myoblast/stem cell assays with recombinant NID1, immunostaining of endomysium","journal":"Matrix biology","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo model combined with in vitro functional assays identifying cellular source and function of NID1","pmids":["35963565"],"is_preprint":false},{"year":2023,"finding":"NID1 is a direct transcriptional target of the EMT transcription factor SNAIL, which occupies an E-box upstream of the NID1 transcription start site; NID1-containing conditioned medium endows non-metastatic CRC cells with lung metastatic capacity after xenotransplantation; ITGAV (αv integrin) is the primary NID1 receptor mediating these effects in CRC.","method":"ChIP for SNAIL occupancy at NID1 E-box, conditioned medium transfer, xenograft lung metastasis assay, ITGAV knockdown","journal":"Cancers","confidence":"High","confidence_rationale":"Tier 2 — ChIP confirming direct transcription factor binding, in vivo metastasis model, and receptor knockdown","pmids":["38001576"],"is_preprint":false},{"year":2023,"finding":"COL4A1 binds to NID1 (confirmed by co-immunoprecipitation) and promotes OSCC cell proliferation, migration, invasion, and EMT; NID1 overexpression reverses the inhibitory effects of COL4A1 knockdown, placing NID1 downstream of COL4A1.","method":"Co-immunoprecipitation, siRNA knockdown, NID1 overexpression rescue, cell proliferation and invasion assays, EMT marker analysis","journal":"Experimental and therapeutic medicine","confidence":"Medium","confidence_rationale":"Tier 3 — single Co-IP with functional rescue experiment demonstrating epistatic relationship","pmids":["37006878"],"is_preprint":false},{"year":2018,"finding":"In C. elegans, NID-1/Nidogen is required for correct dendrite patterning of PVD somatosensory neurons; UNC-52/Perlecan localizes NID-1 via four conserved immunoglobulin domains; genetic epistasis places nid-1 in the same pathway as unc-52 and the netrin axon guidance signaling cassette for dendrite morphogenesis.","method":"C. elegans genetics, null mutant analysis, epistasis assay, confocal imaging of dendrite morphology","journal":"Development (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2 — genetic epistasis in C. elegans ortholog with defined pathway placement","pmids":["29678816"],"is_preprint":false},{"year":2025,"finding":"In C. elegans, NID-1 expressed by body wall muscles or hypodermis promotes guidance of regenerating cholinergic motor axons alongside PVD dendrites; muscle-derived NID-1 specifically is required for synapse reformation and functional recovery; NID-1 acts in coordination with laminin and integrin for axon guidance.","method":"C. elegans nid-1 null mutant, tissue-specific rescue, axon regeneration assay, synapse reformation assay, genetic epistasis with laminin and integrin mutants","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 — tissue-specific rescue and genetic epistasis in C. elegans ortholog; preprint","pmids":["41890084"],"is_preprint":true},{"year":2025,"finding":"Nid1 mediates NASH-related liver fibrosis by activating the JAK2/STAT3 pathway and IL-6 autocrine signaling in hepatic stellate cells; AAV8-mediated Nid1 knockdown attenuates fibrosis; recombinant Nid1 supplementation rescues the protective effect of CP treatment, confirming Nid1 as the mechanistic target.","method":"CDAHFD mouse model, AAV8-mediated knockdown, exogenous recombinant Nid1 rescue, co-culture systems, JAK2/STAT3 pathway analysis, proteomic/metabolomic analysis","journal":"International journal of biological macromolecules","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo knockdown + recombinant rescue confirming Nid1/JAK2/STAT3/IL-6 pathway","pmids":["41349744"],"is_preprint":false},{"year":2024,"finding":"HSPG2 upregulates NID1 expression, leading to activation of the AKT pro-survival signaling pathway and promotion of bladder cancer cell proliferation and chemotherapy resistance.","method":"HSPG2 overexpression in bladder cancer cell lines, Western blotting and immunostaining for NID1/AKT activation, patient-derived tumor organoid mouse models","journal":"Cancer cell international","confidence":"Low","confidence_rationale":"Tier 3 — single lab, overexpression only, no direct binding assay between HSPG2 and NID1","pmids":["39438949"],"is_preprint":false}],"current_model":"NID1 (nidogen-1/entactin) is an ~150 kDa multidomain sulfated glycoprotein with two globular domains (G1, G2) flanking a cysteine-rich EGF-like and thyroglobulin-like stalk (E domain); it forms a tight intracellular complex with laminin and bridges laminin to type IV collagen and fibronectin in basement membrane assembly; it binds calcium ions (N-terminal region), fibrinogen (Aα/Bβ chains), and is cleaved by MMP-7/matrilysin at specific Leu/Ile-preceding sites; cell attachment and neutrophil chemotaxis are mediated by the RGD sequence in the E domain via αvβ3 and the leukocyte response integrin, while a second site in the G2 domain mediates α3β1-dependent adhesion and phagocytosis enhancement; tyrosine sulfation occurs in the medial Golgi; in vivo, NID1 loss selectively disrupts brain capillary and lens capsule basement membranes causing neurological deficits and glomerular permselectivity changes; in cancer contexts, NID1 is a direct transcriptional target of SNAIL that activates ERK/MAPK and PI3K/AKT signaling to promote EMT and metastasis, and is transcriptionally regulated by HIF-1α and the RUNX2/BRD4 axis."},"narrative":{"teleology":[{"year":1981,"claim":"Identification of entactin as a distinct sulfated basement membrane glycoprotein resolved the question of whether basement membranes contained components beyond laminin and collagen IV.","evidence":"Biochemical isolation and immunoelectron microscopy of rodent kidney","pmids":["6262321"],"confidence":"High","gaps":["Protein sequence unknown","Binding partners not identified","Function in BM assembly not tested"]},{"year":1988,"claim":"cDNA sequencing revealed the multidomain architecture (G1-rod-G2 with EGF repeats, thyroglobulin repeat, and an RGD sequence), establishing that entactin possesses intrinsic cell-adhesion capacity through a defined integrin-recognition motif.","evidence":"cDNA cloning, sequence analysis, and RGD peptide cell attachment assay in mammary tumor cells","pmids":["3264556"],"confidence":"High","gaps":["Integrin receptor identity unknown","Domains mediating BM protein interactions not mapped"]},{"year":1990,"claim":"Demonstration that entactin forms a stable intracellular complex with laminin and that its transfection into cells lacking entactin stimulates incorporation of laminin and collagen IV into matrix established entactin as a critical bridging molecule in basement membrane assembly.","evidence":"Transfection of entactin cDNA into JAR cells lacking entactin, with extracellular matrix fractionation and immunofluorescence","pmids":["2119632","2191952"],"confidence":"High","gaps":["Binding domains on