{"gene":"FREM1","run_date":"2026-06-09T23:54:44","timeline":{"discoveries":[{"year":2004,"finding":"FREM1 is an extracellular matrix protein required for epidermal adhesion during embryonic development; loss-of-function mutations cause subepidermal blistering beneath the lamina densa and renal agenesis. Unlike Fras1 and Grip1 mutants, collagen VI and Fras1 deposition in the basement membrane is normal in Frem1 mutants, indicating FREM1 acts independently of Fras1/Grip1 in epidermal differentiation.","method":"Mouse genetics (ENU mutagenesis, classic head blebs mutant characterization), immunostaining, in situ hybridization","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function mouse models with specific molecular phenotypic readout (normal Fras1/collagen VI deposition), replicated across two alleles","pmids":["15345741"],"is_preprint":false},{"year":2006,"finding":"FREM1 (QBRICK), FRAS1, and FREM2 form a ternary complex localized to the basement membrane sublamina densa; their basement membrane deposition is mutually and reciprocally dependent, such that loss of any one protein (Frem1, Frem2, or Grip1) results in coordinated depletion of all three from the basement membrane.","method":"Targeted gene disruption of Frem1/Frem2/Grip1 in mice, immunostaining for basement membrane localization, co-expression and complex formation assay in transfected cells","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal genetic disruption experiments plus in vitro complex formation in transfected cells, confirmed across multiple mutant mouse lines","pmids":["16880404"],"is_preprint":false},{"year":2006,"finding":"FREM1 is secreted from both epithelial and mesenchymal cells (unlike FRAS1 which is exclusively epithelial), yet both proteins co-localize in epithelial basement membranes. FREM1 also displays intracellular distribution in periderm cells and basal keratinocytes around E16, and loss of FRAS1 abolishes FREM1 from the basement membrane but not from periderm cells, indicating FREM1 can act independently in epidermal differentiation processes.","method":"Immunofluorescence, electron microscopy, analysis of Fras1-null mouse embryos","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiments with functional inference in Fras1-null context, single lab, multiple imaging modalities","pmids":["17240369"],"is_preprint":false},{"year":2007,"finding":"FREM3 basement membrane localization is independent of the FRAS1/FREM1/FREM2 complex; loss of FRAS1 does not deplete FREM3 from the basement membrane, in contrast to FREM1 and FREM2 which are completely abolished, demonstrating that FREM3 is anchored independently despite sharing the same sublamina densa location.","method":"Immunostaining of Fras1-null mouse embryos, comparison of Frem1/Frem2/Frem3 localization","journal":"Matrix biology : journal of the International Society for Matrix Biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct immunostaining of knockout mouse embryos with multiple protein markers, single lab","pmids":["17596926"],"is_preprint":false},{"year":2009,"finding":"TILRR (an isoform/alias of FREM1) is a membrane-bound glycosylated protein that acts as a co-receptor for IL-1RI; it is recruited to the IL-1 receptor complex, increases receptor expression and ligand binding, potentiates NF-κB activation, and enhances MyD88 adapter recruitment in a Ras GTPase-dependent manner. Mutagenesis confirmed that TILRR function requires association with the IL-1RI signaling complex.","method":"Co-immunoprecipitation, mutagenesis, NF-κB reporter assays, ligand-binding assays, Ras activation assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, mutagenesis, multiple orthogonal functional assays (ligand binding, NF-κB, MyD88 recruitment, Ras activation)","pmids":["19940113"],"is_preprint":false},{"year":2012,"finding":"TILRR (FREM1 isoform) promotes IL-1-induced anti-apoptotic signals and reduces caspase-3 activity through the IL-1RI TIR domain. Alanine-scanning mutagenesis identified two functionally separable regions: R425A blocked Akt activation and cell survival but not MyD88-dependent NF-κB; D448A blocked MyD88-dependent NF-κB but not cell survival, demonstrating that TILRR controls distinct downstream signaling arms through different receptor conformational states.","method":"Alanine-scanning mutagenesis, caspase-3 activity assay, Akt kinase assay, NF-κB reporter assay, cell survival assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — active-site mutagenesis dissecting two distinct functional domains with orthogonal biochemical readouts, single lab but multiple methods","pmids":["22262840"],"is_preprint":false},{"year":2013,"finding":"FREM1 binds directly to PDGFC, and this interaction regulates downstream PDGFRα signaling. Fibroblasts from Frem1-mutant mice show shorter duration and amplitude of PDGFC-induced signaling, and PDGFC-stimulated Timp1 expression is reduced, leading to decreased basement membrane collagen I deposition.","method":"Co-immunoprecipitation (FREM1–PDGFC binding), fibroblast stimulation assays from Frem1-mutant mice, TIMP1/collagen I quantification","journal":"Disease models & mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding demonstrated by co-IP plus downstream functional readouts in mutant fibroblasts, single lab","pmids":["24046351"],"is_preprint":false},{"year":2013,"finding":"Genetic epistasis experiments in mice revealed that FREM1 interacts genetically with GATA4 in lung lobulation defect development and with SLIT3 in renal agenesis development, placing FREM1 in pathways shared with these factors for organ morphogenesis.","method":"Double-mutant mouse crosses (Frem1 x Gata4; Frem1 x Slit3), phenotypic scoring of lung lobulation and renal agenesis","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo genetic epistasis with specific phenotypic readouts, single lab","pmids":["23536828"],"is_preprint":false},{"year":2015,"finding":"The NF-κB inhibitor IκBα is sequestered to the actin/spectrin cytoskeletal complex in resting cells and is released during IL-1 stimulation through a process controlled by the FREM1 isoform TILRR, providing a mechanism for signal calibration and amplification-sensitive NF-κB regulation.","method":"3D predictive protein modelling, in vitro binding/fractionation assays, agent-based in silico simulation validated against in vitro data","journal":"PloS one","confidence":"Low","confidence_rationale":"Tier 3–4 / Weak — computational modelling plus limited in vitro assays, single lab, abstract does not clearly specify orthogonal biochemical validation of IκBα–cytoskeleton interaction","pmids":["26110282"],"is_preprint":false},{"year":2017,"finding":"Genetic deletion of TILRR (FREM1 isoform 2) or antibody blockade of TILRR reduces atherosclerotic plaque development, with decreased monocyte content and increased collagen and smooth muscle cells in lesions, demonstrating that TILRR-IL-1RI co-receptor signaling drives vascular inflammatory disease progression.","method":"Genetic knockout mouse model, antibody blocking experiments, plaque histomorphometry","journal":"JACC. Basic to translational science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic knockout and antibody blocking with defined cellular phenotypic readouts, single lab, two orthogonal intervention methods","pmids":["28920098"],"is_preprint":false},{"year":2012,"finding":"FREM1 deficiency causes congenital diaphragmatic hernia (CDH) in