{"gene":"RAB11FIP4","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2002,"finding":"RAB11FIP4 was identified as the sixth member of the Rab11-FIP family and interacts with Rab11 in a GTP-dependent manner; its C-terminal region mediates self-interaction and interactions with Rip11, Rab11-FIP2, and Rab11-FIP3, but not with RCP (Rab coupling protein).","method":"Co-immunoprecipitation, pulldown assays with GTP/GDP-loaded Rab11","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal binding assays with GTP/GDP discrimination and domain mapping, single lab","pmids":["12470645"],"is_preprint":false},{"year":2002,"finding":"RAB11FIP4 colocalizes with transferrin and Rab11 in HeLa cells; overexpression condenses the Rab11-positive compartment in the perinuclear region, while expression of the C-terminal region alone disperses it to the cell periphery without inhibiting transferrin recycling, suggesting a Rab11 effector role distinct from transferrin recycling.","method":"Fluorescence microscopy, subcellular fractionation, transferrin recycling assay, overexpression of truncation mutants","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — live-cell imaging with functional readout (transferrin recycling), domain dissection, single lab","pmids":["12470645"],"is_preprint":false},{"year":2002,"finding":"RAB11FIP4 family members can homo- and hetero-interact primarily through their C-terminal region (containing the Rab-binding domain within a predicted coiled-coil or ERM motif), forming potential protein 'platforms' regulated by Rab11 activity.","method":"Co-immunoprecipitation and two-hybrid interaction assays","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP and domain mapping, single lab, two papers reporting consistent findings","pmids":["11944901","12470645"],"is_preprint":false},{"year":2006,"finding":"Zebrafish Rab11-FIP4A (neural-specific isoform) is required for proliferation and cell-cycle exit of retinal progenitors; morpholino knockdown produces small-eye phenotype with impaired proliferation, delayed cell-cycle exit, lack of p57kip2 induction, and enhanced cyclin D1; phenotype rescued by p57Kip2 overexpression or dominant-negative PKA, placing Rab11-FIP4A in a Shh/PKA-regulated pathway.","method":"Antisense morpholino knockdown in zebrafish, in situ hybridization, immunostaining, rescue by p57Kip2 and dominant-negative PKA overexpression","journal":"Developmental biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined cellular phenotype and genetic rescue, single lab, ortholog study","pmids":["16457799"],"is_preprint":false},{"year":2007,"finding":"Mouse Rab11-FIP4A gain-of-function in retina promotes cell cycle exit and increases bipolar cells and Müller glia; loss-of-function reverses this; truncation analysis shows the N-terminal EF-hand-containing region is essential, while the Rab11-binding domain is dispensable, indicating a Rab11-independent mechanism in retinal development.","method":"In vivo retinal electroporation (gain- and loss-of-function), truncation mutant analysis, cell-type immunostaining","journal":"Developmental dynamics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — bidirectional (gain/loss) functional experiments with domain dissection, single lab, ortholog study","pmids":["17089410"],"is_preprint":false},{"year":2010,"finding":"The N-terminal region of Ecm29 binds RAB11FIP4 (and other endocytic proteins), linking the 26S proteasome to endosomal compartments; Ecm29-26S proteasome complexes are present on flotillin-positive endosomes.","method":"Genome-wide two-hybrid screen, mass spectrometry, confocal microscopy, glycerol gradient fractionation","journal":"The Journal of biological chemistry","confidence":"Low","confidence_rationale":"Tier 3 / Weak — RAB11FIP4 identified as a binding partner in a large screen without specific functional follow-up for this protein","pmids":["20682791"],"is_preprint":false},{"year":2015,"finding":"HIF-1α transcriptionally activates RAB11FIP4 under hypoxia by binding its promoter; elevated RAB11FIP4 promotes HCC cell migration and invasion in vitro and lung metastasis in vivo through phosphorylation of PRAS40, regulated by mTOR.","method":"Promoter reporter assay, ChIP, siRNA knockdown and overexpression, migration/invasion assays, in vivo xenograft lung metastasis, Western blot for PRAS40 phosphorylation","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (ChIP, promoter assay, KD/OE with in vitro and in vivo