{"gene":"LRRFIP1","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":2010,"finding":"LRRFIP1 functions as a cytosolic nucleic acid sensor that binds exogenous double-stranded RNA and double-stranded DNA, then interacts with β-catenin to promote its activation; activated β-catenin binds the C-terminal domain of IRF3 and recruits the acetyltransferase p300 to the IFN-β enhanceosome, thereby increasing IFN-β production in macrophages in response to VSV and Listeria monocytogenes.","method":"Co-immunoprecipitation, knockdown (siRNA/shRNA), overexpression, reporter assays, nucleic acid binding assays in macrophages","journal":"Nature immunology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP for LRRFIP1–β-catenin–IRF3 interactions, KD with defined IFN-β phenotype, multiple orthogonal methods in one study, widely replicated by subsequent work","pmids":["20453844"],"is_preprint":false},{"year":2003,"finding":"GCF2/LRRFIP1 is a transcriptional repressor of the EGFR promoter; deletion mutagenesis mapped the DNA-binding and repression domain to amino acids 429–528, and GCF2 also suppresses AP2-mediated activation of the EGFR promoter. GCF2 protein was detected in both nuclear and cytoplasmic compartments.","method":"Deletion mutagenesis, promoter-reporter assays, subcellular fractionation/Western blot, Northern blot","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional deletion mutagenesis plus reporter assay plus fractionation, single lab","pmids":["14522076"],"is_preprint":false},{"year":2005,"finding":"GCF2/LRRFIP1 binds the TNF-α −308 promoter site and acts as a transcriptional repressor; it occupies the −308 site in cells that do not produce TNF-α, whereas Ets-1 binds this site in TNF-α-competent cells. Active transcription is additionally accompanied by NF-κB and c-Jun binding to the proximal promoter.","method":"Affinity purification of binding proteins, chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay (EMSA), surface plasmon resonance","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal biochemical methods (affinity purification, ChIP, EMSA, SPR) in one study establishing direct DNA binding and repressor function","pmids":["16199883"],"is_preprint":false},{"year":2010,"finding":"In human platelets, LRRFIP1 functions as a component of the platelet cytoskeleton, where it interacts with the actin-remodeling proteins Flightless-1 and Drebrin, as identified by proteomic analysis of LRRFIP1-interacting proteins. Morpholino-based silencing in zebrafish demonstrated a significant positive regulatory role for lrrfip1 in thrombus formation.","method":"Proteomic co-immunoprecipitation (LRRFIP1 interactome), morpholino knockdown in Danio rerio, correlation analysis of platelet RNA expression","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS-based interactome plus in vivo morpholino KD with defined thrombosis phenotype, single lab","pmids":["20833976"],"is_preprint":false},{"year":2010,"finding":"LRRFIP1 is phosphorylated on serine residues, and this phosphorylation is altered by poly I:C and nicotine stimulation. Upon dsRNA stimulation, LRRFIP1 colocalizes with labeled dsRNA in monocyte lysosomal structures, whereas it does not colocalize with lysosomes lacking dsRNA.","method":"Western blot for serine phosphorylation, immunofluorescence colocalization with labeled dsRNA and lysosomal markers","journal":"Biochemistry and cell biology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — direct localization experiment with functional context plus phosphorylation detection, single lab, two orthogonal methods","pmids":["21102652"],"is_preprint":false},{"year":2012,"finding":"GCF2/LRRFIP1 acts upstream of the small GTPase RhoA as a transcriptional repressor; overexpression of GCF2 results in loss of RhoA expression, disruption of the actin/filamin network, internalization of membrane transporter MRP1 from the cell surface into cytoplasm, increased doxorubicin accumulation, and increased cisplatin resistance. siRNA knockdown of GCF2 in cisplatin-resistant cells reactivated RhoA, restored actin microfilament structure, and relocated MRP1 to the cell surface.","method":"GCF2 overexpression and siRNA knockdown, Western blot for RhoA and MRP1, immunofluorescence for actin/filamin/MRP1 localization, drug sensitivity assays","journal":"Molecular pharmaceutics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — complementary gain- and loss-of-function with multiple cellular readouts, single lab","pmids":["22571463"],"is_preprint":false},{"year":2012,"finding":"GCF2/LRRFIP1 promotes colorectal cancer metastasis by regulating RhoA interaction with the RGS domain of LARG (Leukemia Associated RhoGEF), thereby driving integrin-dependent RhoA activation, cell adhesion, migration, and invasion.","method":"Stable shRNA knockdown in HT-29 cells, in vivo spleen injection metastasis model (SCID mice), fibronectin-induced adhesion/migration/invasion assays, RhoA-LARG interaction analysis","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo metastasis model plus in vitro pathway analysis, single lab, multiple orthogonal readouts","pmids":["22750095"],"is_preprint":false},{"year":2012,"finding":"The FLI-interacting domain of LRRFIP1 forms a classic parallel homodimeric coiled coil with 10 heptad repeats and 22 helical turns, confirmed as a dimer in solution; a longer construct spanning the coiled-coil and DNA-binding domains assembles into higher-order oligomers in solution.","method":"X-ray crystallography of LRRFIP1 coiled-coil domain, solution biophysics (confirming dimer/oligomer state)","journal":"Journal of structural biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure plus solution biophysics validation, single lab but rigorous structural methods","pmids":["23099021"],"is_preprint":false},{"year":2013,"finding":"LRRFIP1 induces vascular smooth muscle cell (VSMC) proliferation and increases phosphorylation of ERK; miR-132 blocks VSMC proliferation by directly targeting and downregulating LRRFIP1 via its 3′-UTR.","method":"miR-132 mimic/antagomir transfection, luciferase reporter assay with LRRFIP1 3′-UTR, Western blot for p27/SM α-actin/Bcl2, ERK phosphorylation assay, carotid artery injury model in rat","journal":"Atherosclerosis","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase 3′-UTR validation plus in vivo injury model plus pathway readout, single lab","pmids":["23880186"],"is_preprint":false},{"year":2014,"finding":"LRRFIP1 binds directly to long noncoding RNAs upstream of the TNF gene and serves as part of a repressive complex assembled on these noncoding RNAs; knockdown of the noncoding RNAs reduced LRRFIP1 binding to both RNA targets and chromatin, leading to TNF derepression, while overexpression of the noncoding RNAs recruited repressor proteins including LRRFIP1 to the locus.","method":"RNA immunoprecipitation, ChIP, RNA knockdown and overexpression, five complementary identification methods for noncoding RNAs","journal":"Journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNA-IP plus ChIP plus gain/loss-of-function, single lab, multiple orthogonal methods","pmids":["24567534"],"is_preprint":false},{"year":2014,"finding":"In rat cortex after cerebral ischemia, Lrrfip1 (the main isoform) is upregulated from acute to late phases and localizes to the cytoplasm of neurons and astrocytes in the peri-infarct area. In astrocytes, Lrrfip1 activates β-catenin, Akt, and mTOR signaling and positively regulates expression of the glutamate transporter