humans and mice; the Frem1(eyes2) mouse (homozygous truncating mutation) develops retrosternal diaphragmatic hernias, and Frem1 is expressed in the anterior developing diaphragm with decreased cell proliferation in Frem1(eyes2) embryos compared to wild-type.","method":"Mouse genetics (ENU-derived eyes2 allele), immunostaining for Frem1 expression, cell proliferation assay (BrdU/Ki67) in diaphragm","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function mouse model with specific cellular phenotypic readout (proliferation), single lab","pmids":["23221805"],"is_preprint":false},{"year":2022,"finding":"Frem1 expression in cranial neural crest cell (cNCC) mesenchyme during midfacial morphogenesis is transcriptionally regulated by Sonic Hedgehog (Shh) signaling; GLI transcription factors bind the Frem1 transcriptional start site, SHH ligand stimulation or pathway activation induces Frem1 expression in cNCCs, and FREM1 protein is sufficient to induce cNCC proliferation in a concentration-dependent manner.","method":"In situ hybridization, Gli1 reporter assays, SHH ligand stimulation of cNCCs, ChIP (GLI binding at Frem1 TSS), cNCC proliferation assays","journal":"Developmental dynamics : an official publication of the American Association of Anatomists","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP for direct transcription factor binding plus functional rescue/stimulation experiments, single lab, multiple orthogonal methods","pmids":["36495293"],"is_preprint":false},{"year":2023,"finding":"FREM1 is a direct transcriptional target of miR-1825 in head and neck squamous cell carcinoma; luciferase reporter assay confirmed direct miR-1825 binding to FREM1, and miR-1825 overexpression reduced FREM1 expression and promoted cancer cell proliferation, migration, invasion, and tumor formation.","method":"MicroRNA target luciferase reporter assay, microarray, FREM1 immunohistochemistry, in vitro cancer phenotype assays, in vivo xenograft","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct target validation by luciferase assay plus in vitro and in vivo functional assays, single lab","pmids":["37683055"],"is_preprint":false},{"year":2020,"finding":"TILRR (FREM1 isoform) overexpression in cervical epithelial cells causes secretion of pro-inflammatory cytokines/chemokines that promote migration of THP-1 monocytes and MOLT-4 T lymphocytes, as measured by Transwell assay and microfluidic device.","method":"TILRR overexpression in HeLa cells, conditioned medium Transwell migration assay, microfluidic device-based migration quantification","journal":"Frontiers in cell and developmental biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, overexpression with indirect readout (conditioned medium migration), no direct binding or mechanistic epistasis","pmids":["32719797"],"is_preprint":false},{"year":2023,"finding":"A splicing variant in FREM1 (c.3274+4A>G) causes exon 18 skipping resulting in a 62 amino acid deletion in the CSPG6 domain; structural modeling predicts this disrupts the stable β-sheet architecture required for FRAS1/FREM multiprotein complex assembly.","method":"Minigene splicing assay (in vitro and in silico), structural prediction modeling, Sanger sequencing validation","journal":"BMC medical genomics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — minigene functional splicing validation confirmed but structural disruption is based on computational prediction only, no direct complex assembly experiment","pmids":["41923049"],"is_preprint":false},{"year":2023,"finding":"In a bleomycin-induced pulmonary fibrosis model, Frem1 upregulation activates the MyD88/NF-κB signaling pathway and establishes a positive feedback loop amplifying IL-1β production that drives macrophage-to-myofibroblast transition (MMT); genetic ablation of Frem1 confirmed its non-redundant role in this process.","method":"Bleomycin mouse model of IPF, Frem1 gene silencing (siRNA/shRNA), qPCR, Western blot, immunofluorescence, flow cytometry, molecular docking","journal":"International immunopharmacology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — gene silencing with pathway readouts in a single lab, molecular docking is computational; mechanism is indirect (Frem1→NF-κB→IL-1β loop) without direct biochemical reconstitution","pmids":["41833105"],"is_preprint":false},{"year":2025,"finding":"Fraser complex proteins (FREM1, FREM2, FRAS1) form anchoring cords in the sublamina densa of the dermal-epidermal junction; AMACO (VWA2) associates with these anchoring cords but is dispensable for their formation or function, as AMACO-deficient mice show no disruption of Fraser complex basement membrane deposition or anchoring cord formation.","method":"AMACO knockout mouse generation, immunostaining for Fraser complex proteins, electron microscopy of anchoring cords","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — knockout mouse model with direct ultrastructural and immunostaining readouts, establishes the independence of FREM1/FRAS1/FREM2 cord formation from AMACO","pmids":["37047755"],"is_preprint":false}],"current_model":"FREM1 is a multi-functional extracellular matrix protein that localizes to the sublamina densa of basement membranes as part of a reciprocally stabilized ternary complex with FRAS1 and FREM2 (forming anchoring cords), where it is required for epidermal–dermal adhesion during embryogenesis; it also binds PDGFC to regulate downstream PDGFRα signaling and extracellular matrix remodeling, and its alternatively spliced isoform TILRR functions as a membrane-bound IL-1RI co-receptor that recruits MyD88, activates Ras, and potentiates NF-κB-driven inflammatory responses through conformationally distinct TIR-domain interactions, with expression of the Frem1 locus itself regulated by Sonic Hedgehog/GLI signaling in cranial neural crest mesenchyme."},"narrative":{"mechanistic_narrative":"FREM1 is a multifunctional extracellular matrix protein essential for epidermal–dermal adhesion during embryogenesis, where loss of function produces subepidermal blistering beneath the lamina densa and renal agenesis [PMID:15345741]. It localizes to the sublamina densa of basement membranes as part of a reciprocally stabilized ternary complex with FRAS1 and FREM2, in which deposition of all three proteins is mutually dependent—loss of any one coordinately depletes the others—and these proteins assemble into anchoring cords at the dermal–epidermal junction [PMID:16880404, PMID:37047755]. FREM1 is secreted from both epithelial and mesenchymal cells, distinguishing it from the exclusively epithelial FRAS1, and can act in epidermal differentiation independently of the Fras1/Grip1 pathway [PMID:15345741, PMID:17240369]. Beyond its structural role, FREM1 binds directly to PDGFC and shapes downstream PDGFRα signaling, modulating TIMP1 expression and basement membrane collagen I deposition [PMID:24046351], and it participates genetically in organ morphogenesis pathways shared with GATA4 (lung lobulation) and SLIT3 (renal agenesis) [PMID:23536828]. Frem1 expression in cranial neural crest mesenchyme is directly driven by Sonic Hedgehog/GLI signaling, with GLI binding the Frem1 transcriptional start site and FREM1 protein promoting neural crest proliferation [PMID:36495293]. A distinct alternatively spliced isoform, TILRR, is a membrane-bound co-receptor for IL-1RI that increases ligand binding, enhances MyD88 recruitment, and potentiates NF-κB activation in