readouts, signaling readout), single lab","pmids":["25745995"],"is_preprint":false},{"year":2023,"finding":"RAB11FIP4 interacts with ARF5; elevated RAB11FIP4 in HCC promotes cancer stem cell-like features (sphere formation, stemness markers ALDH1A1, CD133, NANOG, OCT4) through modulation of CDK1/cyclin B cell cycle proteins; knockdown reduces stemness and increases sorafenib sensitivity.","method":"Co-immunoprecipitation, siRNA knockdown, overexpression, sphere formation assay, Western blot for stemness markers and CDK1/cyclin B","journal":"Journal of physiology and biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP identifying ARF5 as binding partner, bidirectional functional experiments with multiple readouts, single lab","pmids":["37458957"],"is_preprint":false},{"year":2024,"finding":"Reconstitution of RAB11FIP4 expression in cystinotic (Ctns−/−) fibroblasts restores normal autophagosome levels, decreases LC3B-II, increases LAMP2A localization at the lysosomal membrane, decreases ER stress, and increases megalin at the plasma membrane of proximal tubule cells; a dominant-negative Rab11 partially blocks the ER stress rescue, indicating RAB11FIP4 acts as a Rab11A effector to regulate autophagy, lysosomal trafficking, and endocytic receptor recycling.","method":"mRNA array, Western blot, immunofluorescence/localization of LAMP2A and megalin, LC3B-II quantification, dominant-negative Rab11 epistasis, pharmacological CMA activation","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (localization, autophagy flux, genetic epistasis with dominant-negative Rab11), single lab","pmids":["39434668"],"is_preprint":false},{"year":2025,"finding":"In Drosophila motor neurons, the Rab11FIP4 ortholog (Nuf/Rab11FIP4) acts as a motor adaptor that restricts presynaptic EV cargo levels, opposing the action of MyoV and PI4KIIIα component Rbo; genetic screen demonstrates Rab11FIP4 and PI4KIIIβ homolog Fwd reduce EV cargo at synapses while other Rab11 effectors sustain them.","method":"Directed genetic screen in Drosophila motor neurons, rab11 mutant analysis, fluorescence imaging of EV cargo distribution","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 2 / Weak — genetic epistasis in Drosophila model (ortholog), preprint, single lab, no biochemical reconstitution","pmids":["42124713"],"is_preprint":true},{"year":2025,"finding":"Rab11fip4 interacts with Arf5 in mouse oocytes (confirmed by Co-IP); knockdown of Rab11fip4 impairs oocyte maturation and nanoparticle internalization; Rab11fip4-mediated recycling endosome pathway protects internalized nanoparticles from lysosomal degradation.","method":"Co-immunoprecipitation, siRNA knockdown, transcriptome analysis, endocytic inhibitor experiments, TEM","journal":"ACS applied materials & interfaces","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus functional knockdown with multiple readouts, single lab, consistent with prior ARF5 binding finding","pmids":["40720586"],"is_preprint":false}],"current_model":"RAB11FIP4 is a Rab11A effector protein that uses its C-terminal ERM/Rab-binding domain to interact with GTP-loaded Rab11 and to form homo- and hetero-oligomeric complexes with other Rab11-FIP family members; it localizes to recycling endosomes and regulates endocytic trafficking, autophagy flux, lysosomal function (including LAMP2A membrane localization), and endocytic receptor recycling (megalin) in a manner partially dependent on Rab11; its N-terminal EF-hand region mediates Rab11-independent roles in cell-cycle exit during neural/retinal development via Shh/PKA signaling; it also interacts with ARF5 to influence CDK1/cyclin B-dependent cancer stemness; and it is transcriptionally induced by HIF-1α under hypoxia to promote mTOR/PRAS40-dependent tumor metastasis."},"narrative":{"mechanistic_narrative":"RAB11FIP4 is a member of the Rab11-FIP family of Rab11 effectors that couples GTP-loaded Rab11 to the regulation of endocytic recycling, autophagy, and lysosomal trafficking [PMID:12470645, PMID:39434668]. Through its C-terminal Rab/ERM-binding region it binds GTP-Rab11 in a nucleotide-dependent manner and self-associates as well as heterodimerizes with other Rab11-FIP family members (Rip11, Rab11-FIP2, Rab11-FIP3), forming oligomeric platforms on the perinuclear Rab11-positive recycling compartment where it colocalizes with transferrin [PMID:12470645, PMID:11944901]. Reconstitution in cystinotic fibroblasts shows that RAB11FIP4 acts as a Rab11A effector