GLT-1.","method":"qPCR, immunohistochemistry, subcellular fractionation, in vivo and in vitro ischemia models, Western blot for pathway activation","journal":"Neuroscience","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — direct localization plus pathway activation with multiple readouts in complementary in vivo/in vitro models, single lab","pmids":["24637094"],"is_preprint":false},{"year":2015,"finding":"LRRFIP1 silencing in pancreatic and lung cancer cells reverses the epithelial-mesenchymal transition (EMT), evidenced by increased E-cadherin and decreased vimentin; mechanistically, LRRFIP1 silencing upregulates phosphorylation of β-catenin and decreases its nuclear localization by targeting the β-catenin destruction complex, while increasing β-catenin and E-cadherin in the plasma membrane fraction and inhibiting migration and invasion.","method":"siRNA knockdown, Western blot for EMT markers, subcellular fractionation for β-catenin localization, migration/invasion assays","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with pathway and localization readouts, multiple cancer cell lines, single lab","pmids":["26047573"],"is_preprint":false},{"year":2015,"finding":"LRRFIP1 overexpression in hepatocytes increases IFN-β expression (with or without HCV infection) and inhibits HCV replication, establishing a role for LRRFIP1-mediated type I interferon induction in controlling HCV infection.","method":"LRRFIP1 overexpression in Huh7/Huh7.5.1 cells, qRT-PCR and Western blot for IFN-β, HCV replication assay","journal":"Hepatitis monthly","confidence":"Low","confidence_rationale":"Tier 3 / Weak — overexpression with single readout per endpoint, single lab, no mutagenesis or reciprocal experiment","pmids":["26045710"],"is_preprint":false},{"year":2017,"finding":"Among LRRFIP1 isoforms, LRRFIP1-Iso1 is the strongest enhancer of the canonical Wnt/β-catenin transcription pathway; this activity requires a specific N-terminal domain harboring two critical tryptophan residues (W76, W82) and depends on LRRFIP1-Iso1 homodimerization governed by its specific coiled-coil domain. LRRFIP1-Iso1 and -Iso2 are primarily nuclear due to their shared C-terminal domain, whereas Iso3, -4, and -5 are primarily cytoplasmic and form homo/hetero-multimers.","method":"Topflash β-catenin reporter assay, site-directed mutagenesis (W76A, W82A), subcellular localization by immunofluorescence, co-immunoprecipitation for oligomerization, expression profiling","journal":"Biochimica et biophysica acta. Molecular cell research","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — functional mutagenesis plus reporter assay plus localization plus Co-IP oligomerization, multiple orthogonal methods in one study","pmids":["28322931"],"is_preprint":false},{"year":2019,"finding":"LRRFIP1 expression triggers platelet agglutination by enhancing αIIbβ3 integrin expression; LRRFIP1 knockout in mice significantly decreased αIIbβ3 levels and inhibited platelet agglutination in response to collagen, thrombin, and convulxin.","method":"LRRFIP1 knockout mouse model, platelet aggregation apparatus, flow cytometry for active αIIbβ3","journal":"Experimental and therapeutic medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with defined platelet phenotype and integrin measurement, single lab","pmids":["31258662"],"is_preprint":false},{"year":2020,"finding":"LRRFIP1 is a novel interactor of DAPK1 (Death-Associated Protein Kinase 1) in neurons exposed to oxygen/glucose deprivation (OGD); LRRFIP1 protein levels are increased by pro-oxidant conditions (OGD or the ferroptosis inducer erastin), and the LRRFIP1–DAPK1 interaction was confirmed by reverse Co-IP.","method":"Co-immunoprecipitation (Co-IP and reverse Co-IP), LC-MS/MS proteomics, Western blot, OGD and erastin treatment of primary rat cortical neurons","journal":"Antioxidants","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP validation of MS hit, single lab, functional consequence of interaction not directly tested","pmids":["33265962"],"is_preprint":false},{"year":2021,"finding":"LRRFIP1 silencing in pancreatic cancer cells sensitizes them to gemcitabine by activating the JNK/c-Jun signaling axis; gemcitabine-induced JNK and c-Jun phosphorylation are increased in LRRFIP1 knockdown cells, and this JNK/c-Jun activation depends on Rac activity, as Rac inhibition diminishes the effect.","method":"siRNA knockdown, caspase activity assay, phospho-Western blot for JNK/c-Jun, Rac inhibitor treatment, cell viability assays","journal":"Pancreatology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD with pathway dissection using inhibitor, multiple readouts, single lab","pmids":["33707114"],"is_preprint":false},{"year":2024,"finding":"GCF2/LRRFIP1 mediates nicotine-induced HCC cancer stemness and progression by activating the Wnt/β-catenin/SOX2 signaling pathway; nicotine stabilizes GCF2 protein levels, and silencing GCF2 reduces nicotine-induced stemness and progression.","method":"GCF2 siRNA knockdown, overexpression, Western blot for Wnt/β-catenin/SOX2 pathway components, cancer stemness assays","journal":"Ecotoxicology and environmental safety","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, gain/loss-of-function with pathway readout but limited mechanistic depth on protein stabilization","pmids":["38218109"],"is_preprint":false},{"year":2025,"finding":"LRRFIP1 enhances canonical Wnt/β-catenin signaling in MDS cells by binding to DVL2 and DVL3 (Dishevelled proteins); LRRFIP1 and Dvl synergistically increase Wnt pathway activity, upregulate β-catenin, Dvl2, Dvl3, BCL-2, and CyclinD1, and promote MDS cell proliferation while inhibiting apoptosis.","method":"mRNA transcriptome sequencing, dual luciferase reporter assay, Western blot, co-overexpression experiments (LRRFIP1/Dvl3), CCK8, Annexin-V apoptosis assays","journal":"Journal of translational medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reporter assay plus transcriptome plus functional phenotype, direct DVL interaction inferred from co-overexpression synergy, single lab","pmids":["40420163"],"is_preprint":false},{"year":2025,"finding":"LRRFIP1 inhibits white adipocyte differentiation by binding to the E2F6 promoter and suppressing E2F6 transcription, which in turn downregulates C/EBPα; silencing LRRFIP1 inhibits adipogenic differentiation in C3H10T1/2 cells and reduces differentiation biomarker expression, while overexpression has the opposite effect.","method":"Chromatin immunoprecipitation (ChIP), luciferase promoter assay, qRT-PCR, Western blot, C3H10T1/2 adipogenic differentiation assay, diet-induced obesity mouse model","journal":"Diabetes & metabolism journal","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — ChIP plus luciferase reporter plus complementary gain/loss-of-function, single lab","pmids":["41224206"],"is_preprint":false},{"year":2026,"finding":"In tumor-associated macrophages (TAMs), LRRFIP1 promotes M2-like macrophage polarization via the PI3K/AKT signaling pathway; LRRFIP1 knockdown suppresses M2 phenotype and related cytokine expression, and inhibition of the PI3K pathway or TGF-β receptor abolishes further effects of LRRFIP1 knockdown.","method":"siRNA knockdown in TAMs, flow cytometry, Western blot for PI3K/AKT, ELISA for cytokines, Transwell invasion assay, in vivo tumor/metastasis models, PI3K inhibitor epistasis experiment","journal":"Journal of translational medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis with PI3K inhibitor plus multiple cellular readouts plus in vivo model, single lab","pmids":["41612403"],"is_preprint":false}],"current_model":"LRRFIP1/GCF2 is a multifunctional nucleic acid-binding protein and transcriptional regulator: in innate immunity it acts as a cytosolic sensor for double-stranded RNA/DNA that recruits β-catenin to the IRF3 enhanceosome (via p300) to drive IFN-β production; it also represses transcription of EGFR and TNF-α by directly binding GC-rich promoter elements and assembling repressive complexes on noncoding RNAs; structurally, its FLI-interacting domain forms a homodimeric coiled coil that governs oligomerization and Wnt enhancer activity (with isoform-specific nuclear vs. cytoplasmic localization); and it regulates diverse cellular processes including RhoA/actin/cytoskeletal dynamics, integrin-dependent platelet activation (via αIIbβ3), EMT (through β-catenin/destruction complex), and adipocyte differentiation (via E2F6/C/EBPα), placing it as a pleiotropic scaffold linking nucleic acid sensing, cytoskeletal organization, and Wnt/β-catenin signaling."