laminin and collagen IV not mapped","In vivo requirement not tested"]},{"year":1991,"claim":"Discovery of direct entactin binding to fibrinogen and fibronectin expanded its interaction repertoire beyond classical BM components, suggesting roles in wound healing and provisional matrix.","evidence":"Solid-phase binding assays, affinity chromatography, and transglutaminase cross-linking","pmids":["1680863","1872841"],"confidence":"High","gaps":["In vivo relevance of fibrinogen/fibronectin interactions not shown","Fibronectin-binding domain not mapped"]},{"year":1992,"claim":"Identification of α3β1 as an RGD-independent entactin receptor and of the leukocyte response integrin as the RGD-dependent receptor for neutrophil chemotaxis established that entactin engages at least two distinct integrin pathways with different biological outcomes.","evidence":"Affinity chromatography on entactin-Sepharose, anti-integrin antibody blocking, RGD→RGE site-directed mutagenesis with neutrophil chemotaxis and adhesion assays","pmids":["1527019","1469085"],"confidence":"High","gaps":["Signaling cascades downstream of each integrin not defined","In vivo relevance of neutrophil chemotaxis to entactin not demonstrated"]},{"year":1993,"claim":"Kinetic characterization of MMP-7 (matrilysin) as the most efficient protease for entactin degradation, with cleavage at Leu/Ile-preceding sites, provided a mechanism for regulated BM disassembly.","evidence":"In vitro protease digestion kinetics and Edman degradation for cleavage-site identification","pmids":["8380588"],"confidence":"High","gaps":["In vivo regulation of entactin by MMP-7 not shown at this time","Functional consequences of individual fragments not fully characterized"]},{"year":1995,"claim":"Domain dissection mapped two distinct cell-adhesion sites — the RGD in the E domain engaging αvβ3 and a cysteine-rich EGF repeat in G2 engaging β1 integrin — revealing that entactin is a bifunctional adhesion molecule with domain-specific integrin selectivity.","evidence":"GST-domain fusion protein cell attachment assays, baculovirus-expressed RGD deletion mutant, and anti-integrin antibody blocking","pmids":["7797588"],"confidence":"High","gaps":["Precise β1 integrin heterodimer at G2 site debated (α3β1 vs others)","Structural basis of G2–integrin interaction unknown"]},{"year":1996,"claim":"Functional separation showed the E domain/RGD drives neutrophil chemotaxis via LRI while the G2 domain/α3β1 enhances phagocytosis, and in vivo MMP-3-mediated entactin cleavage in mammary gland was directly linked to epithelial apoptosis, providing the first in vivo consequence of entactin proteolysis.","evidence":"Domain-specific neutrophil activation assays; transgenic mouse cross of stromelysin-1 and TIMP-1 with apoptosis readout","pmids":["8940031","8978831"],"confidence":"High","gaps":["Whether entactin fragments act as direct apoptotic signals or loss of BM support is uncertain","Receptor for apoptotic signaling not identified"]},{"year":2002,"claim":"Nid1-knockout mice revealed selective vulnerability of brain capillary and lens capsule BMs, with neurological deficits and altered glomerular permselectivity, establishing that NID1 is non-redundant in specific tissues despite compensation elsewhere.","evidence":"Gene-targeted knockout mouse with behavioral, immunohistochemical, and electron microscopy phenotyping; glomerular filtration analysis","pmids":["12480912","14566019"],"confidence":"High","gaps":["Compensatory role of nidogen-2 not fully delineated","Molecular basis of tissue-selective BM sensitivity unknown"]},{"year":2013,"claim":"Whole-exome sequencing linked NID1 mutations to autosomal dominant Dandy-Walker malformation, with structural modeling showing disruption of the NID1-LAMC1 interaction, connecting NID1 to a human developmental brain disorder.","evidence":"Whole-exome sequencing of families with Dandy-Walker malformation, structural modeling of NID1-LAMC1 complex","pmids":["23674478"],"confidence":"Medium","gaps":["Small number of families; independent replication in larger cohorts not reported","No functional rescue experiment confirming causality of specific mutations"]},{"year":2017,"claim":"NID1 was shown to activate ERK/MAPK signaling to promote EMT in cancer cells, opening a new functional dimension as a secreted pro-metastatic factor beyond its classical BM structural role.","evidence":"Ectopic overexpression and siRNA knockdown in ovarian cancer cells with EMT marker, migration/invasion, and pathway analysis","pmids":["28416770"],"confidence":"Medium","gaps":["Receptor mediating ERK activation not identified","In vivo metastasis not demonstrated in this study"]},{"year":2019,"claim":"The p53/miR-192/215 axis was identified as a negative regulator of NID1 expression, and NID1-containing conditioned medium was shown to induce EMT in epithelial CRC cells in a paracrine manner, establishing NID1 as a secreted intercellular EMT signal regulated by tumor suppressors.","evidence":"Conditioned medium transfer, miRNA target validation, p53 activation experiments in CRC cell lines","pmids":["30831320"],"confidence":"High","gaps":["Receptor on recipient cells not identified in this study","Contribution of other secreted factors in conditioned medium not fully excluded"]},{"year":2020,"claim":"ChIP demonstrated direct RUNX2 binding at the NID1 promoter, placing NID1 downstream of the BRD4/RUNX2 transcriptional axis and explaining how BET inhibitors suppress metastasis in gastric cancer.","evidence":"ChIP, luciferase reporter, ATAC-seq/RNA-seq, and in vivo tumor models in gastric cancer","pmids":["32157097"],"confidence":"High","gaps":["Whether RUNX2 regulation of NID1 operates in non-cancer contexts unknown","Other transcriptional regulators of NID1 not surveyed systematically"]},{"year":2022,"claim":"HIF-1α was shown to directly bind the NID1 promoter and drive transcription under hypoxia, linking NID1 upregulation to the hypoxic tumor microenvironment and PI3K/AKT-mediated metastasis.","evidence":"ChIP and dual-luciferase reporter in salivary gland adenoid cystic carcinoma cells; in vivo lung metastasis model","pmids":["35689951"],"confidence":"Medium","gaps":["Whether HIF-1α regulation is tissue-general or cancer-specific not determined","Direct NID1 receptor activating PI3K/AKT not identified"]},{"year":2023,"claim":"SNAIL was identified as a direct transcriptional activator of NID1 through E-box occupancy, and ITGAV (αv integrin) was shown to be the primary NID1 receptor mediating paracrine lung metastasis in CRC, closing a key gap in receptor identity.","evidence":"ChIP for SNAIL at NID1 E-box, conditioned medium xenograft lung metastasis assay, ITGAV knockdown in CRC cells","pmids":["38001576"],"confidence":"High","gaps":["Whether ITGAV partners with β3 or another β subunit in this context not resolved","Downstream signaling from ITGAV/NID1 not fully mapped"]},{"year":2025,"claim":"NID1 was placed in the JAK2/STAT3/IL-6 autocrine signaling axis in hepatic stellate cells, establishing a role for NID1 in NASH-related liver fibrosis beyond its classical BM and cancer contexts.","evidence":"CDAHFD mouse model of NASH, AAV8-mediated Nid1 knockdown, recombinant Nid1 rescue, JAK2/STAT3 pathway analysis","pmids":["41349744"],"confidence":"Medium","gaps":["Mechanism by which NID1 activates JAK2 not defined","Whether NID1 acts through a cell-surface receptor or intracellularly in stellate cells unknown"]},{"year":null,"claim":"Key unresolved questions include: how NID1 selectively activates distinct signaling cascades (ERK, PI3K/AKT, JAK2/STAT3) in different cellular contexts; the structural basis of integrin heterodimer selectivity at the G2 domain; and whether nidogen-2 compensates for NID1 loss in tissues that appear unaffected in knockouts.