a Ras-dependent manner [PMID:19940113], with separable receptor regions controlling MyD88-dependent NF-κB versus Akt-driven cell survival arms [PMID:22262840]. FREM1 deficiency causes congenital diaphragmatic hernia in humans and mice through reduced diaphragm cell proliferation [PMID:23221805].","teleology":[{"year":2004,"claim":"Established FREM1 as an extracellular matrix protein required for epidermal adhesion, and showed it acts independently of the Fras1/Grip1 differentiation pathway since collagen VI and Fras1 deposition remain normal in its absence.","evidence":"ENU mutagenesis mouse genetics with immunostaining and in situ hybridization of head blebs mutants","pmids":["15345741"],"confidence":"High","gaps":["Molecular partners stabilizing FREM1 in the basement membrane not yet defined","Mechanism of adhesion function unresolved"]},{"year":2006,"claim":"Defined the FRAS1/FREM1/FREM2 ternary complex and its reciprocal codependence, explaining why loss of any single member abolishes all three from the sublamina densa.","evidence":"Targeted Frem1/Frem2/Grip1 gene disruption in mice plus co-expression complex formation assays in transfected cells","pmids":["16880404"],"confidence":"High","gaps":["Stoichiometry and structural architecture of the complex not determined","Direct binding interfaces between subunits not mapped"]},{"year":2006,"claim":"Distinguished FREM1's dual epithelial/mesenchymal secretion and intracellular periderm distribution from FRAS1, supporting a Fras1-independent role in epidermal differentiation.","evidence":"Immunofluorescence and electron microscopy in Fras1-null mouse embryos","pmids":["17240369"],"confidence":"Medium","gaps":["Functional significance of intracellular FREM1 in periderm unclear","No reciprocal validation of independent activity"]},{"year":2009,"claim":"Identified the FREM1 isoform TILRR as a membrane-bound IL-1RI co-receptor that amplifies inflammatory signaling, linking the locus to immune regulation beyond its ECM role.","evidence":"Reciprocal co-IP, mutagenesis, NF-κB reporter, ligand-binding, and Ras activation assays","pmids":["19940113"],"confidence":"High","gaps":["Physiological context of TILRR expression not established","Relationship between TILRR isoform and ECM FREM1 not reconciled"]},{"year":2012,"claim":"Dissected TILRR control of two separable signaling arms—MyD88-dependent NF-κB versus Akt-driven cell survival—through distinct receptor conformational states.","evidence":"Alanine-scanning mutagenesis (R425A, D448A) with caspase-3, Akt, NF-κB, and survival assays","pmids":["22262840"],"confidence":"High","gaps":["Structural basis of conformational switching not solved","In vivo relevance of survival vs inflammatory arms untested"]},{"year":2012,"claim":"Linked FREM1 deficiency to congenital diaphragmatic hernia via reduced diaphragm cell proliferation, expanding its developmental phenotype.","evidence":"ENU-derived eyes2 truncating allele mouse with Frem1 immunostaining and BrdU/Ki67 proliferation assay","pmids":["23221805"],"confidence":"Medium","gaps":["Molecular driver of the proliferation defect unknown","Pathway connecting FREM1 to diaphragm morphogenesis unmapped"]},{"year":2013,"claim":"Showed FREM1 binds PDGFC and tunes PDGFRα signaling duration and amplitude, providing a signaling-modulatory mechanism linking it to ECM remodeling.","evidence":"Co-IP of FREM1–PDGFC, fibroblast stimulation from Frem1-mutant mice, TIMP1/collagen I quantification","pmids":["24046351"],"confidence":"Medium","gaps":["Binding interface and affinity not characterized","Whether modulation occurs in vivo during morphogenesis unclear"]},{"year":2013,"claim":"Placed FREM1 in genetic pathways with GATA4 and SLIT3 for lung and kidney morphogenesis through epistasis.","evidence":"Double-mutant mouse crosses with phenotypic scoring of lung lobulation and renal agenesis","pmids":["23536828"],"confidence":"Medium","gaps":["Biochemical basis of genetic interactions not established","Whether interactions are direct or pathway-level unknown"]},{"year":2015,"claim":"Proposed that TILRR calibrates NF-κB signaling by controlling IκBα release from the actin/spectrin cytoskeleton.","evidence":"3D predictive modelling, in vitro binding/fractionation, and agent-based in silico simulation","pmids":["26110282"],"confidence":"Low","gaps":["Largely computational; IκBα–cytoskeleton interaction lacks orthogonal biochemical validation","Direct role of TILRR in sequestration not demonstrated"]},{"year":2017,"claim":"Demonstrated TILRR-IL-1RI co-receptor signaling drives atherosclerotic plaque progression, giving the inflammatory arm a disease phenotype.","evidence":"TILRR knockout mouse and antibody blockade with plaque histomorphometry","pmids":["28920098"],"confidence":"Medium","gaps":["Cell-type-specific contribution not resolved","Mechanistic link from TILRR signaling to monocyte content not fully traced"]},{"year":2020,"claim":"Indicated TILRR overexpression in cervical epithelium drives cytokine secretion that recruits immune cells.","evidence":"TILRR overexpression in HeLa cells with conditioned-medium Transwell and microfluidic migration assays","pmids":["32719797"],"confidence":"Low","gaps":["Overexpression with indirect migration readout; no direct binding or epistasis","Endogenous TILRR contribution untested"]},{"year":2022,"claim":"Established that Shh/GLI signaling directly transcribes Frem1 in cranial neural crest, and that FREM1 protein promotes neural crest proliferation, embedding FREM1 in midfacial morphogenesis.","evidence":"In situ hybridization, Gli1 reporter, SHH stimulation, ChIP at Frem1 TSS, and cNCC proliferation assays","pmids":["36495293"],"confidence":"Medium","gaps":["Downstream effectors of FREM1-induced proliferation unknown","Receptor mediating FREM1 proliferative effect unidentified"]},{"year":2023,"claim":"Identified FREM1 as a direct miR-1825 target whose suppression promotes head and neck squamous cell carcinoma progression, implicating a tumor-suppressive role.","evidence":"Luciferase reporter, microarray, IHC, in vitro phenotype assays, and xenograft","pmids":["37683055"],"confidence":"Medium","gaps":["Mechanism by which FREM1 restrains tumor phenotypes unknown","Whether ECM or signaling function mediates suppression unclear"]},{"year":2023,"claim":"Showed a CSPG6-domain splicing variant predicted to disrupt the β-sheet architecture needed for Fraser complex assembly, connecting genotype to complex integrity.","evidence":"Minigene splicing assay with structural prediction modeling and Sanger validation","pmids":["41923049"],"confidence":"Low","gaps":["Structural disruption is computational only","No direct complex assembly experiment performed"]},{"year":2023,"claim":"Implicated Frem1 in pulmonary fibrosis via a MyD88/NF-κB/IL-1β positive feedback loop driving macrophage-to-myofibroblast transition.","evidence":"Bleomycin mouse model with Frem1 silencing, qPCR, Western, flow cytometry, and molecular docking","pmids":["41833105"],"confidence":"Low","gaps":["Mechanism indirect without biochemical reconstitution","Docking is computational; direct Frem1 interactions in the loop unverified"]},{"year":2025,"claim":"Confirmed FREM1/FRAS1/FREM2 form anchoring cords whose assembly is independent of AMACO (VWA2), refining the boundary of obligate complex partners.","evidence":"AMACO knockout mouse with immunostaining and electron microscopy of anchoring