},"narrative":{"mechanistic_narrative":"LRRFIP1 (also termed GCF2) is a pleiotropic nucleic acid-binding scaffold and transcriptional regulator that links cytosolic nucleic acid sensing, Wnt/β-catenin signaling, and cytoskeletal organization [PMID:20453844, PMID:16199883, PMID:28322931]. In innate immunity it binds exogenous double-stranded RNA and DNA and activates β-catenin, which engages the C-terminal domain of IRF3 and recruits p300 to the IFN-β enhanceosome to amplify type I interferon production in response to viral and bacterial challenge [PMID:20453844]. Independently of its sensing role, LRRFIP1/GCF2 functions as a sequence-specific transcriptional repressor, binding GC-rich elements of the EGFR promoter through a DNA-binding/repression domain mapped to residues 429–528 [PMID:14522076] and occupying the TNF-α −308 promoter site to keep the gene silent, with derepression occurring when it is displaced by activating factors [PMID:16199883]; this repressive activity at the TNF locus is extended through direct binding to upstream long noncoding RNAs that template a repressive complex on chromatin [PMID:24567534]. Structurally, its FLI-interacting domain forms a parallel homodimeric coiled coil, and longer constructs assemble into higher-order oligomers, providing the multimerization framework for its activities [PMID:23099021]; isoform-specific behavior follows from this architecture, with LRRFIP1-Iso1 acting as the strongest enhancer of canonical Wnt/β-catenin transcription via an N-terminal domain bearing critical tryptophans W76/W82 and obligate homodimerization, while shared C-terminal sequence dictates nuclear versus cytoplasmic isoform distribution [PMID:28322931]. Through β-catenin and Dishevelled (DVL2/DVL3) engagement it modulates Wnt-dependent proliferation and survival and drives epithelial-mesenchymal transition by acting on the β-catenin destruction complex [PMID:26047573, PMID:40420163]. LRRFIP1 also controls cytoskeletal and adhesion programs: it interacts with the actin-remodeling proteins Flightless-1 and Drebrin in platelets and promotes thrombus formation and αIIbβ3 integrin-dependent platelet activation [PMID:20833976, PMID:31258662], and it acts upstream of RhoA to govern actin/filamin architecture, cell migration, and invasion [PMID:22571463, PMID:22750095]. Additional roles in adipocyte differentiation via repression of E2F6 and downstream C/EBPα [PMID:41224206] and in tumor-associated macrophage M2 polarization via PI3K/AKT signaling [PMID:41612403] mark it as a broadly acting regulatory node.","teleology":[{"year":2003,"claim":"Established LRRFIP1/GCF2 as a sequence-specific transcriptional repressor by mapping a discrete DNA-binding and repression domain on the EGFR promoter, defining its earliest known molecular function.","evidence":"Deletion mutagenesis, promoter-reporter assays, and subcellular fractionation","pmids":["14522076"],"confidence":"Medium","gaps":["Did not resolve whether repression is direct or requires cofactor complexes","Endogenous physiological context of EGFR repression untested"]},{"year":2005,"claim":"Showed direct, sequence-specific DNA binding to the TNF-α −308 site and a switch-like repressor role, distinguishing TNF-competent from non-competent cells.","evidence":"Affinity purification, ChIP, EMSA, and surface plasmon resonance","pmids":["16199883"],"confidence":"High","gaps":["Repressive complex composition at the locus not defined","How LRRFIP1 is displaced to permit activation not resolved"]},{"year":2010,"claim":"Defined a novel innate-immune function: LRRFIP1 senses cytosolic dsRNA/dsDNA and routes signal through β-catenin to the IRF3/p300 IFN-β enhanceosome, connecting nucleic acid binding to interferon induction.","evidence":"Reciprocal Co-IP, siRNA/shRNA knockdown, reporter assays, and nucleic acid binding assays in macrophages challenged with VSV and Listeria","pmids":["20453844"],"confidence":"High","gaps":["Structural basis of dsRNA/dsDNA recognition not defined","Relationship between sensing and transcriptional repressor activity unclear"]},{"year":2010,"claim":"Placed LRRFIP1 in the platelet cytoskeleton via interactions with actin-remodeling proteins and demonstrated an in vivo role in thrombus formation.","evidence":"Proteomic interactome (Flightless-1, Drebrin) and morpholino knockdown in zebrafish","pmids":["20833976"],"confidence":"Medium","gaps":["Direct binding interfaces with Flightless-1/Drebrin not mapped","Mechanism linking cytoskeletal role to thrombosis not detailed"]},{"year":2010,"claim":"Provided localization and post-translational evidence that LRRFIP1 is serine-phosphorylated and traffics to dsRNA-containing lysosomal structures upon stimulation.","evidence":"Western blot for serine phosphorylation and immunofluorescence colocalization with labeled dsRNA in monocytes","pmids":["21102652"],"confidence":"Medium","gaps":["Kinase responsible for phosphorylation not identified","Functional consequence of lysosomal colocalization untested"]},{"year":2012,"claim":"Connected LRRFIP1/GCF2 to RhoA-dependent cytoskeletal and drug-resistance phenotypes, showing it acts upstream of RhoA and through LARG to drive integrin-dependent migration and metastasis.","evidence":"Gain/loss-of-function with RhoA/actin/MRP1 readouts plus an in vivo colorectal metastasis model and RhoA-LARG interaction analysis","pmids":["22571463","22750095"],"confidence":"Medium","gaps":["Whether RhoA regulation is transcriptional or post-translational not fully resolved","Direct vs. indirect control of LARG-RhoA coupling unclear"]},{"year":2012,"claim":"Resolved the oligomerization architecture by solving the FLI-interacting domain as a parallel homodimeric coiled coil, with longer constructs forming higher-order oligomers.","evidence":"X-ray crystallography and solution biophysics","pmids":["23099021"],"confidence":"High","gaps":["No full-length structure or DNA/RNA-bound complex","Functional role of higher-order oligomers not directly tested"]},{"year":2014,"claim":"Extended TNF repression to an RNA-scaffolded mechanism, showing LRRFIP1 binds upstream long noncoding RNAs that recruit it to chromatin as part of a repressive complex.","evidence":"RNA-IP, ChIP, and RNA knockdown/overexpression","pmids":["24567534"],"confidence":"Medium","gaps":["Other components of the repressive complex not fully cataloged","RNA-binding domain within LRRFIP1 not mapped"]},{"year":2014,"claim":"Demonstrated isoform- and tissue-specific cytoplasmic