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of NID1–integrin complexes exists","Systematic comparison of NID1 vs NID2 function in vivo is lacking","Receptor identity for JAK2/STAT3 activation is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[4,11,21]},{"term_id":"GO:0098631","term_label":"cell adhesion mediator activity","supporting_discovery_ids":[1,7,8,15,16]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[24,25,29]}],"localization":[{"term_id":"GO:0031012","term_label":"extracellular matrix","supporting_discovery_ids":[0,4,6,11]},{"term_id":"GO:0005576","term_label":"extracellular region","supporting_discovery_ids":[0,11,25,28]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-1474244","term_label":"Extracellular matrix organization","supporting_discovery_ids":[4,11,21,26]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[24,29,35]},{"term_id":"R-HSA-1500931","term_label":"Cell-Cell communication","supporting_discovery_ids":[7,8,15,16]}],"complexes":["Laminin-nidogen complex"],"partners":["LAMC1","COL4A1","FN1","ITGAV","ITGB3","ITGA3","ITGB1","HSPG2"],"other_free_text":[]},"mechanistic_narrative":"NID1 (nidogen-1/entactin) is a secreted basement membrane glycoprotein that bridges laminin to type IV collagen and fibronectin, thereby organizing and stabilizing basement membrane architecture [PMID:2119632, PMID:8433553]. Its multidomain structure harbors two distinct cell-adhesion sites: an RGD sequence in the EGF-like E domain that engages αvβ3 integrin and the leukocyte response integrin to mediate cell attachment and neutrophil chemotaxis, and a cysteine-rich repeat in the G2 domain that binds α3β1 integrin to promote adhesion and enhance phagocytosis [PMID:7797588, PMID:8940031, PMID:1469085]. In vivo, NID1 loss selectively disrupts brain capillary and lens capsule basement membranes causing neurological deficits and altered glomerular permselectivity, and mutations in NID1 and its partner LAMC1 cause autosomal dominant Dandy-Walker malformation [PMID:12480912, PMID:14566019, PMID:23674478]. In cancer contexts, NID1 is transcriptionally activated by SNAIL, HIF-1α, and the RUNX2/BRD4 axis, and functions as a secreted paracrine signal that drives epithelial-mesenchymal transition and metastasis through ERK/MAPK and PI3K/AKT pathways [PMID:38001576, PMID:32157097, PMID:35689951, PMID:28416770]."},"prefetch_data":{"uniprot":{"accession":"P14543","full_name":"Nidogen-1","aliases":["Entactin"],"length_aa":1247,"mass_kda":136.4,"function":"Sulfated glycoprotein widely distributed in basement membranes and tightly associated with laminin. Also binds to collagen IV and perlecan. 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domain shows homology to EGF precursor and LDL receptor; the molecule contains six EGF-type cysteine-rich repeats, one thyroglobulin repeat, and an RGD cell-recognition sequence in one EGF-type repeat; synthetic RGD-containing peptide promotes mammary tumor cell attachment.\",\n      \"method\": \"cDNA sequencing, sequence analysis, synthetic peptide cell attachment assay\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — complete cDNA sequence with functional validation of RGD peptide\",\n      \"pmids\": [\"3264556\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1988,\n      \"finding\": \"Entactin tyrosine sulfation occurs in the medial Golgi cisternae and is not the last modification before secretion; N-linked glycosylation and terminal glycosylation in the trans-Golgi occur after sulfation.\",\n      \"method\": \"Metabolic labeling with [35S]methionine and H2[35S]O4, tunicamycin and monensin inhibitor treatments, pulse-chase analysis\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple inhibitor conditions in a single study defining post-translational modification order\",\n      \"pmids\": [\"3042455\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1990,\n      \"finding\": \"Entactin promotes cell attachment through the integrin RGD recognition sequence; additionally, entactin directly binds calcium ions through sites in the N-terminal region, demonstrated with recombinant peptides containing the first 330 amino acids.\",\n      \"method\": \"Cell attachment assay with synthetic peptides and recombinant entactin, calcium binding assay with recombinant N-terminal fragment\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted cell attachment and direct calcium-binding assay with recombinant proteins and mutagenic peptides\",\n      \"pmids\": [\"2191952\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1990,\n      \"finding\": \"Entactin forms a highly stable noncovalent complex with laminin intracellularly; transfection of entactin into JAR choriocarcinoma cells (which lack entactin but make laminin and collagen IV) stimulates incorporation of all three into extracellular matrix, indicating entactin bridges laminin and type IV collagen in basement membrane assembly.\",\n      \"method\": \"Cell transfection, immunofluorescence, extracellular matrix fractionation\",\n      \"journal\": \"American journal of respiratory cell and molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reconstitution by transfection with functional readout of matrix assembly, replicated in multiple papers\",\n      \"pmids\": [\"2119632\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1991,\n      \"finding\": \"Entactin specifically binds fibrinogen through interactions with the Aα and Bβ chains of fibrinogen in a divalent cation-independent manner; entactin can be cross-linked to fibrinogen by transglutaminase.\",\n      \"method\": \"Solid phase binding assay with radiolabeled entactin, antibody inhibition, transglutaminase cross-linking\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct in vitro binding assay with saturability, antibody inhibition, and cross-linking\",\n      \"pmids\": [\"1680863\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1991,\n      \"finding\": \"Entactin forms a complex with fibronectin (independent of laminin) and co-localizes in the extracellular matrix of 4CQ embryonal carcinoma cells; direct binding between entactin and fibronectin was demonstrated by affinity chromatography and solid phase assay.