cords","pmids":["37047755"],"confidence":"Medium","gaps":["Functional role of AMACO association with cords unresolved","Other accessory factors at anchoring cords not catalogued"]},{"year":null,"claim":"How the structural ECM/Fraser-complex function of FREM1 relates mechanistically to the TILRR isoform's IL-1RI co-receptor activity, and whether they share regulatory or expression control, remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of FREM1 or the Fraser complex","Isoform switching control between FREM1 and TILRR unknown","Receptor for FREM1's proliferative/signaling effects unidentified"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1,16]},{"term_id":"GO:0038024","term_label":"cargo receptor activity","supporting_discovery_ids":[4]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[4,5]}],"localization":[{"term_id":"GO:0031012","term_label":"extracellular matrix","supporting_discovery_ids":[0,1,16]},{"term_id":"GO:0005576","term_label":"extracellular region","supporting_discovery_ids":[2,6]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-1474244","term_label":"Extracellular matrix organization","supporting_discovery_ids":[0,1,16]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[4,5,9]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[4,6,11]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[0,10,11]}],"complexes":["Fraser complex (FRAS1/FREM1/FREM2)","IL-1RI signaling complex (TILRR isoform)"],"partners":["FRAS1","FREM2","PDGFC","IL1R1","MYD88"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5H8C1","full_name":"FRAS1-related extracellular matrix protein 1","aliases":["Protein QBRICK"],"length_aa":2179,"mass_kda":244.2,"function":"Extracellular matrix protein that plays a role in epidermal differentiation and is required for epidermal adhesion during embryonic development","subcellular_location":"Secreted, extracellular space, extracellular matrix, basement membrane","url":"https://www.uniprot.org/uniprotkb/Q5H8C1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FREM1","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/FREM1","total_profiled":1310},"omim":[{"mim_id":"617667","title":"FRASER SYNDROME 3; FRASRS3","url":"https://www.omim.org/entry/617667"},{"mim_id":"617666","title":"FRASER SYNDROME 2; FRASRS2","url":"https://www.omim.org/entry/617666"},{"mim_id":"614485","title":"TRIGONOCEPHALY 2; TRIGNO2","url":"https://www.omim.org/entry/614485"},{"mim_id":"608980","title":"BIFID NOSE WITH OR WITHOUT ANORECTAL AND RENAL ANOMALIES; BNAR","url":"https://www.omim.org/entry/608980"},{"mim_id":"608946","title":"FRAS1-RELATED EXTRACELLULAR MATRIX PROTEIN 3; FREM3","url":"https://www.omim.org/entry/608946"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"epididymis","ntpm":34.4}],"url":"https://www.proteinatlas.org/search/FREM1"},"hgnc":{"alias_symbol":["FLJ25461","C9orf145","C9orf143","DKFZp686M16108","TILRR"],"prev_symbol":["C9orf154"]},"alphafold":{"accession":"Q5H8C1","domains":[{"cath_id":"2.60.40,2.60.40","chopping":"24-132","consensus_level":"medium","plddt":82.7966,"start":24,"end":132},{"cath_id":"2.60.40","chopping":"136-194_227-287","consensus_level":"high","plddt":79.4513,"start":136,"end":287},{"cath_id":"2.60.40","chopping":"324-410","consensus_level":"medium","plddt":84.4432,"start":324,"end":410},{"cath_id":"2.60.40.60","chopping":"412-518","consensus_level":"medium","plddt":83.7386,"start":412,"end":518},{"cath_id":"2.60.40.10","chopping":"524-635","consensus_level":"high","plddt":80.7237,"start":524,"end":635},{"cath_id":"2.60.40","chopping":"646-772","consensus_level":"high","plddt":80.73,"start":646,"end":772},{"cath_id":"2.60.40,2.60.40","chopping":"780-881","consensus_level":"high","plddt":79.3004,"start":780,"end":881},{"cath_id":"2.60.40,2.60.40","chopping":"890-985_1008-1019","consensus_level":"high","plddt":80.4137,"start":890,"end":1019},{"cath_id":"-","chopping":"1024-1063","consensus_level":"medium","plddt":83.5823,"start":1024,"end":1063},{"cath_id":"2.60.40.10","chopping":"1278-1389","consensus_level":"high","plddt":77.0434,"start":1278,"end":1389},{"cath_id":"2.60.40,2.60.40","chopping":"1393-1503","consensus_level":"medium","plddt":76.7953,"start":1393,"end":1503},{"cath_id":"-","chopping":"1517-1625","consensus_level":"medium","plddt":74.3804,"start":1517,"end":1625},{"cath_id":"-","chopping":"1628-1732","consensus_level":"medium","plddt":81.6592,"start":1628,"end":1732},{"cath_id":"2.60.40.2030","chopping":"1742-1849","consensus_level":"high","plddt":82.4582,"start":1742,"end":1849},{"cath_id":"-","chopping":"2014-2048","consensus_level":"medium","plddt":65.9086,"start":2014,"end":2048},{"cath_id":"3.10.100.10","chopping":"2059-2179","consensus_level":"high","plddt":80.8274,"start":2059,"end":2179}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5H8C1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5H8C1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5H8C1-F1-predicted_aligned_error_v6.png","plddt_mean":75.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FREM1","jax_strain_url":"https://www.jax.org/strain/search?query=FREM1"},"sequence":{"accession":"Q5H8C1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5H8C1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5H8C1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5H8C1"}},"corpus_meta":[{"pmid":"15345741","id":"PMC_15345741","title":"The extracellular matrix gene Frem1 is essential for the normal adhesion of the embryonic epidermis.","date":"2004","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/15345741","citation_count":113,"is_preprint":false},{"pmid":"16880404","id":"PMC_16880404","title":"Breakdown of the reciprocal stabilization of QBRICK/Frem1, Fras1, and Frem2 at the basement membrane provokes Fraser syndrome-like defects.","date":"2006","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/16880404","citation_count":110,"is_preprint":false},{"pmid":"19732862","id":"PMC_19732862","title":"FREM1 mutations cause bifid nose, renal agenesis, and anorectal malformations syndrome.","date":"2009","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/19732862","citation_count":76,"is_preprint":false},{"pmid":"21931569","id":"PMC_21931569","title":"Heterozygous mutations of FREM1 are associated with an increased risk of isolated metopic craniosynostosis in humans and mice.","date":"2011","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/21931569","citation_count":67,"is_preprint":false},{"pmid":"21507892","id":"PMC_21507892","title":"Manitoba-oculo-tricho-anal (MOTA) syndrome is caused by mutations in FREM1.","date":"2011","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/21507892","citation_count":56,"is_preprint":false},{"pmid":"17240369","id":"PMC_17240369","title":"Overlapping and divergent localization of Frem1 and Fras1 and its functional implications during mouse embryonic development.","date":"2006","source":"Experimental cell 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QBRICK/Frem1.","date":"2007","source":"Matrix biology : journal of the International Society for Matrix Biology","url":"https://pubmed.ncbi.nlm.nih.gov/17462874","citation_count":21,"is_preprint":false},{"pmid":"23401257","id":"PMC_23401257","title":"Novel FREM1 mutations expand the phenotypic spectrum associated with Manitoba-oculo-tricho-anal (MOTA) syndrome and bifid nose renal agenesis anorectal malformations (BNAR) syndrome.","date":"2013","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/23401257","citation_count":21,"is_preprint":false},{"pmid":"28920098","id":"PMC_28920098","title":"The IL-1RI Co-Receptor TILRR (FREM1 Isoform 2) Controls Aberrant Inflammatory Responses and Development of Vascular Disease.","date":"2017","source":"JACC. 