to normalize autophagosome levels, drive LAMP2A localization to the lysosomal membrane, relieve ER stress, and restore megalin recycling to the plasma membrane, with the ER-stress component being partially Rab11-dependent [PMID:39434668]. Distinct from its endosomal effector role, the N-terminal EF-hand-containing region mediates a Rab11-independent function in cell-cycle exit during retinal development, acting within a Shh/PKA-regulated pathway that controls p57Kip2 induction and cyclin D1 levels and the production of bipolar cells and Müller glia [PMID:16457799, PMID:17089410]. In hepatocellular carcinoma, RAB11FIP4 is transcriptionally induced by HIF-1α under hypoxia and promotes migration, invasion, and lung metastasis through mTOR-dependent PRAS40 phosphorylation [PMID:25745995], and it interacts with ARF5 to promote cancer stem cell-like features via CDK1/cyclin B cell-cycle proteins [PMID:37458957]. The ARF5 interaction is conserved in mouse oocytes, where RAB11FIP4 supports a recycling-endosome pathway that protects internalized cargo from lysosomal degradation [PMID:40720586].","teleology":[{"year":2002,"claim":"Established RAB11FIP4 as a bona fide Rab11 effector by showing GTP-dependent Rab11 binding and defining the C-terminal region as the module for Rab binding and for homo/hetero-oligomerization with other Rab11-FIPs.","evidence":"Co-immunoprecipitation, two-hybrid, and pulldowns with GTP/GDP-loaded Rab11 plus truncation mapping in cultured cells","pmids":["12470645","11944901"],"confidence":"Medium","gaps":["No structure of the Rab-binding interface","Functional consequence of FIP heterodimerization not resolved","Selectivity against RCP unexplained mechanistically"]},{"year":2002,"claim":"Placed RAB11FIP4 on the perinuclear Rab11 recycling compartment but distinguished its role from bulk transferrin recycling, indicating a regulatory rather than core-transport effector function.","evidence":"Fluorescence microscopy, subcellular fractionation, and transferrin recycling assays with truncation mutants in HeLa cells","pmids":["12470645"],"confidence":"Medium","gaps":["The specific recycling cargo it does control was not identified","Mechanism by which it condenses the Rab11 compartment unknown"]},{"year":2007,"claim":"Revealed a Rab11-independent developmental function: the N-terminal EF-hand region, not the Rab11-binding domain, drives retinal progenitor cell-cycle exit within Shh/PKA signaling controlling p57Kip2 and cyclin D1.","evidence":"Morpholino knockdown in zebrafish with p57Kip2/dominant-negative PKA rescue, and bidirectional retinal electroporation with truncation analysis in mouse","pmids":["16457799","17089410"],"confidence":"Medium","gaps":["Molecular partners of the EF-hand region not identified","Direct mechanistic link to Shh/PKA components missing","Relevance to mammalian development beyond retina untested"]},{"year":2010,"claim":"Linked RAB11FIP4 to the proteasome by identifying it as an Ecm29-binding partner tethering 26S proteasomes to endosomes, hinting at a broader endosomal scaffolding role.","evidence":"Genome-wide two-hybrid, mass spectrometry, and confocal microscopy","pmids":["20682791"],"confidence":"Low","gaps":["Identified only as a screen hit with no functional follow-up for RAB11FIP4","Interaction not validated reciprocally for this protein","Physiological role of proteasome-endosome link via RAB11FIP4 unknown"]},{"year":2015,"claim":"Defined an oncogenic axis: HIF-1α transcriptionally induces RAB11FIP4 under hypoxia to drive HCC metastasis through mTOR-dependent PRAS40 phosphorylation.","evidence":"Promoter reporter, ChIP, knockdown/overexpression with migration/invasion assays and in vivo xenograft lung metastasis","pmids":["25745995"],"confidence":"Medium","gaps":["How an endosomal effector engages mTOR/PRAS40 is unresolved","Whether the metastatic effect requires Rab11 binding untested","Direct versus indirect regulation of PRAS40 not distinguished"]},{"year":2023,"claim":"Identified ARF5 as a RAB11FIP4 partner and connected RAB11FIP4 to cancer stemness and chemoresistance via CDK1/cyclin B cell-cycle proteins.","evidence":"Co-immunoprecipitation, bidirectional knockdown/overexpression, sphere formation, and stemness/CDK1-cyclin B Western blots in HCC","pmids":["37458957"],"confidence":"Medium","gaps":["Direct versus indirect ARF5 binding not mapped","Mechanism connecting ARF5 to CDK1/cyclin B regulation unclear","Relationship to the HIF-1α/mTOR