localization driving β-catenin/Akt/mTOR activation and GLT-1 regulation in CNS ischemia.","evidence":"qPCR, immunohistochemistry, fractionation, and pathway Western blot in ischemia models","pmids":["24637094"],"confidence":"Medium","gaps":["Direct molecular targets in the β-catenin/Akt/mTOR axis not defined","Causality between LRRFIP1 and GLT-1 regulation not mechanistically dissected"]},{"year":2015,"claim":"Linked LRRFIP1 to EMT control by acting on the β-catenin destruction complex to govern β-catenin phosphorylation and nuclear localization in cancer cells.","evidence":"siRNA knockdown with EMT markers, β-catenin fractionation, and migration/invasion assays in pancreatic and lung cancer lines","pmids":["26047573"],"confidence":"Medium","gaps":["Direct interaction with destruction complex components not shown","Distinction between sensing-independent and Wnt-dependent roles unclear"]},{"year":2017,"claim":"Defined the structure-function determinants of Wnt enhancement: Iso1 is the strongest activator, requiring W76/W82 and coiled-coil-mediated homodimerization, with C-terminal sequence dictating nuclear vs cytoplasmic isoform distribution.","evidence":"Topflash reporter, site-directed mutagenesis (W76A/W82A), immunofluorescence localization, and Co-IP oligomerization","pmids":["28322931"],"confidence":"High","gaps":["Direct binding partner engaged by the W76/W82 surface not identified","How isoform localization tunes downstream outputs not resolved"]},{"year":2019,"claim":"Genetic knockout established that LRRFIP1 is required for αIIbβ3 integrin expression and agonist-induced platelet agglutination, formalizing its in vivo platelet role.","evidence":"LRRFIP1 knockout mouse, aggregometry, and flow cytometry for active αIIbβ3","pmids":["31258662"],"confidence":"Medium","gaps":["Mechanism by which LRRFIP1 controls αIIbβ3 levels not defined","Link to earlier cytoskeletal interactome not directly tested"]},{"year":2020,"claim":"Identified DAPK1 as a stress-induced LRRFIP1 interactor in neurons under oxygen/glucose deprivation, extending its interaction network into oxidative stress responses.","evidence":"LC-MS/MS, Co-IP and reverse Co-IP in primary cortical neurons under OGD/erastin","pmids":["33265962"],"confidence":"Low","gaps":["Functional consequence of the LRRFIP1–DAPK1 interaction not tested","Single Co-IP validation of an MS hit without structural mapping"]},{"year":2021,"claim":"Connected LRRFIP1 to chemoresistance by showing its silencing sensitizes pancreatic cancer cells to gemcitabine through Rac-dependent JNK/c-Jun activation.","evidence":"siRNA knockdown, phospho-Western blot, Rac inhibitor epistasis, and viability/caspase assays","pmids":["33707114"],"confidence":"Medium","gaps":["Direct molecular link between LRRFIP1 and Rac not established","Whether effect generalizes beyond pancreatic cancer untested"]},{"year":2025,"claim":"Identified Dishevelled proteins (DVL2/DVL3) as Wnt-pathway partners through which LRRFIP1 synergistically amplifies β-catenin signaling and proliferation/survival in MDS cells.","evidence":"Transcriptome sequencing, dual luciferase reporter, co-overexpression synergy, and proliferation/apoptosis assays","pmids":["40420163"],"confidence":"Medium","gaps":["Direct LRRFIP1–DVL binding inferred from synergy, not biochemically mapped","Domain mediating DVL engagement not defined"]},{"year":2025,"claim":"Extended transcriptional repressor activity to adipogenesis, showing LRRFIP1 binds the E2F6 promoter to suppress E2F6 and downstream C/EBPα, inhibiting white adipocyte differentiation.","evidence":"ChIP, luciferase promoter assay, gain/loss-of-function in C3H10T1/2 cells, and diet-induced obesity mouse model","pmids":["41224206"],"confidence":"Medium","gaps":["Cofactors at the E2F6 promoter not identified","Relation to GC-rich binding seen at EGFR/TNF promoters not tested"]},{"year":2026,"claim":"Defined a role in the tumor microenvironment, with LRRFIP1 promoting M2-like macrophage polarization via PI3K/AKT and TGF-β receptor signaling.","evidence":"siRNA knockdown in TAMs, flow cytometry, cytokine ELISA, PI3K inhibitor epistasis, and in vivo tumor/metastasis models","pmids":["41612403"],"confidence":"Medium","gaps":["Direct molecular targets upstream of PI3K/AKT not identified","Whether nucleic acid sensing contributes to this role untested"]},{"year":null,"claim":"How a single protein integrates cytosolic nucleic acid sensing, GC-rich/lncRNA-templated transcriptional repression, and Wnt/β-catenin enhancement into a coherent regulatory logic — and which activities are isoform-, tissue-, or stimulus-specific — remains unresolved.","evidence":"No single study reconciles the sensing, repressor, and Wnt-enhancer functions mechanistically","pmids":[],"confidence":"Low","gaps":["No full-length structure bound to nucleic acid or partners","Domain assignment of RNA binding vs DNA binding vs partner engagement incomplete","Isoform-specific division of labor across tissues not systematically mapped"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[1,2,19]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,9]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[1,2,9,19]},{"term_id":"GO:0140299","term_label":"molecular sensor activity","supporting_discovery_ids":[0]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[3,5]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,18]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,13]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,10,13]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[3,5]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,20]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[13,18,11]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[1,2,9,19]},{"term_id":"R-HSA-109582","term_label":"Hemostasis","supporting_discovery_ids":[3,14]}],"complexes":[],"partners":["CTNNB1","IRF3","EP300","FLII","DBN1","DVL2","DVL3","DAPK1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q32MZ4","full_name":"Leucine-rich repeat flightless-interacting protein 1","aliases":["GC-binding factor 2","TAR RNA-interacting protein"],"length_aa":808,"mass_kda":89.3,"function":"Transcriptional repressor which preferentially binds to the GC-rich consensus sequence (5'-AGCCCCCGGCG-3') and may regulate expression of TNF, EGFR and PDGFA. May control smooth muscle cells proliferation following artery injury through PDGFA repression. May also bind double-stranded RNA. Positively regulates Toll-like receptor (TLR) signaling in response to agonist probably by competing with the negative FLII regulator for MYD88-binding","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q32MZ4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/LRRFIP1","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"ACTB","stoichiometry":0.2},{"gene":"ACTG1","stoichiometry":0.2},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"MYL12A","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/LRRFIP1","total_profiled":1310},"omim":[{"mim_id":"614043","title":"LEUCINE-RICH REPEAT IN FLII-INTERACTING PROTEIN 2; LRRFIP2","url":"https://www.omim.org/entry/614043"},{"mim_id":"603256","title":"LEUCINE-RICH REPEAT IN FLII-INTERACTING PROTEIN 1; LRRFIP1","url":"https://www.omim.org/entry/603256"},{"mim_id":"600300","title":"SOLUTE CARRIER FAMILY 1 (GLIAL HIGH AFFINITY GLUTAMATE TRANSPORTER), MEMBER 2; SLC1A2","url":"https://www.omim.org/entry/600300"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Plasma membrane","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in 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double-stranded RNA and double-stranded DNA, then interacts with β-catenin to promote its activation; activated β-catenin binds the C-terminal domain of IRF3 and recruits the acetyltransferase p300 to the IFN-β enhanceosome, thereby increasing IFN-β production in macrophages in response to VSV and Listeria monocytogenes.