\",\n      \"method\": \"Affinity column chromatography, solid phase binding assay, immunofluorescence\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — two orthogonal binding methods in a single lab\",\n      \"pmids\": [\"1872841\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"The cell surface receptor for entactin on PC-3 prostate carcinoma cells is integrin α3β1; binding requires divalent cations (Ca2+, Mg2+, Mn2+) and is not inhibited by RGD-containing peptides; α3β1 purified from cells binds entactin-Sepharose, while α2β1 does not.\",\n      \"method\": \"Affinity chromatography on entactin-Sepharose, anti-integrin antibody identification, purified integrin binding assay, liposome reconstitution, antibody inhibition of cell attachment\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — receptor isolated by affinity chromatography, identified by antibodies, confirmed with purified integrin and liposome reconstitution\",\n      \"pmids\": [\"1527019\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"Entactin mediates neutrophil (PMN) adhesion and chemotaxis through its RGD domain and the leukocyte response integrin (LRI); a recombinant RGE-substituted entactin mutant (Asp674→Glu) lost both adhesive and chemotactic activities; anti-β1 and anti-β2 antibodies did not block the response whereas anti-LRI did.\",\n      \"method\": \"Adhesion assay, chemotaxis assay, RGD/RGE synthetic peptides, recombinant site-directed mutant entactin, monoclonal antibody blocking, leukocyte adhesion deficiency patient PMNs\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — site-directed mutagenesis of RGD, multiple antibody blocking experiments, patient cell validation\",\n      \"pmids\": [\"1469085\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"Entactin is required for long-term maintenance and adhesion of contractile skeletal myotubes; anti-entactin antibodies did not inhibit satellite cell attachment or fusion but caused myotube detachment after spontaneous contractions began, demonstrating a specific role for entactin in myotube maintenance.\",\n      \"method\": \"Anti-entactin antibody perturbation on Matrigel cultures of regenerated satellite cells, myotube adhesion assay\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — specific antibody perturbation with defined cellular phenotype (myotube detachment)\",\n      \"pmids\": [\"1734030\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Entactin is specifically degraded by matrix metalloproteinases; matrilysin (MMP-7) is ~100-fold more effective than interstitial collagenase and ~600-fold more effective than 92 kDa gelatinase; matrilysin cleaves entactin at sites amino-terminal to leucine or isoleucine residues producing fragments of 29–115 kDa.\",\n      \"method\": \"In vitro protease digestion assay, kinetic analysis (Km, Vmax), Edman degradation for cleavage site identification\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — quantitative in vitro enzyme assay with precise cleavage site determination\",\n      \"pmids\": [\"8380588\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Entactin binds laminin, collagen IV, fibrinogen, and fibronectin; the laminin-entactin complex is formed intracellularly in M1536-B3 cells and transported in membrane-enclosed vesicles to the extracellular compartment.\",\n      \"method\": \"Co-immunoprecipitation, cell fractionation, transfection experiments, indirect immunofluorescence\",\n      \"journal\": \"Kidney international\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple binding partners confirmed by multiple orthogonal methods, intracellular complex formation demonstrated\",\n      \"pmids\": [\"8433553\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Recombinant entactin promotes primary trophoblast cell adhesion and migration through the RGD recognition sequence; a mutated entactin with Glu replacing Asp at the RGD site provided no trophoblast adhesive activity.\",\n      \"method\": \"Blastocyst outgrowth assay, RGD peptide inhibition, recombinant RGD→RGE mutant entactin, anti-entactin antibody\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — site-directed mutagenesis of RGD with loss-of-function confirmation in cell migration assay\",\n      \"pmids\": [\"8491783\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"The binding of fibronectin to entactin is mediated through the 29 kDa amino-terminal fragment of fibronectin and the G2 domain of entactin (but not G1, E, or G3 domains); half-saturation for binding is ~5 nM.\",\n      \"method\": \"Solid phase binding assay with GST-domain fusion proteins of entactin and radiolabeled fibronectin fragment\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — domain-mapping by solid-phase assay with defined recombinant fragments\",\n      \"pmids\": [\"8147897\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"A novel epitope of entactin at the neuromuscular junction is dependent on glycosylation; N-glycanase treatment reduces entactin molecular mass and eliminates the synaptic-specific 9H6 antibody epitope, indicating that synaptic entactin bears a distinct N-glycosylation pattern not found at extrasynaptic sites.\",\n      \"method\": \"Monoclonal antibody generation, Western blot, N-glycanase treatment, immunostaining of NMJ\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — glycosylation-dependent epitope demonstrated by N-glycanase treatment with specific antibody\",\n      \"pmids\": [\"7514212\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"Entactin has two distinct cell attachment sites: (1) the RGD sequence in the EGF-like stalk (E domain) recognized by αvβ3 integrin, and (2) a second site in a 39-amino acid cysteine-rich EGF repeat of the G2 domain recognized by a β1 integrin family member; deletion/mutation of RGD reveals the second site.\",\n      \"method\": \"GST-domain fusion protein cell attachment assay, baculovirus-expressed full-length RGD deletion mutant, anti-integrin antibody inhibition\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — domain dissection with mutagenesis, antibody blocking, and reconstitution in baculovirus system\",\n      \"pmids\": [\"7797588\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Entactin E domain (containing RGD) ligates the leukocyte response integrin (LRI/β3-like) and signals for neutrophil chemotaxis, while the G2 domain ligates α3β1 and signals for enhancement of Fc receptor-mediated phagocytosis; matrilysin cleavage of entactin liberates fragments retaining both activities.