axis not integrated"]},{"year":2024,"claim":"Demonstrated that RAB11FIP4 acts as a Rab11A effector regulating autophagy flux, LAMP2A lysosomal membrane localization, and megalin recycling, with rescue activity in a cystinosis model.","evidence":"Reconstitution in Ctns-/- fibroblasts with autophagy flux, LAMP2A/megalin localization, and dominant-negative Rab11 epistasis","pmids":["39434668"],"confidence":"Medium","gaps":["Which steps are Rab11-dependent versus independent only partly delineated","Direct substrate/cargo handling not biochemically reconstituted","Connection to the EF-hand developmental role unaddressed"]},{"year":2025,"claim":"Extended the ARF5-linked recycling role to mouse oocytes, where RAB11FIP4 supports maturation and protects internalized cargo from lysosomal degradation via recycling endosomes.","evidence":"Co-immunoprecipitation, siRNA knockdown, transcriptome and endocytic inhibitor experiments, TEM in mouse oocytes","pmids":["40720586"],"confidence":"Medium","gaps":["Mechanism of cargo diversion from lysosome to recycling route unresolved","Role of Rab11 binding in this context untested"]},{"year":2025,"claim":"Genetic screening in Drosophila motor neurons positioned the Nuf/Rab11FIP4 ortholog as a motor adaptor restricting presynaptic EV cargo, opposing MyoV/Rbo and partitioning Rab11 effectors into cargo-promoting versus cargo-restricting roles.","evidence":"Directed genetic screen and rab11 mutant analysis with EV cargo imaging in Drosophila (preprint)","pmids":["42124713"],"confidence":"Low","gaps":["Preprint without biochemical reconstitution","Ortholog finding not confirmed in mammals","Direct motor adaptor activity not demonstrated biochemically"]},{"year":null,"claim":"How RAB11FIP4 toggles between its Rab11-dependent endosomal/lysosomal effector functions and its Rab11-independent EF-hand developmental and oncogenic signaling roles remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model integrating the EF-hand and Rab-binding domains","Mechanism coupling endosomal scaffolding to mTOR/PRAS40 and CDK1/cyclin B signaling unknown","Direct cargo and substrate identities largely undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,2,8]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,8]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[1,5,8]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1,8]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[8]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[3,4,7]}],"complexes":["Rab11-FIP oligomeric complex"],"partners":["RAB11A","RAB11FIP3","RAB11FIP2","RAB11FIP5","ARF5","ECM29"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q86YS3","full_name":"Rab11 family-interacting protein 4","aliases":["Arfophilin-2"],"length_aa":637,"mass_kda":71.9,"function":"Acts as a regulator of endocytic traffic by participating in membrane delivery. Required for the abscission step in cytokinesis, possibly by acting as an 'address tag' delivering recycling endosome membranes to the cleavage furrow during late cytokinesis. In case of infection by HCMV (human cytomegalovirus), may participate in egress of the virus out of nucleus; this function is independent of ARF6","subcellular_location":"Endosome; Cytoplasm, cytoskeleton, spindle; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome; Recycling endosome membrane; Cleavage furrow; Midbody; Cytoplasmic vesicle","url":"https://www.uniprot.org/uniprotkb/Q86YS3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RAB11FIP4","classification":"Not Classified","n_dependent_lines":14,"n_total_lines":1208,"dependency_fraction":0.011589403973509934},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/RAB11FIP4","total_profiled":1310},"omim":[{"mim_id":"616694","title":"ECM29 PROTEASOME ADAPTOR AND SCAFFOLD PROTEIN; ECPAS","url":"https://www.omim.org/entry/616694"},{"mim_id":"611999","title":"RAB11 FAMILY-INTERACTING PROTEIN 4; RAB11FIP4","url":"https://www.omim.org/entry/611999"},{"mim_id":"608738","title":"RAB11 FAMILY-INTERACTING PROTEIN 3; RAB11FIP3","url":"https://www.omim.org/entry/608738"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Golgi apparatus","reliability":"Approved"},{"location":"Vesicles","reliability":"Approved"},{"location":"Connecting piece","reliability":"Approved"},{"location":"Mid piece","reliability":"Approved"},{"location":"Principal piece","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":52.7},{"tissue":"testis","ntpm":47.0}],"url":"https://www.proteinatlas.org/search/RAB11FIP4"},"hgnc":{"alias_symbol":["RAB11-FIP4","KIAA1821","MGC11316","FLJ00131"],"prev_symbol":[]},"alphafold":{"accession":"Q86YS3","domains":[{"cath_id":"1.10.238.10","chopping":"11-92","consensus_level":"high","plddt":80.7488,"start":11,"end":92},{"cath_id":"1.20.5","chopping":"341-486","consensus_level":"medium","plddt":96.6974,"start":341,"end":486}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86YS3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86YS3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86YS3-F1-predicted_aligned_error_v6.png","plddt_mean":70.