\",\n      \"method\": \"Co-immunoprecipitation, knockdown (siRNA/shRNA), overexpression, reporter assays, nucleic acid binding assays in macrophages\",\n      \"journal\": \"Nature immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP for LRRFIP1–β-catenin–IRF3 interactions, KD with defined IFN-β phenotype, multiple orthogonal methods in one study, widely replicated by subsequent work\",\n      \"pmids\": [\"20453844\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"GCF2/LRRFIP1 is a transcriptional repressor of the EGFR promoter; deletion mutagenesis mapped the DNA-binding and repression domain to amino acids 429–528, and GCF2 also suppresses AP2-mediated activation of the EGFR promoter. GCF2 protein was detected in both nuclear and cytoplasmic compartments.\",\n      \"method\": \"Deletion mutagenesis, promoter-reporter assays, subcellular fractionation/Western blot, Northern blot\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional deletion mutagenesis plus reporter assay plus fractionation, single lab\",\n      \"pmids\": [\"14522076\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"GCF2/LRRFIP1 binds the TNF-α −308 promoter site and acts as a transcriptional repressor; it occupies the −308 site in cells that do not produce TNF-α, whereas Ets-1 binds this site in TNF-α-competent cells. Active transcription is additionally accompanied by NF-κB and c-Jun binding to the proximal promoter.\",\n      \"method\": \"Affinity purification of binding proteins, chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay (EMSA), surface plasmon resonance\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal biochemical methods (affinity purification, ChIP, EMSA, SPR) in one study establishing direct DNA binding and repressor function\",\n      \"pmids\": [\"16199883\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"In human platelets, LRRFIP1 functions as a component of the platelet cytoskeleton, where it interacts with the actin-remodeling proteins Flightless-1 and Drebrin, as identified by proteomic analysis of LRRFIP1-interacting proteins. Morpholino-based silencing in zebrafish demonstrated a significant positive regulatory role for lrrfip1 in thrombus formation.\",\n      \"method\": \"Proteomic co-immunoprecipitation (LRRFIP1 interactome), morpholino knockdown in Danio rerio, correlation analysis of platelet RNA expression\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS-based interactome plus in vivo morpholino KD with defined thrombosis phenotype, single lab\",\n      \"pmids\": [\"20833976\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"LRRFIP1 is phosphorylated on serine residues, and this phosphorylation is altered by poly I:C and nicotine stimulation. Upon dsRNA stimulation, LRRFIP1 colocalizes with labeled dsRNA in monocyte lysosomal structures, whereas it does not colocalize with lysosomes lacking dsRNA.\",\n      \"method\": \"Western blot for serine phosphorylation, immunofluorescence colocalization with labeled dsRNA and lysosomal markers\",\n      \"journal\": \"Biochemistry and cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — direct localization experiment with functional context plus phosphorylation detection, single lab, two orthogonal methods\",\n      \"pmids\": [\"21102652\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"GCF2/LRRFIP1 acts upstream of the small GTPase RhoA as a transcriptional repressor; overexpression of GCF2 results in loss of RhoA expression, disruption of the actin/filamin network, internalization of membrane transporter MRP1 from the cell surface into cytoplasm, increased doxorubicin accumulation, and increased cisplatin resistance. siRNA knockdown of GCF2 in cisplatin-resistant cells reactivated RhoA, restored actin microfilament structure, and relocated MRP1 to the cell surface.\",\n      \"method\": \"GCF2 overexpression and siRNA knockdown, Western blot for RhoA and MRP1, immunofluorescence for actin/filamin/MRP1 localization, drug sensitivity assays\",\n      \"journal\": \"Molecular pharmaceutics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — complementary gain- and loss-of-function with multiple cellular readouts, single lab\",\n      \"pmids\": [\"22571463\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"GCF2/LRRFIP1 promotes colorectal cancer metastasis by regulating RhoA interaction with the RGS domain of LARG (Leukemia Associated RhoGEF), thereby driving integrin-dependent RhoA activation, cell adhesion, migration, and invasion.\",\n      \"method\": \"Stable shRNA knockdown in HT-29 cells, in vivo spleen injection metastasis model (SCID mice), fibronectin-induced adhesion/migration/invasion assays, RhoA-LARG interaction analysis\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo metastasis model plus in vitro pathway analysis, single lab, multiple orthogonal readouts\",\n      \"pmids\": [\"22750095\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The FLI-interacting domain of LRRFIP1 forms a classic parallel homodimeric coiled coil with 10 heptad repeats and 22 helical turns, confirmed as a dimer in solution; a longer construct spanning the coiled-coil and DNA-binding domains assembles into higher-order oligomers in solution.\",\n      \"method\": \"X-ray crystallography of LRRFIP1 coiled-coil domain, solution biophysics (confirming dimer/oligomer state)\",\n      \"journal\": \"Journal of structural biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure plus solution biophysics validation, single lab but rigorous structural methods\",\n      \"pmids\": [\"23099021\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"LRRFIP1 induces vascular smooth muscle cell (VSMC) proliferation and increases phosphorylation of ERK; miR-132 blocks VSMC proliferation by directly targeting and downregulating LRRFIP1 via its 3′-UTR.\",\n      \"method\": \"miR-132 mimic/antagomir transfection, luciferase reporter assay with LRRFIP1 3′-UTR, Western blot for p27/SM α-actin/Bcl2, ERK phosphorylation assay, carotid artery injury model in rat\",\n      \"journal\": \"Atherosclerosis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase 3′-UTR validation plus in vivo injury model plus pathway readout, single lab\",\n      \"pmids\": [\"23880186\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"LRRFIP1 binds directly to long noncoding RNAs upstream of the TNF gene and serves as part of a repressive complex assembled on these noncoding RNAs; knockdown of the noncoding RNAs reduced LRRFIP1 binding to both RNA targets and chromatin, leading to TNF derepression, while overexpression of the noncoding RNAs recruited repressor proteins including LRRFIP1 to the locus.\",\n      \"method\": \"RNA immunoprecipitation, ChIP, RNA knockdown and overexpression, five complementary identification methods for noncoding RNAs\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNA-IP plus ChIP plus gain/loss-of-function, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"24567534\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In rat cortex after cerebral ischemia, Lrrfip1 (the main isoform) is upregulated from acute to late phases and localizes to the cytoplasm of neurons and astrocytes in the peri-infarct area. In astrocytes, Lrrfip1 activates β-catenin, Akt, and mTOR signaling and positively regulates expression of the glutamate transporter GLT-1.