\",\n      \"method\": \"GST-domain fusion protein neutrophil activation assays (chemotaxis, phagocytosis), matrilysin cleavage, anti-integrin antibody blocking\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — domain-specific functional dissection with defined receptor identification and protease cleavage experiments\",\n      \"pmids\": [\"8940031\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Stromelysin-1 (MMP-3) cleaves entactin in mammary gland basement membrane in vivo; enhanced cleavage of entactin correlates directly with apoptosis of overlying mammary epithelial cells; TIMP-1 overexpression blocks both entactin cleavage and apoptosis.\",\n      \"method\": \"Transgenic mouse cross (stromelysin-1 × TIMP-1 overexpressing mice), apoptosis assay, in vivo entactin protein quantification\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo genetic evidence with dose-response across multiple genotypes linking entactin cleavage to apoptosis\",\n      \"pmids\": [\"8978831\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Human mesangial cells adhere to native entactin via both αvβ3 (binding to the RGD sequence on the E domain) and a β1 integrin receptor (binding to a non-RGD site); cation dependence was demonstrated and tertiary molecular structure of entactin contributes to binding.\",\n      \"method\": \"Anti-integrin antibody inhibition of adhesion, wild-type and mutant recombinant entactin fragments, immunoprecipitation of integrin receptors\",\n      \"journal\": \"Cell adhesion and communication\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — domain-specific adhesion mapped with mutant entactin and antibody blocking\",\n      \"pmids\": [\"9686320\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Nidogen-1/entactin-1 is exclusively produced and secreted by mesenchymal peritubular cells (not Sertoli cells) in the testis; monoclonal antibody perturbation against entactin-1 caused loss of peritubular cell adhesion (autocrine function) while Sertoli cells remained adherent.\",\n      \"method\": \"DD-RT-PCR, Western blotting of cell fractions and supernatants, monoclonal antibody perturbation of cell adhesion\",\n      \"journal\": \"European journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — cell-type-specific expression confirmed and function demonstrated by antibody perturbation\",\n      \"pmids\": [\"10727019\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Entactin inhibits amyloid β-protein (Aβ1-40) fibril formation in vitro in a dose-dependent manner at a molar ratio of 50:1 (Aβ:entactin); entactin induces a random coil structure in Aβ40 as shown by circular dichroism spectroscopy.\",\n      \"method\": \"Thioflavin T fluorometric assay, electron microscopy, circular dichroism spectroscopy\",\n      \"journal\": \"Neuroscience letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — in vitro assay with multiple orthogonal methods confirming mechanism\",\n      \"pmids\": [\"11376898\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Targeted disruption of entactin-1/nidogen-1 in mice results in neurological deficits (seizure-like symptoms, loss of hind-leg muscle control) and selective structural alterations in basement membranes of brain capillaries and lens capsule, while other basement membranes appear morphologically normal.\",\n      \"method\": \"Gene targeting/knockout mouse, behavioral phenotyping, immunohistochemistry, electron microscopy\",\n      \"journal\": \"Laboratory investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo knockout with defined neurological and tissue-specific phenotypes\",\n      \"pmids\": [\"12480912\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"In entactin-1-null mice, the glomerular basement membrane is thickened; distribution of anionic charges is significantly altered; αv-integrin density on glomerular cells is increased; glomerular filtration permselectivity (albumin distribution) is altered; type IV collagen and laminin distributions remain unchanged.\",\n      \"method\": \"Immunocytochemistry in knockout mice, morphometry, glomerular filtration analysis with endogenous albumin\",\n      \"journal\": \"The journal of histochemistry and cytochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo knockout with multiple functional readouts of glomerular function\",\n      \"pmids\": [\"14566019\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Mutations in NID1 and its binding partner LAMC1 cause autosomal dominant Dandy-Walker malformation; structural modeling of the NID1-LAMC1 complex shows each mutation disrupts the protein-protein interaction.\",\n      \"method\": \"Whole-exome sequencing, protein interaction network analysis, structural modeling of NID1-LAMC1 complex\",\n      \"journal\": \"Human mutation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — human genetics combined with structural modeling showing disruption of defined interaction\",\n      \"pmids\": [\"23674478\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"NID1 activates ERK/MAPK signaling to promote epithelial-mesenchymal transition (EMT) in ovarian cancer cells; ectopic NID1 expression induces EMT with enhanced motility, invasiveness, and cisplatin resistance, while NID1 knockdown reverses these effects.\",\n      \"method\": \"Ectopic overexpression and siRNA knockdown, EMT marker analysis, migration/invasion assays, ERK/MAPK pathway analysis\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — bidirectional manipulation (overexpression and knockdown) with pathway identification\",\n      \"pmids\": [\"28416770\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"NID1 is secreted by mesenchymal-like colorectal cancer cells and induces EMT in neighboring epithelial-like CRC cells via paracrine signaling; p53 suppresses NID1 expression by inducing miR-192 and miR-215, which directly target the NID1 mRNA; NID1 is required and sufficient for inducing EMT in recipient cells.\",\n      \"method\": \"Conditioned medium transfer, cytokine array, miRNA target validation, p53 activation experiments, rescue assays\",\n      \"journal\": \"Cellular and molecular gastroenterology and hepatology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods identifying p53/miR-192/215/NID1 regulatory axis with functional EMT readout\",\n      \"pmids\": [\"30831320\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Drosophila Nidogen/entactin (NDG) is not essential for basement membrane assembly but mediates BM stability and ECM-dependent neural plasticity; loss of Laminin strongly affects BM localization of NDG; Ndg-null mutants have ultrastructural BM defects compromising barrier function, impaired larval crawling, and defects in chordotonal organs and neuromuscular junction.\",\n      \"method\": \"Drosophila Ndg-null mutants, TEM ultrastructure, in vivo barrier function assay, behavioral assays, confocal immunostaining\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — comprehensive in vivo loss-of-function in Drosophila ortholog with multiple phenotypic readouts\",\n      \"pmids\": [\"30567930\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"BRD4 inhibitor JQ1 reduces NID1 expression in gastric cancer cells via RUNX2; RUNX2 directly binds the NID1 promoter region (demonstrated by ChIP), and RUNX2/NID1 axis mediates JQ1-inhibited metastasis; NID1 knockdown inhibits migration and invasion by inducing MET.