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RAB11FIP4","jax_strain_url":"https://www.jax.org/strain/search?query=RAB11FIP4"},"sequence":{"accession":"Q86YS3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86YS3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86YS3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86YS3"}},"corpus_meta":[{"pmid":"15304524","id":"PMC_15304524","title":"The 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its C-terminal region mediates self-interaction and interactions with Rip11, Rab11-FIP2, and Rab11-FIP3, but not with RCP (Rab coupling protein).\",\n      \"method\": \"Co-immunoprecipitation, pulldown assays with GTP/GDP-loaded Rab11\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal binding assays with GTP/GDP discrimination and domain mapping, single lab\",\n      \"pmids\": [\"12470645\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"RAB11FIP4 colocalizes with transferrin and Rab11 in HeLa cells; overexpression condenses the Rab11-positive compartment in the perinuclear region, while expression of the C-terminal region alone disperses it to the cell periphery without inhibiting transferrin recycling, suggesting a Rab11 effector role distinct from transferrin recycling.\",\n      \"method\": \"Fluorescence microscopy, subcellular fractionation, transferrin recycling assay, overexpression of truncation mutants\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — live-cell imaging with functional readout (transferrin recycling), domain dissection, single lab\",\n      \"pmids\": [\"12470645\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"RAB11FIP4 family members can homo- and hetero-interact primarily through their C-terminal region (containing the Rab-binding domain within a predicted coiled-coil or ERM motif), forming potential protein 'platforms' regulated by Rab11 activity.\",\n      \"method\": \"Co-immunoprecipitation and two-hybrid interaction assays\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP and domain mapping, single lab, two papers reporting consistent findings\",\n      \"pmids\": [\"11944901\", \"12470645\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Zebrafish Rab11-FIP4A (neural-specific isoform) is required for proliferation and cell-cycle exit of retinal progenitors; morpholino knockdown produces small-eye phenotype with impaired proliferation, delayed cell-cycle exit, lack of p57kip2 induction, and enhanced cyclin D1; phenotype rescued by p57Kip2 overexpression or dominant-negative PKA, placing Rab11-FIP4A in a Shh/PKA-regulated pathway.\",\n      \"method\": \"Antisense morpholino knockdown in zebrafish, in situ hybridization, immunostaining, rescue by p57Kip2 and dominant-negative PKA overexpression\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined cellular phenotype and genetic rescue, single lab, ortholog study\",\n      \"pmids\": [\"16457799\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Mouse Rab11-FIP4A gain-of-function in retina promotes cell cycle exit and increases bipolar cells and Müller glia; loss-of-function reverses this; truncation analysis shows the N-terminal EF-hand-containing region is essential, while the Rab11-binding domain is dispensable, indicating a Rab11-independent mechanism in retinal development.\",\n      \"method\": \"In vivo retinal electroporation (gain- and loss-of-function), truncation mutant analysis, cell-type immunostaining\",\n      \"journal\": \"Developmental dynamics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — bidirectional (gain/loss) functional experiments with domain dissection, single lab, ortholog study\",\n      \"pmids\": [\"17089410\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The N-terminal region of Ecm29 binds RAB11FIP4 (and other endocytic proteins), linking the 26S proteasome to endosomal compartments; Ecm29-26S proteasome complexes are present on flotillin-positive endosomes.