\",\n      \"method\": \"qPCR, immunohistochemistry, subcellular fractionation, in vivo and in vitro ischemia models, Western blot for pathway activation\",\n      \"journal\": \"Neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — direct localization plus pathway activation with multiple readouts in complementary in vivo/in vitro models, single lab\",\n      \"pmids\": [\"24637094\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"LRRFIP1 silencing in pancreatic and lung cancer cells reverses the epithelial-mesenchymal transition (EMT), evidenced by increased E-cadherin and decreased vimentin; mechanistically, LRRFIP1 silencing upregulates phosphorylation of β-catenin and decreases its nuclear localization by targeting the β-catenin destruction complex, while increasing β-catenin and E-cadherin in the plasma membrane fraction and inhibiting migration and invasion.\",\n      \"method\": \"siRNA knockdown, Western blot for EMT markers, subcellular fractionation for β-catenin localization, migration/invasion assays\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with pathway and localization readouts, multiple cancer cell lines, single lab\",\n      \"pmids\": [\"26047573\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"LRRFIP1 overexpression in hepatocytes increases IFN-β expression (with or without HCV infection) and inhibits HCV replication, establishing a role for LRRFIP1-mediated type I interferon induction in controlling HCV infection.\",\n      \"method\": \"LRRFIP1 overexpression in Huh7/Huh7.5.1 cells, qRT-PCR and Western blot for IFN-β, HCV replication assay\",\n      \"journal\": \"Hepatitis monthly\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — overexpression with single readout per endpoint, single lab, no mutagenesis or reciprocal experiment\",\n      \"pmids\": [\"26045710\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Among LRRFIP1 isoforms, LRRFIP1-Iso1 is the strongest enhancer of the canonical Wnt/β-catenin transcription pathway; this activity requires a specific N-terminal domain harboring two critical tryptophan residues (W76, W82) and depends on LRRFIP1-Iso1 homodimerization governed by its specific coiled-coil domain. LRRFIP1-Iso1 and -Iso2 are primarily nuclear due to their shared C-terminal domain, whereas Iso3, -4, and -5 are primarily cytoplasmic and form homo/hetero-multimers.\",\n      \"method\": \"Topflash β-catenin reporter assay, site-directed mutagenesis (W76A, W82A), subcellular localization by immunofluorescence, co-immunoprecipitation for oligomerization, expression profiling\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — functional mutagenesis plus reporter assay plus localization plus Co-IP oligomerization, multiple orthogonal methods in one study\",\n      \"pmids\": [\"28322931\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"LRRFIP1 expression triggers platelet agglutination by enhancing αIIbβ3 integrin expression; LRRFIP1 knockout in mice significantly decreased αIIbβ3 levels and inhibited platelet agglutination in response to collagen, thrombin, and convulxin.\",\n      \"method\": \"LRRFIP1 knockout mouse model, platelet aggregation apparatus, flow cytometry for active αIIbβ3\",\n      \"journal\": \"Experimental and therapeutic medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with defined platelet phenotype and integrin measurement, single lab\",\n      \"pmids\": [\"31258662\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"LRRFIP1 is a novel interactor of DAPK1 (Death-Associated Protein Kinase 1) in neurons exposed to oxygen/glucose deprivation (OGD); LRRFIP1 protein levels are increased by pro-oxidant conditions (OGD or the ferroptosis inducer erastin), and the LRRFIP1–DAPK1 interaction was confirmed by reverse Co-IP.\",\n      \"method\": \"Co-immunoprecipitation (Co-IP and reverse Co-IP), LC-MS/MS proteomics, Western blot, OGD and erastin treatment of primary rat cortical neurons\",\n      \"journal\": \"Antioxidants\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP validation of MS hit, single lab, functional consequence of interaction not directly tested\",\n      \"pmids\": [\"33265962\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"LRRFIP1 silencing in pancreatic cancer cells sensitizes them to gemcitabine by activating the JNK/c-Jun signaling axis; gemcitabine-induced JNK and c-Jun phosphorylation are increased in LRRFIP1 knockdown cells, and this JNK/c-Jun activation depends on Rac activity, as Rac inhibition diminishes the effect.\",\n      \"method\": \"siRNA knockdown, caspase activity assay, phospho-Western blot for JNK/c-Jun, Rac inhibitor treatment, cell viability assays\",\n      \"journal\": \"Pancreatology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD with pathway dissection using inhibitor, multiple readouts, single lab\",\n      \"pmids\": [\"33707114\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"GCF2/LRRFIP1 mediates nicotine-induced HCC cancer stemness and progression by activating the Wnt/β-catenin/SOX2 signaling pathway; nicotine stabilizes GCF2 protein levels, and silencing GCF2 reduces nicotine-induced stemness and progression.\",\n      \"method\": \"GCF2 siRNA knockdown, overexpression, Western blot for Wnt/β-catenin/SOX2 pathway components, cancer stemness assays\",\n      \"journal\": \"Ecotoxicology and environmental safety\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, gain/loss-of-function with pathway readout but limited mechanistic depth on protein stabilization\",\n      \"pmids\": [\"38218109\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"LRRFIP1 enhances canonical Wnt/β-catenin signaling in MDS cells by binding to DVL2 and DVL3 (Dishevelled proteins); LRRFIP1 and Dvl synergistically increase Wnt pathway activity, upregulate β-catenin, Dvl2, Dvl3, BCL-2, and CyclinD1, and promote MDS cell proliferation while inhibiting apoptosis.\",\n      \"method\": \"mRNA transcriptome sequencing, dual luciferase reporter assay, Western blot, co-overexpression experiments (LRRFIP1/Dvl3), CCK8, Annexin-V apoptosis assays\",\n      \"journal\": \"Journal of translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reporter assay plus transcriptome plus functional phenotype, direct DVL interaction inferred from co-overexpression synergy, single lab\",\n      \"pmids\": [\"40420163\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"LRRFIP1 inhibits white adipocyte differentiation by binding to the E2F6 promoter and suppressing E2F6 transcription, which in turn downregulates C/EBPα; silencing LRRFIP1 inhibits adipogenic differentiation in C3H10T1/2 cells and reduces differentiation biomarker expression, while overexpression has the opposite effect.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), luciferase promoter assay, qRT-PCR, Western blot, C3H10T1/2 adipogenic differentiation assay, diet-induced obesity mouse model\",\n      \"journal\": \"Diabetes & metabolism journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — ChIP plus luciferase reporter plus complementary gain/loss-of-function, single lab\",\n      \"pmids\": [\"41224206\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"In tumor-associated macrophages (TAMs), LRRFIP1 promotes M2-like macrophage polarization via the PI3K/AKT signaling pathway; LRRFIP1 knockdown suppresses M2 phenotype and related cytokine expression, and inhibition of the PI3K pathway or TGF-β receptor abolishes further effects of LRRFIP1 knockdown.