\",\n      \"method\": \"ATAC-seq, RNA-seq, ChIP, luciferase reporter assay, rescue experiments, in vivo tumor models\",\n      \"journal\": \"Oncogenesis\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — ChIP demonstrating direct RUNX2 occupancy at NID1 promoter, luciferase reporter, and rescue experiments\",\n      \"pmids\": [\"32157097\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Enteric neuron-derived Nidogen-1 (NID1) is secreted by enteric neurons and promotes colorectal cancer cell migration; the NID1-enriched secretome of Ndrg4-/- ENS cells boosts intestinal organoid growth; NID1 is enriched in human CRC secretomes.\",\n      \"method\": \"Ndrg4 knockout mouse models, indirect co-culture, quantitative proteomics, in vitro migration assay, immunostaining\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo and in vitro models with proteomics identifying NID1 as functional secreted factor\",\n      \"pmids\": [\"33890711\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"NID1 overexpression promotes salivary gland adenoid cystic carcinoma (SACC) metastasis via PI3K/AKT pathway activation and subsequent EMT; HIF-1α directly binds the NID1 promoter and drives NID1 transcription under hypoxia, as confirmed by ChIP and dual-luciferase reporter assay.\",\n      \"method\": \"ChIP, dual-luciferase reporter assay, NID1 overexpression, PI3K/AKT pathway analysis, in vivo lung metastasis mouse model\",\n      \"journal\": \"Oral oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP and reporter assay confirming HIF-1α binding; PI3K/AKT pathway mechanistically linked\",\n      \"pmids\": [\"35689951\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Skeletal muscle fibro-adipogenic progenitors (FAPs) are the primary source of elevated NID1 during obesity; increased NID1 impairs muscle stem cell proliferation and primes FAPs toward fibrogenic differentiation, causing excessive ECM deposition.\",\n      \"method\": \"High-fat diet mouse model, cell fractionation, in vitro myoblast/stem cell assays with recombinant NID1, immunostaining of endomysium\",\n      \"journal\": \"Matrix biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo model combined with in vitro functional assays identifying cellular source and function of NID1\",\n      \"pmids\": [\"35963565\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NID1 is a direct transcriptional target of the EMT transcription factor SNAIL, which occupies an E-box upstream of the NID1 transcription start site; NID1-containing conditioned medium endows non-metastatic CRC cells with lung metastatic capacity after xenotransplantation; ITGAV (αv integrin) is the primary NID1 receptor mediating these effects in CRC.\",\n      \"method\": \"ChIP for SNAIL occupancy at NID1 E-box, conditioned medium transfer, xenograft lung metastasis assay, ITGAV knockdown\",\n      \"journal\": \"Cancers\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ChIP confirming direct transcription factor binding, in vivo metastasis model, and receptor knockdown\",\n      \"pmids\": [\"38001576\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"COL4A1 binds to NID1 (confirmed by co-immunoprecipitation) and promotes OSCC cell proliferation, migration, invasion, and EMT; NID1 overexpression reverses the inhibitory effects of COL4A1 knockdown, placing NID1 downstream of COL4A1.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, NID1 overexpression rescue, cell proliferation and invasion assays, EMT marker analysis\",\n      \"journal\": \"Experimental and therapeutic medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single Co-IP with functional rescue experiment demonstrating epistatic relationship\",\n      \"pmids\": [\"37006878\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"In C. elegans, NID-1/Nidogen is required for correct dendrite patterning of PVD somatosensory neurons; UNC-52/Perlecan localizes NID-1 via four conserved immunoglobulin domains; genetic epistasis places nid-1 in the same pathway as unc-52 and the netrin axon guidance signaling cassette for dendrite morphogenesis.\",\n      \"method\": \"C. elegans genetics, null mutant analysis, epistasis assay, confocal imaging of dendrite morphology\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis in C. elegans ortholog with defined pathway placement\",\n      \"pmids\": [\"29678816\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In C. elegans, NID-1 expressed by body wall muscles or hypodermis promotes guidance of regenerating cholinergic motor axons alongside PVD dendrites; muscle-derived NID-1 specifically is required for synapse reformation and functional recovery; NID-1 acts in coordination with laminin and integrin for axon guidance.\",\n      \"method\": \"C. elegans nid-1 null mutant, tissue-specific rescue, axon regeneration assay, synapse reformation assay, genetic epistasis with laminin and integrin mutants\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — tissue-specific rescue and genetic epistasis in C. elegans ortholog; preprint\",\n      \"pmids\": [\"41890084\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Nid1 mediates NASH-related liver fibrosis by activating the JAK2/STAT3 pathway and IL-6 autocrine signaling in hepatic stellate cells; AAV8-mediated Nid1 knockdown attenuates fibrosis; recombinant Nid1 supplementation rescues the protective effect of CP treatment, confirming Nid1 as the mechanistic target.\",\n      \"method\": \"CDAHFD mouse model, AAV8-mediated knockdown, exogenous recombinant Nid1 rescue, co-culture systems, JAK2/STAT3 pathway analysis, proteomic/metabolomic analysis\",\n      \"journal\": \"International journal of biological macromolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo knockdown + recombinant rescue confirming Nid1/JAK2/STAT3/IL-6 pathway\",\n      \"pmids\": [\"41349744\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"HSPG2 upregulates NID1 expression, leading to activation of the AKT pro-survival signaling pathway and promotion of bladder cancer cell proliferation and chemotherapy resistance.