\",\n      \"method\": \"Genome-wide two-hybrid screen, mass spectrometry, confocal microscopy, glycerol gradient fractionation\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — RAB11FIP4 identified as a binding partner in a large screen without specific functional follow-up for this protein\",\n      \"pmids\": [\"20682791\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"HIF-1α transcriptionally activates RAB11FIP4 under hypoxia by binding its promoter; elevated RAB11FIP4 promotes HCC cell migration and invasion in vitro and lung metastasis in vivo through phosphorylation of PRAS40, regulated by mTOR.\",\n      \"method\": \"Promoter reporter assay, ChIP, siRNA knockdown and overexpression, migration/invasion assays, in vivo xenograft lung metastasis, Western blot for PRAS40 phosphorylation\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (ChIP, promoter assay, KD/OE with in vitro and in vivo readouts, signaling readout), single lab\",\n      \"pmids\": [\"25745995\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RAB11FIP4 interacts with ARF5; elevated RAB11FIP4 in HCC promotes cancer stem cell-like features (sphere formation, stemness markers ALDH1A1, CD133, NANOG, OCT4) through modulation of CDK1/cyclin B cell cycle proteins; knockdown reduces stemness and increases sorafenib sensitivity.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, overexpression, sphere formation assay, Western blot for stemness markers and CDK1/cyclin B\",\n      \"journal\": \"Journal of physiology and biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP identifying ARF5 as binding partner, bidirectional functional experiments with multiple readouts, single lab\",\n      \"pmids\": [\"37458957\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Reconstitution of RAB11FIP4 expression in cystinotic (Ctns−/−) fibroblasts restores normal autophagosome levels, decreases LC3B-II, increases LAMP2A localization at the lysosomal membrane, decreases ER stress, and increases megalin at the plasma membrane of proximal tubule cells; a dominant-negative Rab11 partially blocks the ER stress rescue, indicating RAB11FIP4 acts as a Rab11A effector to regulate autophagy, lysosomal trafficking, and endocytic receptor recycling.\",\n      \"method\": \"mRNA array, Western blot, immunofluorescence/localization of LAMP2A and megalin, LC3B-II quantification, dominant-negative Rab11 epistasis, pharmacological CMA activation\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (localization, autophagy flux, genetic epistasis with dominant-negative Rab11), single lab\",\n      \"pmids\": [\"39434668\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In Drosophila motor neurons, the Rab11FIP4 ortholog (Nuf/Rab11FIP4) acts as a motor adaptor that restricts presynaptic EV cargo levels, opposing the action of MyoV and PI4KIIIα component Rbo; genetic screen demonstrates Rab11FIP4 and PI4KIIIβ homolog Fwd reduce EV cargo at synapses while other Rab11 effectors sustain them.\",\n      \"method\": \"Directed genetic screen in Drosophila motor neurons, rab11 mutant analysis, fluorescence imaging of EV cargo distribution\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic epistasis in Drosophila model (ortholog), preprint, single lab, no biochemical reconstitution\",\n      \"pmids\": [\"42124713\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Rab11fip4 interacts with Arf5 in mouse oocytes (confirmed by Co-IP); knockdown of Rab11fip4 impairs oocyte maturation and nanoparticle internalization; Rab11fip4-mediated recycling endosome pathway protects internalized nanoparticles from lysosomal degradation.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, transcriptome analysis, endocytic inhibitor experiments, TEM\",\n      \"journal\": \"ACS applied materials & interfaces\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus functional knockdown with multiple readouts, single lab, consistent with prior ARF5 binding finding\",\n      \"pmids\": [\"40720586\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RAB11FIP4 is a Rab11A effector protein that uses its C-terminal ERM/Rab-binding domain to interact with GTP-loaded Rab11 and to form homo- and hetero-oligomeric complexes with other Rab11-FIP family members; it localizes to recycling endosomes and regulates endocytic trafficking, autophagy flux, lysosomal function (including LAMP2A membrane