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biology","url":"https://pubmed.ncbi.nlm.nih.gov/32719797","citation_count":9,"is_preprint":false},{"pmid":"24746155","id":"PMC_24746155","title":"Development of monoclonal antibodies to interrogate functional domains and isoforms of FREM1 protein.","date":"2014","source":"Monoclonal antibodies in immunodiagnosis and immunotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/24746155","citation_count":8,"is_preprint":false},{"pmid":"34594127","id":"PMC_34594127","title":"TILRR (Toll-like Interleukin-1 Receptor Regulator), an Important Modulator of Inflammatory Responsive Genes, is Circulating in the Blood.","date":"2021","source":"Journal of inflammation research","url":"https://pubmed.ncbi.nlm.nih.gov/34594127","citation_count":8,"is_preprint":false},{"pmid":"35726312","id":"PMC_35726312","title":"Integrated Bioinformatics Identifies FREM1 as a Diagnostic Gene Signature for Heart Failure.","date":"2022","source":"Applied bionics and 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hedgehog signaling in the cranial neural crest mesenchyme during midfacial morphogenesis.","date":"2022","source":"Developmental dynamics : an official publication of the American Association of Anatomists","url":"https://pubmed.ncbi.nlm.nih.gov/36495293","citation_count":1,"is_preprint":false},{"pmid":"39819863","id":"PMC_39819863","title":"De Novo Missense Mutation in FREM1 Identified in a Chinese Patient with Comorbid Congenital Microtia and Pulmonary Hypoplasia.","date":"2024","source":"The Journal of craniofacial surgery","url":"https://pubmed.ncbi.nlm.nih.gov/39819863","citation_count":1,"is_preprint":false},{"pmid":"40605465","id":"PMC_40605465","title":"Non-Canonical Splice Site Variant in FREM1 Result in Fetal Renal Agenesis.","date":"2025","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40605465","citation_count":1,"is_preprint":false},{"pmid":"35592073","id":"PMC_35592073","title":"Toll-like Interleukin -1 Receptor Regulator (TILRR) Protein, a Major Modulator of Inflammation, is Expressed in Normal Human and Macaque Tissues and PBMCs.","date":"2022","source":"Journal of inflammation research","url":"https://pubmed.ncbi.nlm.nih.gov/35592073","citation_count":0,"is_preprint":false},{"pmid":"37470964","id":"PMC_37470964","title":"Variants in FREM1 and trisomy 18 identified in a neonatal progeria patient.","date":"2023","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/37470964","citation_count":0,"is_preprint":false},{"pmid":"41833105","id":"PMC_41833105","title":"Sinominine alleviates pulmonary fibrosis by suppressing macrophage-to-myofibroblast transition via inhibition of the Frem1/NF-κB/IL-1β axis.","date":"2026","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/41833105","citation_count":0,"is_preprint":false},{"pmid":"38075139","id":"PMC_38075139","title":"Retracted: Integrated Bioinformatics Identifies FREM1 as a Diagnostic Gene Signature for Heart Failure.","date":"2023","source":"Applied bionics and biomechanics","url":"https://pubmed.ncbi.nlm.nih.gov/38075139","citation_count":0,"is_preprint":false},{"pmid":"37387989","id":"PMC_37387989","title":"Retracted: TILRR Aggravates Sepsis-Induced Acute Lung Injury by Suppressing the PI3K/Akt Pathway.","date":"2023","source":"Evidence-based complementary and alternative medicine : eCAM","url":"https://pubmed.ncbi.nlm.nih.gov/37387989","citation_count":0,"is_preprint":false},{"pmid":"41923049","id":"PMC_41923049","title":"A novel homozygous splicing variant in FREM1 expands the phenotypic spectrum of BNAR syndrome: functional validation and successful PGT-M.","date":"2026","source":"BMC medical genomics","url":"https://pubmed.ncbi.nlm.nih.gov/41923049","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.10.28.620501","title":"<i>Frem2</i>  Knockout Mice Exhibit Fraser Syndrome Phenotypes and Neonatal Lethality Due to Bilateral Renal Agenesis","date":"2024-10-28","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.28.620501","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":20414,"output_tokens":4369,"usd":0.063389,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12439,"output_tokens":4757,"usd":0.09056,"stage2_stop_reason":"end_turn"},"total_usd":0.153949,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2004,\n      \"finding\": \"FREM1 is an extracellular matrix protein required for epidermal adhesion during embryonic development; loss-of-function mutations cause subepidermal blistering beneath the lamina densa and renal agenesis. Unlike Fras1 and Grip1 mutants, collagen VI and Fras1 deposition in the basement membrane is normal in Frem1 mutants, indicating FREM1 acts independently of Fras1/Grip1 in epidermal differentiation.\",\n      \"method\": \"Mouse genetics (ENU mutagenesis, classic head blebs mutant characterization), immunostaining, in situ hybridization\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function mouse models with specific molecular phenotypic readout (normal Fras1/collagen VI deposition), replicated across two alleles\",\n      \"pmids\": [\"15345741\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"FREM1 (QBRICK), FRAS1, and FREM2 form a ternary complex localized to the basement membrane sublamina densa; their basement membrane deposition is mutually and reciprocally dependent, such that loss of any one protein (Frem1, Frem2, or Grip1) results in coordinated depletion of all three from the basement membrane.\",\n      \"method\": \"Targeted gene disruption of Frem1/Frem2/Grip1 in mice, immunostaining for basement membrane localization, co-expression and complex formation assay in transfected cells\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal genetic disruption experiments plus in vitro complex formation in transfected cells, confirmed across multiple mutant mouse lines\",\n      \"pmids\": [\"16880404\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"FREM1 is secreted from both epithelial and mesenchymal cells (unlike FRAS1 which is exclusively epithelial), yet both proteins co-localize in epithelial basement membranes. FREM1 also displays intracellular distribution in periderm cells and basal keratinocytes around E16, and loss of FRAS1 abolishes FREM1 from the basement membrane but not from periderm cells, indicating FREM1 can act independently in epidermal differentiation processes.\",\n      \"method\": \"Immunofluorescence, electron microscopy, analysis of Fras1-null mouse embryos\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiments with functional inference in Fras1-null context, single lab, multiple imaging modalities\",\n      \"pmids\": [\"17240369\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"FREM3 basement membrane localization is independent of the FRAS1/FREM1/FREM2 complex; loss of FRAS1 does not deplete FREM3 from the basement membrane, in contrast to FREM1 and FREM2 which are completely abolished, demonstrating that FREM3 is anchored independently despite sharing the same sublamina densa location.