\",\n      \"method\": \"HSPG2 overexpression in bladder cancer cell lines, Western blotting and immunostaining for NID1/AKT activation, patient-derived tumor organoid mouse models\",\n      \"journal\": \"Cancer cell international\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, overexpression only, no direct binding assay between HSPG2 and NID1\",\n      \"pmids\": [\"39438949\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NID1 (nidogen-1/entactin) is an ~150 kDa multidomain sulfated glycoprotein with two globular domains (G1, G2) flanking a cysteine-rich EGF-like and thyroglobulin-like stalk (E domain); it forms a tight intracellular complex with laminin and bridges laminin to type IV collagen and fibronectin in basement membrane assembly; it binds calcium ions (N-terminal region), fibrinogen (Aα/Bβ chains), and is cleaved by MMP-7/matrilysin at specific Leu/Ile-preceding sites; cell attachment and neutrophil chemotaxis are mediated by the RGD sequence in the E domain via αvβ3 and the leukocyte response integrin, while a second site in the G2 domain mediates α3β1-dependent adhesion and phagocytosis enhancement; tyrosine sulfation occurs in the medial Golgi; in vivo, NID1 loss selectively disrupts brain capillary and lens capsule basement membranes causing neurological deficits and glomerular permselectivity changes; in cancer contexts, NID1 is a direct transcriptional target of SNAIL that activates ERK/MAPK and PI3K/AKT signaling to promote EMT and metastasis, and is transcriptionally regulated by HIF-1α and the RUNX2/BRD4 axis.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"NID1 (nidogen-1/entactin) is a secreted basement membrane glycoprotein that bridges laminin to type IV collagen and fibronectin, thereby organizing and stabilizing basement membrane architecture [PMID:2119632, PMID:8433553]. Its multidomain structure harbors two distinct cell-adhesion sites: an RGD sequence in the EGF-like E domain that engages αvβ3 integrin and the leukocyte response integrin to mediate cell attachment and neutrophil chemotaxis, and a cysteine-rich repeat in the G2 domain that binds α3β1 integrin to promote adhesion and enhance phagocytosis [PMID:7797588, PMID:8940031, PMID:1469085]. In vivo, NID1 loss selectively disrupts brain capillary and lens capsule basement membranes causing neurological deficits and altered glomerular permselectivity, and mutations in NID1 and its partner LAMC1 cause autosomal dominant Dandy-Walker malformation [PMID:12480912, PMID:14566019, PMID:23674478]. In cancer contexts, NID1 is transcriptionally activated by SNAIL, HIF-1α, and the RUNX2/BRD4 axis, and functions as a secreted paracrine signal that drives epithelial-mesenchymal transition and metastasis through ERK/MAPK and PI3K/AKT pathways [PMID:38001576, PMID:32157097, PMID:35689951, PMID:28416770].\",\n  \"teleology\": [\n    {\n      \"year\": 1981,\n      \"claim\": \"Identification of entactin as a distinct sulfated basement membrane glycoprotein resolved the question of whether basement membranes contained components beyond laminin and collagen IV.\",\n      \"evidence\": \"Biochemical isolation and immunoelectron microscopy of rodent kidney\",\n      \"pmids\": [\"6262321\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Protein sequence unknown\", \"Binding partners not identified\", \"Function in BM assembly not tested\"]\n    },\n    {\n      \"year\": 1988,\n      \"claim\": \"cDNA sequencing revealed the multidomain architecture (G1-rod-G2 with EGF repeats, thyroglobulin repeat, and an RGD sequence), establishing that entactin possesses intrinsic cell-adhesion capacity through a defined integrin-recognition motif.\",\n      \"evidence\": \"cDNA cloning, sequence analysis, and RGD peptide cell attachment assay in mammary tumor cells\",\n      \"pmids\": [\"3264556\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Integrin receptor identity unknown\", \"Domains mediating BM protein interactions not mapped\"]\n    },\n    {\n      \"year\": 1990,\n      \"claim\": \"Demonstration that entactin forms a stable intracellular complex with laminin and that its transfection into cells lacking entactin stimulates incorporation of laminin and collagen IV into matrix established entactin as a critical bridging molecule in basement membrane assembly.\",\n      \"evidence\": \"Transfection of entactin cDNA into JAR cells lacking entactin, with extracellular matrix fractionation and immunofluorescence\",\n      \"pmids\": [\"2119632\", \"2191952\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Binding domains on laminin and collagen IV not mapped\", \"In vivo requirement not tested\"]\n    },\n    {\n      \"year\": 1991,\n      \"claim\": \"Discovery of direct entactin binding to fibrinogen and fibronectin expanded its interaction repertoire beyond classical BM components, suggesting roles in wound healing and provisional matrix.\",\n      \"evidence\": \"Solid-phase binding assays, affinity chromatography, and transglutaminase cross-linking\",\n      \"pmids\": [\"1680863\", \"1872841\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo relevance of fibrinogen/fibronectin interactions not shown\", \"Fibronectin-binding domain not mapped\"]\n    },\n    {\n      \"year\": 1992,\n      \"claim\": \"Identification of α3β1 as an RGD-independent entactin receptor and of the leukocyte response integrin as the RGD-dependent receptor for neutrophil chemotaxis established that entactin engages at least two distinct integrin pathways with different biological outcomes.\",\n      \"evidence\": \"Affinity chromatography on entactin-Sepharose, anti-integrin antibody blocking, RGD→RGE site-directed mutagenesis with neutrophil chemotaxis and adhesion assays\",\n      \"pmids\": [\"1527019\", \"1469085\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signaling cascades downstream of each integrin not defined\", \"In vivo relevance of neutrophil chemotaxis to entactin not demonstrated\"]\n    },\n    {\n      \"year\": 1993,\n      \"claim\": \"Kinetic characterization of MMP-7 (matrilysin) as the most efficient protease for entactin degradation, with cleavage at Leu/Ile-preceding sites, provided a mechanism for regulated BM disassembly.\",\n      \"evidence\": \"In vitro protease digestion kinetics and Edman degradation for cleavage-site identification\",\n      \"pmids\": [\"8380588\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo regulation of entactin by MMP-7 not shown at this time\", \"Functional consequences of individual fragments not fully characterized\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Domain dissection mapped two distinct cell-adhesion sites — the RGD in the E domain engaging αvβ3 and a cysteine-rich EGF repeat in G2 engaging β1 integrin — revealing that entactin is a bifunctional adhesion molecule with domain-specific integrin selectivity.\",\n      \"evidence\": \"GST-domain fusion protein cell attachment assays, baculovirus-expressed RGD deletion mutant, and anti-integrin antibody blocking\",\n      \"pmids\": [\"7797588\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Precise β1 integrin heterodimer at G2 site debated (α3β1 vs others)\", \"Structural basis of G2–integrin interaction unknown\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Functional separation showed the E domain/RGD drives neutrophil chemotaxis via LRI while the G2 domain/α3β1 enhances phagocytosis, and in vivo MMP-3-mediated entactin cleavage in mammary gland was directly linked to epithelial apoptosis, providing the first in vivo consequence of entactin proteolysis.