localization), and endocytic receptor recycling (megalin) in a manner partially dependent on Rab11; its N-terminal EF-hand region mediates Rab11-independent roles in cell-cycle exit during neural/retinal development via Shh/PKA signaling; it also interacts with ARF5 to influence CDK1/cyclin B-dependent cancer stemness; and it is transcriptionally induced by HIF-1α under hypoxia to promote mTOR/PRAS40-dependent tumor metastasis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RAB11FIP4 is a member of the Rab11-FIP family of Rab11 effectors that couples GTP-loaded Rab11 to the regulation of endocytic recycling, autophagy, and lysosomal trafficking [#0, #8]. Through its C-terminal Rab/ERM-binding region it binds GTP-Rab11 in a nucleotide-dependent manner and self-associates as well as heterodimerizes with other Rab11-FIP family members (Rip11, Rab11-FIP2, Rab11-FIP3), forming oligomeric platforms on the perinuclear Rab11-positive recycling compartment where it colocalizes with transferrin [#0, #1, #2]. Reconstitution in cystinotic fibroblasts shows that RAB11FIP4 acts as a Rab11A effector to normalize autophagosome levels, drive LAMP2A localization to the lysosomal membrane, relieve ER stress, and restore megalin recycling to the plasma membrane, with the ER-stress component being partially Rab11-dependent [#8]. Distinct from its endosomal effector role, the N-terminal EF-hand-containing region mediates a Rab11-independent function in cell-cycle exit during retinal development, acting within a Shh/PKA-regulated pathway that controls p57Kip2 induction and cyclin D1 levels and the production of bipolar cells and Müller glia [#3, #4]. In hepatocellular carcinoma, RAB11FIP4 is transcriptionally induced by HIF-1\\u03b1 under hypoxia and promotes migration, invasion, and lung metastasis through mTOR-dependent PRAS40 phosphorylation [#6], and it interacts with ARF5 to promote cancer stem cell-like features via CDK1/cyclin B cell-cycle proteins [#7]. The ARF5 interaction is conserved in mouse oocytes, where RAB11FIP4 supports a recycling-endosome pathway that protects internalized cargo from lysosomal degradation [#10].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Established RAB11FIP4 as a bona fide Rab11 effector by showing GTP-dependent Rab11 binding and defining the C-terminal region as the module for Rab binding and for homo/hetero-oligomerization with other Rab11-FIPs.\",\n      \"evidence\": \"Co-immunoprecipitation, two-hybrid, and pulldowns with GTP/GDP-loaded Rab11 plus truncation mapping in cultured cells\",\n      \"pmids\": [\"12470645\", \"11944901\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of the Rab-binding interface\", \"Functional consequence of FIP heterodimerization not resolved\", \"Selectivity against RCP unexplained mechanistically\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Placed RAB11FIP4 on the perinuclear Rab11 recycling compartment but distinguished its role from bulk transferrin recycling, indicating a regulatory rather than core-transport effector function.\",\n      \"evidence\": \"Fluorescence microscopy, subcellular fractionation, and transferrin recycling assays with truncation mutants in HeLa cells\",\n      \"pmids\": [\"12470645\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The specific recycling cargo it does control was not identified\", \"Mechanism by which it condenses the Rab11 compartment unknown\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Revealed a Rab11-independent developmental function: the N-terminal EF-hand region, not the Rab11-binding domain, drives retinal progenitor cell-cycle exit within Shh/PKA signaling controlling p57Kip2 and cyclin D1.\",\n      \"evidence\": \"Morpholino knockdown in zebrafish with p57Kip2/dominant-negative PKA rescue, and bidirectional retinal electroporation with truncation analysis in mouse\",\n      \"pmids\": [\"16457799\", \"17089410\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular partners of the EF-hand region not identified\", \"Direct mechanistic link to Shh/PKA components missing\", \"Relevance to mammalian development beyond retina untested\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Linked RAB11FIP4 to the proteasome by identifying it as an Ecm29-binding partner tethering 26S proteasomes to endosomes, hinting at a broader endosomal scaffolding role.