\",\n      \"method\": \"Immunostaining of Fras1-null mouse embryos, comparison of Frem1/Frem2/Frem3 localization\",\n      \"journal\": \"Matrix biology : journal of the International Society for Matrix Biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct immunostaining of knockout mouse embryos with multiple protein markers, single lab\",\n      \"pmids\": [\"17596926\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"TILRR (an isoform/alias of FREM1) is a membrane-bound glycosylated protein that acts as a co-receptor for IL-1RI; it is recruited to the IL-1 receptor complex, increases receptor expression and ligand binding, potentiates NF-κB activation, and enhances MyD88 adapter recruitment in a Ras GTPase-dependent manner. Mutagenesis confirmed that TILRR function requires association with the IL-1RI signaling complex.\",\n      \"method\": \"Co-immunoprecipitation, mutagenesis, NF-κB reporter assays, ligand-binding assays, Ras activation assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, mutagenesis, multiple orthogonal functional assays (ligand binding, NF-κB, MyD88 recruitment, Ras activation)\",\n      \"pmids\": [\"19940113\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"TILRR (FREM1 isoform) promotes IL-1-induced anti-apoptotic signals and reduces caspase-3 activity through the IL-1RI TIR domain. Alanine-scanning mutagenesis identified two functionally separable regions: R425A blocked Akt activation and cell survival but not MyD88-dependent NF-κB; D448A blocked MyD88-dependent NF-κB but not cell survival, demonstrating that TILRR controls distinct downstream signaling arms through different receptor conformational states.\",\n      \"method\": \"Alanine-scanning mutagenesis, caspase-3 activity assay, Akt kinase assay, NF-κB reporter assay, cell survival assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — active-site mutagenesis dissecting two distinct functional domains with orthogonal biochemical readouts, single lab but multiple methods\",\n      \"pmids\": [\"22262840\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"FREM1 binds directly to PDGFC, and this interaction regulates downstream PDGFRα signaling. Fibroblasts from Frem1-mutant mice show shorter duration and amplitude of PDGFC-induced signaling, and PDGFC-stimulated Timp1 expression is reduced, leading to decreased basement membrane collagen I deposition.\",\n      \"method\": \"Co-immunoprecipitation (FREM1–PDGFC binding), fibroblast stimulation assays from Frem1-mutant mice, TIMP1/collagen I quantification\",\n      \"journal\": \"Disease models & mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding demonstrated by co-IP plus downstream functional readouts in mutant fibroblasts, single lab\",\n      \"pmids\": [\"24046351\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Genetic epistasis experiments in mice revealed that FREM1 interacts genetically with GATA4 in lung lobulation defect development and with SLIT3 in renal agenesis development, placing FREM1 in pathways shared with these factors for organ morphogenesis.\",\n      \"method\": \"Double-mutant mouse crosses (Frem1 x Gata4; Frem1 x Slit3), phenotypic scoring of lung lobulation and renal agenesis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo genetic epistasis with specific phenotypic readouts, single lab\",\n      \"pmids\": [\"23536828\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The NF-κB inhibitor IκBα is sequestered to the actin/spectrin cytoskeletal complex in resting cells and is released during IL-1 stimulation through a process controlled by the FREM1 isoform TILRR, providing a mechanism for signal calibration and amplification-sensitive NF-κB regulation.\",\n      \"method\": \"3D predictive protein modelling, in vitro binding/fractionation assays, agent-based in silico simulation validated against in vitro data\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3–4 / Weak — computational modelling plus limited in vitro assays, single lab, abstract does not clearly specify orthogonal biochemical validation of IκBα–cytoskeleton interaction\",\n      \"pmids\": [\"26110282\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Genetic deletion of TILRR (FREM1 isoform 2) or antibody blockade of TILRR reduces atherosclerotic plaque development, with decreased monocyte content and increased collagen and smooth muscle cells in lesions, demonstrating that TILRR-IL-1RI co-receptor signaling drives vascular inflammatory disease progression.\",\n      \"method\": \"Genetic knockout mouse model, antibody blocking experiments, plaque histomorphometry\",\n      \"journal\": \"JACC. Basic to translational science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic knockout and antibody blocking with defined cellular phenotypic readouts, single lab, two orthogonal intervention methods\",\n      \"pmids\": [\"28920098\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"FREM1 deficiency causes congenital diaphragmatic hernia (CDH) in humans and mice; the Frem1(eyes2) mouse (homozygous truncating mutation) develops retrosternal diaphragmatic hernias, and Frem1 is expressed in the anterior developing diaphragm with decreased cell proliferation in Frem1(eyes2) embryos compared to wild-type.\",\n      \"method\": \"Mouse genetics (ENU-derived eyes2 allele), immunostaining for Frem1 expression, cell proliferation assay (BrdU/Ki67) in diaphragm\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function mouse model with specific cellular phenotypic readout (proliferation), single lab\",\n      \"pmids\": [\"23221805\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Frem1 expression in cranial neural crest cell (cNCC) mesenchyme during midfacial morphogenesis is transcriptionally regulated by Sonic Hedgehog (Shh) signaling; GLI transcription factors bind the Frem1 transcriptional start site, SHH ligand stimulation or pathway activation induces Frem1 expression in cNCCs, and FREM1 protein is sufficient to induce cNCC proliferation in a concentration-dependent manner.\",\n      \"method\": \"In situ hybridization, Gli1 reporter assays, SHH ligand stimulation of cNCCs, ChIP (GLI binding at Frem1 TSS), cNCC proliferation assays\",\n      \"journal\": \"Developmental dynamics : an official publication of the American Association of Anatomists\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP for direct transcription factor binding plus functional rescue/stimulation experiments, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"36495293\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"FREM1 is a direct transcriptional target of miR-1825 in head and neck squamous cell carcinoma; luciferase reporter assay confirmed direct miR-1825 binding to FREM1, and miR-1825 overexpression reduced FREM1 expression and promoted cancer cell proliferation, migration, invasion, and tumor formation.\",\n      \"method\": \"MicroRNA target luciferase reporter assay, microarray, FREM1 immunohistochemistry, in vitro cancer phenotype assays, in vivo xenograft\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct target validation by luciferase assay plus in vitro and in vivo functional assays, single lab\",\n      \"pmids\": [\"37683055\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TILRR (FREM1 isoform) overexpression in cervical epithelial cells causes secretion of pro-inflammatory cytokines/chemokines that promote migration of THP-1 monocytes and MOLT-4 T lymphocytes, as measured by Transwell assay and microfluidic device.