\",\n      \"evidence\": \"Domain-specific neutrophil activation assays; transgenic mouse cross of stromelysin-1 and TIMP-1 with apoptosis readout\",\n      \"pmids\": [\"8940031\", \"8978831\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether entactin fragments act as direct apoptotic signals or loss of BM support is uncertain\", \"Receptor for apoptotic signaling not identified\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Nid1-knockout mice revealed selective vulnerability of brain capillary and lens capsule BMs, with neurological deficits and altered glomerular permselectivity, establishing that NID1 is non-redundant in specific tissues despite compensation elsewhere.\",\n      \"evidence\": \"Gene-targeted knockout mouse with behavioral, immunohistochemical, and electron microscopy phenotyping; glomerular filtration analysis\",\n      \"pmids\": [\"12480912\", \"14566019\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Compensatory role of nidogen-2 not fully delineated\", \"Molecular basis of tissue-selective BM sensitivity unknown\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Whole-exome sequencing linked NID1 mutations to autosomal dominant Dandy-Walker malformation, with structural modeling showing disruption of the NID1-LAMC1 interaction, connecting NID1 to a human developmental brain disorder.\",\n      \"evidence\": \"Whole-exome sequencing of families with Dandy-Walker malformation, structural modeling of NID1-LAMC1 complex\",\n      \"pmids\": [\"23674478\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Small number of families; independent replication in larger cohorts not reported\", \"No functional rescue experiment confirming causality of specific mutations\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"NID1 was shown to activate ERK/MAPK signaling to promote EMT in cancer cells, opening a new functional dimension as a secreted pro-metastatic factor beyond its classical BM structural role.\",\n      \"evidence\": \"Ectopic overexpression and siRNA knockdown in ovarian cancer cells with EMT marker, migration/invasion, and pathway analysis\",\n      \"pmids\": [\"28416770\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Receptor mediating ERK activation not identified\", \"In vivo metastasis not demonstrated in this study\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"The p53/miR-192/215 axis was identified as a negative regulator of NID1 expression, and NID1-containing conditioned medium was shown to induce EMT in epithelial CRC cells in a paracrine manner, establishing NID1 as a secreted intercellular EMT signal regulated by tumor suppressors.\",\n      \"evidence\": \"Conditioned medium transfer, miRNA target validation, p53 activation experiments in CRC cell lines\",\n      \"pmids\": [\"30831320\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Receptor on recipient cells not identified in this study\", \"Contribution of other secreted factors in conditioned medium not fully excluded\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"ChIP demonstrated direct RUNX2 binding at the NID1 promoter, placing NID1 downstream of the BRD4/RUNX2 transcriptional axis and explaining how BET inhibitors suppress metastasis in gastric cancer.\",\n      \"evidence\": \"ChIP, luciferase reporter, ATAC-seq/RNA-seq, and in vivo tumor models in gastric cancer\",\n      \"pmids\": [\"32157097\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether RUNX2 regulation of NID1 operates in non-cancer contexts unknown\", \"Other transcriptional regulators of NID1 not surveyed systematically\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"HIF-1α was shown to directly bind the NID1 promoter and drive transcription under hypoxia, linking NID1 upregulation to the hypoxic tumor microenvironment and PI3K/AKT-mediated metastasis.\",\n      \"evidence\": \"ChIP and dual-luciferase reporter in salivary gland adenoid cystic carcinoma cells; in vivo lung metastasis model\",\n      \"pmids\": [\"35689951\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether HIF-1α regulation is tissue-general or cancer-specific not determined\", \"Direct NID1 receptor activating PI3K/AKT not identified\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"SNAIL was identified as a direct transcriptional activator of NID1 through E-box occupancy, and ITGAV (αv integrin) was shown to be the primary NID1 receptor mediating paracrine lung metastasis in CRC, closing a key gap in receptor identity.\",\n      \"evidence\": \"ChIP for SNAIL at NID1 E-box, conditioned medium xenograft lung metastasis assay, ITGAV knockdown in CRC cells\",\n      \"pmids\": [\"38001576\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether ITGAV partners with β3 or another β subunit in this context not resolved\", \"Downstream signaling from ITGAV/NID1 not fully mapped\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"NID1 was placed in the JAK2/STAT3/IL-6 autocrine signaling axis in hepatic stellate cells, establishing a role for NID1 in NASH-related liver fibrosis beyond its classical BM and cancer contexts.\",\n      \"evidence\": \"CDAHFD mouse model of NASH, AAV8-mediated Nid1 knockdown, recombinant Nid1 rescue, JAK2/STAT3 pathway analysis\",\n      \"pmids\": [\"41349744\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which NID1 activates JAK2 not defined\", \"Whether NID1 acts through a cell-surface receptor or intracellularly in stellate cells unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include: how NID1 selectively activates distinct signaling cascades (ERK, PI3K/AKT, JAK2/STAT3) in different cellular contexts; the structural basis of integrin heterodimer selectivity at the G2 domain; and whether nidogen-2 compensates for NID1 loss in tissues that appear unaffected in knockouts.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of NID1–integrin complexes exists\", \"Systematic comparison of NID1 vs NID2 function in vivo is lacking\", \"Receptor identity for JAK2/STAT3 activation is unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [4, 11, 21]},\n      {\"term_id\": \"GO:0098631\", \"supporting_discovery_ids\": [1, 7, 8, 15, 16]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [24, 25, 29]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0031012\", \"supporting_discovery_ids\": [0, 4, 6, 11]},\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [0, 11, 25, 28]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1474244\", \"supporting_discovery_ids\": [4, 11, 21, 26]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [24, 29, 35]},\n      {\"term_id\": \"R-HSA-1500931\", \"supporting_discovery_ids\": [7, 8, 15, 16]}\n    ],\n    \"complexes\": [\n      \"Laminin-nidogen complex\"\n    ],\n    \"partners\": [\n      \"LAMC1\",\n      \"COL4A1\",\n      \"FN1\",\n      \"ITGAV\",\n      \"ITGB3\",\n      \"ITGA3\",\n      \"ITGB1\",\n      \"HSPG2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}