\",\n      \"method\": \"siRNA knockdown in TAMs, flow cytometry, Western blot for PI3K/AKT, ELISA for cytokines, Transwell invasion assay, in vivo tumor/metastasis models, PI3K inhibitor epistasis experiment\",\n      \"journal\": \"Journal of translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis with PI3K inhibitor plus multiple cellular readouts plus in vivo model, single lab\",\n      \"pmids\": [\"41612403\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LRRFIP1/GCF2 is a multifunctional nucleic acid-binding protein and transcriptional regulator: in innate immunity it acts as a cytosolic sensor for double-stranded RNA/DNA that recruits β-catenin to the IRF3 enhanceosome (via p300) to drive IFN-β production; it also represses transcription of EGFR and TNF-α by directly binding GC-rich promoter elements and assembling repressive complexes on noncoding RNAs; structurally, its FLI-interacting domain forms a homodimeric coiled coil that governs oligomerization and Wnt enhancer activity (with isoform-specific nuclear vs. cytoplasmic localization); and it regulates diverse cellular processes including RhoA/actin/cytoskeletal dynamics, integrin-dependent platelet activation (via αIIbβ3), EMT (through β-catenin/destruction complex), and adipocyte differentiation (via E2F6/C/EBPα), placing it as a pleiotropic scaffold linking nucleic acid sensing, cytoskeletal organization, and Wnt/β-catenin signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LRRFIP1 (also termed GCF2) is a pleiotropic nucleic acid-binding scaffold and transcriptional regulator that links cytosolic nucleic acid sensing, Wnt/β-catenin signaling, and cytoskeletal organization [#0, #2, #13]. In innate immunity it binds exogenous double-stranded RNA and DNA and activates β-catenin, which engages the C-terminal domain of IRF3 and recruits p300 to the IFN-β enhanceosome to amplify type I interferon production in response to viral and bacterial challenge [#0]. Independently of its sensing role, LRRFIP1/GCF2 functions as a sequence-specific transcriptional repressor, binding GC-rich elements of the EGFR promoter through a DNA-binding/repression domain mapped to residues 429–528 [#1] and occupying the TNF-α −308 promoter site to keep the gene silent, with derepression occurring when it is displaced by activating factors [#2]; this repressive activity at the TNF locus is extended through direct binding to upstream long noncoding RNAs that template a repressive complex on chromatin [#9]. Structurally, its FLI-interacting domain forms a parallel homodimeric coiled coil, and longer constructs assemble into higher-order oligomers, providing the multimerization framework for its activities [#7]; isoform-specific behavior follows from this architecture, with LRRFIP1-Iso1 acting as the strongest enhancer of canonical Wnt/β-catenin transcription via an N-terminal domain bearing critical tryptophans W76/W82 and obligate homodimerization, while shared C-terminal sequence dictates nuclear versus cytoplasmic isoform distribution [#13]. Through β-catenin and Dishevelled (DVL2/DVL3) engagement it modulates Wnt-dependent proliferation and survival and drives epithelial-mesenchymal transition by acting on the β-catenin destruction complex [#11, #18]. LRRFIP1 also controls cytoskeletal and adhesion programs: it interacts with the actin-remodeling proteins Flightless-1 and Drebrin in platelets and promotes thrombus formation and αIIbβ3 integrin-dependent platelet activation [#3, #14], and it acts upstream of RhoA to govern actin/filamin architecture, cell migration, and invasion [#5, #6]. Additional roles in adipocyte differentiation via repression of E2F6 and downstream C/EBPα [#19] and in tumor-associated macrophage M2 polarization via PI3K/AKT signaling [#20] mark it as a broadly acting regulatory node.\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Established LRRFIP1/GCF2 as a sequence-specific transcriptional repressor by mapping a discrete DNA-binding and repression domain on the EGFR promoter, defining its earliest known molecular function.\",\n      \"evidence\": \"Deletion mutagenesis, promoter-reporter assays, and subcellular fractionation\",\n      \"pmids\": [\"14522076\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not resolve whether repression is direct or requires cofactor complexes\", \"Endogenous physiological context of EGFR repression untested\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Showed direct, sequence-specific DNA binding to the TNF-α −308 site and a switch-like repressor role, distinguishing TNF-competent from non-competent cells.\",\n      \"evidence\": \"Affinity purification, ChIP, EMSA, and surface plasmon resonance\",\n      \"pmids\": [\"16199883\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Repressive complex composition at the locus not defined\", \"How LRRFIP1 is displaced to permit activation not resolved\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Defined a novel innate-immune function: LRRFIP1 senses cytosolic dsRNA/dsDNA and routes signal through β-catenin to the IRF3/p300 IFN-β enhanceosome, connecting nucleic acid binding to interferon induction.\",\n      \"evidence\": \"Reciprocal Co-IP, siRNA/shRNA knockdown, reporter assays, and nucleic acid binding assays in macrophages challenged with VSV and Listeria\",\n      \"pmids\": [\"20453844\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of dsRNA/dsDNA recognition not defined\", \"Relationship between sensing and transcriptional repressor activity unclear\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Placed LRRFIP1 in the platelet cytoskeleton via interactions with actin-remodeling proteins and demonstrated an in vivo role in thrombus formation.\",\n      \"evidence\": \"Proteomic interactome (Flightless-1, Drebrin) and morpholino knockdown in zebrafish\",\n      \"pmids\": [\"20833976\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding interfaces with Flightless-1/Drebrin not mapped\", \"Mechanism linking cytoskeletal role to thrombosis not detailed\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Provided localization and post-translational evidence that LRRFIP1 is serine-phosphorylated and traffics to dsRNA-containing lysosomal structures upon stimulation.\",\n      \"evidence\": \"Western blot for serine phosphorylation and immunofluorescence colocalization with labeled dsRNA in monocytes\",\n      \"pmids\": [\"21102652\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Kinase responsible for phosphorylation not identified\", \"Functional consequence of lysosomal colocalization untested\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Connected LRRFIP1/GCF2 to RhoA-dependent cytoskeletal and drug-resistance phenotypes, showing it acts upstream of RhoA and through LARG to drive integrin-dependent migration and metastasis.\",\n      \"evidence\": \"Gain/loss-of-function with RhoA/actin/MRP1 readouts plus an in vivo colorectal metastasis model and RhoA-LARG interaction analysis\",\n      \"pmids\": [\"22571463\", \"22750095\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether RhoA regulation is transcriptional or post-translational not fully resolved\", \"Direct vs. indirect control of LARG-RhoA coupling unclear\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Resolved the oligomerization architecture by solving the FLI-interacting domain as a parallel homodimeric coiled coil, with longer constructs forming higher-order oligomers.