\",\n      \"evidence\": \"Genome-wide two-hybrid, mass spectrometry, and confocal microscopy\",\n      \"pmids\": [\"20682791\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Identified only as a screen hit with no functional follow-up for RAB11FIP4\", \"Interaction not validated reciprocally for this protein\", \"Physiological role of proteasome-endosome link via RAB11FIP4 unknown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined an oncogenic axis: HIF-1\\u03b1 transcriptionally induces RAB11FIP4 under hypoxia to drive HCC metastasis through mTOR-dependent PRAS40 phosphorylation.\",\n      \"evidence\": \"Promoter reporter, ChIP, knockdown/overexpression with migration/invasion assays and in vivo xenograft lung metastasis\",\n      \"pmids\": [\"25745995\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How an endosomal effector engages mTOR/PRAS40 is unresolved\", \"Whether the metastatic effect requires Rab11 binding untested\", \"Direct versus indirect regulation of PRAS40 not distinguished\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified ARF5 as a RAB11FIP4 partner and connected RAB11FIP4 to cancer stemness and chemoresistance via CDK1/cyclin B cell-cycle proteins.\",\n      \"evidence\": \"Co-immunoprecipitation, bidirectional knockdown/overexpression, sphere formation, and stemness/CDK1-cyclin B Western blots in HCC\",\n      \"pmids\": [\"37458957\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct versus indirect ARF5 binding not mapped\", \"Mechanism connecting ARF5 to CDK1/cyclin B regulation unclear\", \"Relationship to the HIF-1\\u03b1/mTOR axis not integrated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated that RAB11FIP4 acts as a Rab11A effector regulating autophagy flux, LAMP2A lysosomal membrane localization, and megalin recycling, with rescue activity in a cystinosis model.\",\n      \"evidence\": \"Reconstitution in Ctns-/- fibroblasts with autophagy flux, LAMP2A/megalin localization, and dominant-negative Rab11 epistasis\",\n      \"pmids\": [\"39434668\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Which steps are Rab11-dependent versus independent only partly delineated\", \"Direct substrate/cargo handling not biochemically reconstituted\", \"Connection to the EF-hand developmental role unaddressed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended the ARF5-linked recycling role to mouse oocytes, where RAB11FIP4 supports maturation and protects internalized cargo from lysosomal degradation via recycling endosomes.\",\n      \"evidence\": \"Co-immunoprecipitation, siRNA knockdown, transcriptome and endocytic inhibitor experiments, TEM in mouse oocytes\",\n      \"pmids\": [\"40720586\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of cargo diversion from lysosome to recycling route unresolved\", \"Role of Rab11 binding in this context untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Genetic screening in Drosophila motor neurons positioned the Nuf/Rab11FIP4 ortholog as a motor adaptor restricting presynaptic EV cargo, opposing MyoV/Rbo and partitioning Rab11 effectors into cargo-promoting versus cargo-restricting roles.\",\n      \"evidence\": \"Directed genetic screen and rab11 mutant analysis with EV cargo imaging in Drosophila (preprint)\",\n      \"pmids\": [\"42124713\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Preprint without biochemical reconstitution\", \"Ortholog finding not confirmed in mammals\", \"Direct motor adaptor activity not demonstrated biochemically\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RAB11FIP4 toggles between its Rab11-dependent endosomal/lysosomal effector functions and its Rab11-independent EF-hand developmental and oncogenic signaling roles remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model integrating the EF-hand and Rab-binding domains\", \"Mechanism coupling endosomal scaffolding to mTOR/PRAS40 and CDK1/cyclin B signaling unknown\", \"Direct cargo and substrate identities largely undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 2, 8]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0055037\", \"supporting_discovery_ids\": [1, 8]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [1, 5, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1, 8]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [3, 4, 7]}\n    ],\n    \"complexes\": [\"Rab11-FIP oligomeric complex\"],\n    \"partners\": [\"RAB11A\", \"RAB11FIP3\", \"RAB11FIP2\", \"RAB11FIP5\", \"ARF5\", \"ECM29\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":6,"faith_pct":83.33333333333333}}