\",\n      \"method\": \"TILRR overexpression in HeLa cells, conditioned medium Transwell migration assay, microfluidic device-based migration quantification\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, overexpression with indirect readout (conditioned medium migration), no direct binding or mechanistic epistasis\",\n      \"pmids\": [\"32719797\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"A splicing variant in FREM1 (c.3274+4A>G) causes exon 18 skipping resulting in a 62 amino acid deletion in the CSPG6 domain; structural modeling predicts this disrupts the stable β-sheet architecture required for FRAS1/FREM multiprotein complex assembly.\",\n      \"method\": \"Minigene splicing assay (in vitro and in silico), structural prediction modeling, Sanger sequencing validation\",\n      \"journal\": \"BMC medical genomics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — minigene functional splicing validation confirmed but structural disruption is based on computational prediction only, no direct complex assembly experiment\",\n      \"pmids\": [\"41923049\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In a bleomycin-induced pulmonary fibrosis model, Frem1 upregulation activates the MyD88/NF-κB signaling pathway and establishes a positive feedback loop amplifying IL-1β production that drives macrophage-to-myofibroblast transition (MMT); genetic ablation of Frem1 confirmed its non-redundant role in this process.\",\n      \"method\": \"Bleomycin mouse model of IPF, Frem1 gene silencing (siRNA/shRNA), qPCR, Western blot, immunofluorescence, flow cytometry, molecular docking\",\n      \"journal\": \"International immunopharmacology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — gene silencing with pathway readouts in a single lab, molecular docking is computational; mechanism is indirect (Frem1→NF-κB→IL-1β loop) without direct biochemical reconstitution\",\n      \"pmids\": [\"41833105\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Fraser complex proteins (FREM1, FREM2, FRAS1) form anchoring cords in the sublamina densa of the dermal-epidermal junction; AMACO (VWA2) associates with these anchoring cords but is dispensable for their formation or function, as AMACO-deficient mice show no disruption of Fraser complex basement membrane deposition or anchoring cord formation.\",\n      \"method\": \"AMACO knockout mouse generation, immunostaining for Fraser complex proteins, electron microscopy of anchoring cords\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — knockout mouse model with direct ultrastructural and immunostaining readouts, establishes the independence of FREM1/FRAS1/FREM2 cord formation from AMACO\",\n      \"pmids\": [\"37047755\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FREM1 is a multi-functional extracellular matrix protein that localizes to the sublamina densa of basement membranes as part of a reciprocally stabilized ternary complex with FRAS1 and FREM2 (forming anchoring cords), where it is required for epidermal–dermal adhesion during embryogenesis; it also binds PDGFC to regulate downstream PDGFRα signaling and extracellular matrix remodeling, and its alternatively spliced isoform TILRR functions as a membrane-bound IL-1RI co-receptor that recruits MyD88, activates Ras, and potentiates NF-κB-driven inflammatory responses through conformationally distinct TIR-domain interactions, with expression of the Frem1 locus itself regulated by Sonic Hedgehog/GLI signaling in cranial neural crest mesenchyme.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"FREM1 is a multifunctional extracellular matrix protein essential for epidermal–dermal adhesion during embryogenesis, where loss of function produces subepidermal blistering beneath the lamina densa and renal agenesis [#0]. It localizes to the sublamina densa of basement membranes as part of a reciprocally stabilized ternary complex with FRAS1 and FREM2, in which deposition of all three proteins is mutually dependent—loss of any one coordinately depletes the others—and these proteins assemble into anchoring cords at the dermal–epidermal junction [#1, #16]. FREM1 is secreted from both epithelial and mesenchymal cells, distinguishing it from the exclusively epithelial FRAS1, and can act in epidermal differentiation independently of the Fras1/Grip1 pathway [#0, #2]. Beyond its structural role, FREM1 binds directly to PDGFC and shapes downstream PDGFRα signaling, modulating TIMP1 expression and basement membrane collagen I deposition [#6], and it participates genetically in organ morphogenesis pathways shared with GATA4 (lung lobulation) and SLIT3 (renal agenesis) [#7]. Frem1 expression in cranial neural crest mesenchyme is directly driven by Sonic Hedgehog/GLI signaling, with GLI binding the Frem1 transcriptional start site and FREM1 protein promoting neural crest proliferation [#11]. A distinct alternatively spliced isoform, TILRR, is a membrane-bound co-receptor for IL-1RI that increases ligand binding, enhances MyD88 recruitment, and potentiates NF-κB activation in a Ras-dependent manner [#4], with separable receptor regions controlling MyD88-dependent NF-κB versus Akt-driven cell survival arms [#5]. FREM1 deficiency causes congenital diaphragmatic hernia in humans and mice through reduced diaphragm cell proliferation [#10].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Established FREM1 as an extracellular matrix protein required for epidermal adhesion, and showed it acts independently of the Fras1/Grip1 differentiation pathway since collagen VI and Fras1 deposition remain normal in its absence.\",\n      \"evidence\": \"ENU mutagenesis mouse genetics with immunostaining and in situ hybridization of head blebs mutants\",\n      \"pmids\": [\"15345741\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular partners stabilizing FREM1 in the basement membrane not yet defined\", \"Mechanism of adhesion function unresolved\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Defined the FRAS1/FREM1/FREM2 ternary complex and its reciprocal codependence, explaining why loss of any single member abolishes all three from the sublamina densa.\",\n      \"evidence\": \"Targeted Frem1/Frem2/Grip1 gene disruption in mice plus co-expression complex formation assays in transfected cells\",\n      \"pmids\": [\"16880404\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and structural architecture of the complex not determined\", \"Direct binding interfaces between subunits not mapped\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Distinguished FREM1's dual epithelial/mesenchymal secretion and intracellular periderm distribution from FRAS1, supporting a Fras1-independent role in epidermal differentiation.\",\n      \"evidence\": \"Immunofluorescence and electron microscopy in Fras1-null mouse embryos\",\n      \"pmids\": [\"17240369\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional significance of intracellular FREM1 in periderm unclear\", \"No reciprocal validation of independent activity\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Identified the FREM1 isoform TILRR as a membrane-bound IL-1RI co-receptor that amplifies inflammatory signaling, linking the locus to immune regulation beyond its ECM role.\",\n      \"evidence\": \"Reciprocal co-IP, mutagenesis, NF-κB reporter, ligand-binding, and Ras activation assays\",\n      \"pmids\": [\"19940113\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological context of TILRR expression not established\", \"Relationship between TILRR isoform and ECM FREM1 not reconciled\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Dissected TILRR control of two separable signaling arms—MyD88-dependent NF-κB versus Akt-driven cell survival—through distinct receptor conformational states.