\",\n      \"evidence\": \"X-ray crystallography and solution biophysics\",\n      \"pmids\": [\"23099021\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No full-length structure or DNA/RNA-bound complex\", \"Functional role of higher-order oligomers not directly tested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Extended TNF repression to an RNA-scaffolded mechanism, showing LRRFIP1 binds upstream long noncoding RNAs that recruit it to chromatin as part of a repressive complex.\",\n      \"evidence\": \"RNA-IP, ChIP, and RNA knockdown/overexpression\",\n      \"pmids\": [\"24567534\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Other components of the repressive complex not fully cataloged\", \"RNA-binding domain within LRRFIP1 not mapped\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Demonstrated isoform- and tissue-specific cytoplasmic localization driving β-catenin/Akt/mTOR activation and GLT-1 regulation in CNS ischemia.\",\n      \"evidence\": \"qPCR, immunohistochemistry, fractionation, and pathway Western blot in ischemia models\",\n      \"pmids\": [\"24637094\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular targets in the β-catenin/Akt/mTOR axis not defined\", \"Causality between LRRFIP1 and GLT-1 regulation not mechanistically dissected\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Linked LRRFIP1 to EMT control by acting on the β-catenin destruction complex to govern β-catenin phosphorylation and nuclear localization in cancer cells.\",\n      \"evidence\": \"siRNA knockdown with EMT markers, β-catenin fractionation, and migration/invasion assays in pancreatic and lung cancer lines\",\n      \"pmids\": [\"26047573\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct interaction with destruction complex components not shown\", \"Distinction between sensing-independent and Wnt-dependent roles unclear\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined the structure-function determinants of Wnt enhancement: Iso1 is the strongest activator, requiring W76/W82 and coiled-coil-mediated homodimerization, with C-terminal sequence dictating nuclear vs cytoplasmic isoform distribution.\",\n      \"evidence\": \"Topflash reporter, site-directed mutagenesis (W76A/W82A), immunofluorescence localization, and Co-IP oligomerization\",\n      \"pmids\": [\"28322931\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct binding partner engaged by the W76/W82 surface not identified\", \"How isoform localization tunes downstream outputs not resolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Genetic knockout established that LRRFIP1 is required for αIIbβ3 integrin expression and agonist-induced platelet agglutination, formalizing its in vivo platelet role.\",\n      \"evidence\": \"LRRFIP1 knockout mouse, aggregometry, and flow cytometry for active αIIbβ3\",\n      \"pmids\": [\"31258662\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which LRRFIP1 controls αIIbβ3 levels not defined\", \"Link to earlier cytoskeletal interactome not directly tested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified DAPK1 as a stress-induced LRRFIP1 interactor in neurons under oxygen/glucose deprivation, extending its interaction network into oxidative stress responses.\",\n      \"evidence\": \"LC-MS/MS, Co-IP and reverse Co-IP in primary cortical neurons under OGD/erastin\",\n      \"pmids\": [\"33265962\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Functional consequence of the LRRFIP1–DAPK1 interaction not tested\", \"Single Co-IP validation of an MS hit without structural mapping\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Connected LRRFIP1 to chemoresistance by showing its silencing sensitizes pancreatic cancer cells to gemcitabine through Rac-dependent JNK/c-Jun activation.\",\n      \"evidence\": \"siRNA knockdown, phospho-Western blot, Rac inhibitor epistasis, and viability/caspase assays\",\n      \"pmids\": [\"33707114\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular link between LRRFIP1 and Rac not established\", \"Whether effect generalizes beyond pancreatic cancer untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified Dishevelled proteins (DVL2/DVL3) as Wnt-pathway partners through which LRRFIP1 synergistically amplifies β-catenin signaling and proliferation/survival in MDS cells.\",\n      \"evidence\": \"Transcriptome sequencing, dual luciferase reporter, co-overexpression synergy, and proliferation/apoptosis assays\",\n      \"pmids\": [\"40420163\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct LRRFIP1–DVL binding inferred from synergy, not biochemically mapped\", \"Domain mediating DVL engagement not defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended transcriptional repressor activity to adipogenesis, showing LRRFIP1 binds the E2F6 promoter to suppress E2F6 and downstream C/EBPα, inhibiting white adipocyte differentiation.\",\n      \"evidence\": \"ChIP, luciferase promoter assay, gain/loss-of-function in C3H10T1/2 cells, and diet-induced obesity mouse model\",\n      \"pmids\": [\"41224206\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cofactors at the E2F6 promoter not identified\", \"Relation to GC-rich binding seen at EGFR/TNF promoters not tested\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined a role in the tumor microenvironment, with LRRFIP1 promoting M2-like macrophage polarization via PI3K/AKT and TGF-β receptor signaling.\",\n      \"evidence\": \"siRNA knockdown in TAMs, flow cytometry, cytokine ELISA, PI3K inhibitor epistasis, and in vivo tumor/metastasis models\",\n      \"pmids\": [\"41612403\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular targets upstream of PI3K/AKT not identified\", \"Whether nucleic acid sensing contributes to this role untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single protein integrates cytosolic nucleic acid sensing, GC-rich/lncRNA-templated transcriptional repression, and Wnt/β-catenin enhancement into a coherent regulatory logic — and which activities are isoform-, tissue-, or stimulus-specific — remains unresolved.\",\n      \"evidence\": \"No single study reconciles the sensing, repressor, and Wnt-enhancer functions mechanistically\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No full-length structure bound to nucleic acid or partners\", \"Domain assignment of RNA binding vs DNA binding vs partner engagement incomplete\", \"Isoform-specific division of labor across tissues not systematically mapped\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [1, 2, 19]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 9]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [1, 2, 9, 19]},\n      {\"term_id\": \"GO:0140299\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 18]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 13]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 10, 13]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 20]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [13, 18, 11]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 2, 9, 19]},\n      {\"term_id\": \"R-HSA-109582\", \"supporting_discovery_ids\": [3, 14]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"CTNNB1\", \"IRF3\", \"EP300\", \"FLII\", \"DBN1\", \"DVL2\", \"DVL3\", \"DAPK1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}