\",\n      \"evidence\": \"Alanine-scanning mutagenesis (R425A, D448A) with caspase-3, Akt, NF-κB, and survival assays\",\n      \"pmids\": [\"22262840\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of conformational switching not solved\", \"In vivo relevance of survival vs inflammatory arms untested\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Linked FREM1 deficiency to congenital diaphragmatic hernia via reduced diaphragm cell proliferation, expanding its developmental phenotype.\",\n      \"evidence\": \"ENU-derived eyes2 truncating allele mouse with Frem1 immunostaining and BrdU/Ki67 proliferation assay\",\n      \"pmids\": [\"23221805\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular driver of the proliferation defect unknown\", \"Pathway connecting FREM1 to diaphragm morphogenesis unmapped\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Showed FREM1 binds PDGFC and tunes PDGFRα signaling duration and amplitude, providing a signaling-modulatory mechanism linking it to ECM remodeling.\",\n      \"evidence\": \"Co-IP of FREM1–PDGFC, fibroblast stimulation from Frem1-mutant mice, TIMP1/collagen I quantification\",\n      \"pmids\": [\"24046351\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding interface and affinity not characterized\", \"Whether modulation occurs in vivo during morphogenesis unclear\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Placed FREM1 in genetic pathways with GATA4 and SLIT3 for lung and kidney morphogenesis through epistasis.\",\n      \"evidence\": \"Double-mutant mouse crosses with phenotypic scoring of lung lobulation and renal agenesis\",\n      \"pmids\": [\"23536828\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Biochemical basis of genetic interactions not established\", \"Whether interactions are direct or pathway-level unknown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Proposed that TILRR calibrates NF-κB signaling by controlling IκBα release from the actin/spectrin cytoskeleton.\",\n      \"evidence\": \"3D predictive modelling, in vitro binding/fractionation, and agent-based in silico simulation\",\n      \"pmids\": [\"26110282\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Largely computational; IκBα–cytoskeleton interaction lacks orthogonal biochemical validation\", \"Direct role of TILRR in sequestration not demonstrated\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrated TILRR-IL-1RI co-receptor signaling drives atherosclerotic plaque progression, giving the inflammatory arm a disease phenotype.\",\n      \"evidence\": \"TILRR knockout mouse and antibody blockade with plaque histomorphometry\",\n      \"pmids\": [\"28920098\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cell-type-specific contribution not resolved\", \"Mechanistic link from TILRR signaling to monocyte content not fully traced\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Indicated TILRR overexpression in cervical epithelium drives cytokine secretion that recruits immune cells.\",\n      \"evidence\": \"TILRR overexpression in HeLa cells with conditioned-medium Transwell and microfluidic migration assays\",\n      \"pmids\": [\"32719797\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Overexpression with indirect migration readout; no direct binding or epistasis\", \"Endogenous TILRR contribution untested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Established that Shh/GLI signaling directly transcribes Frem1 in cranial neural crest, and that FREM1 protein promotes neural crest proliferation, embedding FREM1 in midfacial morphogenesis.\",\n      \"evidence\": \"In situ hybridization, Gli1 reporter, SHH stimulation, ChIP at Frem1 TSS, and cNCC proliferation assays\",\n      \"pmids\": [\"36495293\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream effectors of FREM1-induced proliferation unknown\", \"Receptor mediating FREM1 proliferative effect unidentified\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified FREM1 as a direct miR-1825 target whose suppression promotes head and neck squamous cell carcinoma progression, implicating a tumor-suppressive role.\",\n      \"evidence\": \"Luciferase reporter, microarray, IHC, in vitro phenotype assays, and xenograft\",\n      \"pmids\": [\"37683055\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which FREM1 restrains tumor phenotypes unknown\", \"Whether ECM or signaling function mediates suppression unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showed a CSPG6-domain splicing variant predicted to disrupt the β-sheet architecture needed for Fraser complex assembly, connecting genotype to complex integrity.\",\n      \"evidence\": \"Minigene splicing assay with structural prediction modeling and Sanger validation\",\n      \"pmids\": [\"41923049\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Structural disruption is computational only\", \"No direct complex assembly experiment performed\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Implicated Frem1 in pulmonary fibrosis via a MyD88/NF-κB/IL-1β positive feedback loop driving macrophage-to-myofibroblast transition.\",\n      \"evidence\": \"Bleomycin mouse model with Frem1 silencing, qPCR, Western, flow cytometry, and molecular docking\",\n      \"pmids\": [\"41833105\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Mechanism indirect without biochemical reconstitution\", \"Docking is computational; direct Frem1 interactions in the loop unverified\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Confirmed FREM1/FRAS1/FREM2 form anchoring cords whose assembly is independent of AMACO (VWA2), refining the boundary of obligate complex partners.\",\n      \"evidence\": \"AMACO knockout mouse with immunostaining and electron microscopy of anchoring cords\",\n      \"pmids\": [\"37047755\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional role of AMACO association with cords unresolved\", \"Other accessory factors at anchoring cords not catalogued\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the structural ECM/Fraser-complex function of FREM1 relates mechanistically to the TILRR isoform's IL-1RI co-receptor activity, and whether they share regulatory or expression control, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of FREM1 or the Fraser complex\", \"Isoform switching control between FREM1 and TILRR unknown\", \"Receptor for FREM1's proliferative/signaling effects unidentified\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1, 16]},\n      {\"term_id\": \"GO:0038024\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0031012\", \"supporting_discovery_ids\": [0, 1, 16]},\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [2, 6]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1474244\", \"supporting_discovery_ids\": [0, 1, 16]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [4, 5, 9]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [4, 6, 11]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [0, 10, 11]}\n    ],\n    \"complexes\": [\"Fraser complex (FRAS1/FREM1/FREM2)\", \"IL-1RI signaling complex (TILRR isoform)\"],\n    \"partners\": [\"FRAS1\", \"FREM2\", \"PDGFC\", \"IL1R1\", \"MyD88\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}