{"gene":"WDR91","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":2016,"finding":"C. elegans SORF-1 (WDR91 ortholog) and SORF-2 (WDR81 ortholog) act in a complex with BEC-1/Beclin1 to inhibit PI3-kinase complex activity, thereby preventing excessive PtdIns3P synthesis on early endosomes; loss of sorf-1 or sorf-2 leads to greatly elevated endosomal PtdIns3P and excessive early endosome fusion, blocking early-to-late endosome conversion. In mammalian cells, WDR91 and WDR81 physically interact with Beclin1 and inhibit PI3K complex activity; their inactivation causes Beclin1-dependent enlargement of PtdIns3P-enriched endosomes and defective EGFR degradation.","method":"Genetic loss-of-function in C. elegans, epistasis with Rab switching genes, co-immunoprecipitation (complex with Beclin1), PI3K activity assay, mammalian cell inactivation with EGFR degradation readout, live imaging of endosomal PtdIns3P","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, in vivo genetic epistasis in C. elegans, enzymatic activity assay, validated in mammalian cells with orthogonal functional readouts; independently replicated in subsequent papers","pmids":["26783301"],"is_preprint":false},{"year":2017,"finding":"WDR91 is a Rab7 effector: it is recruited to endosomes by interacting with GTP-Rab7, and once there it inhibits Rab7-associated PI3-kinase activity to reduce PtdIns3P levels, coupling Rab switching with PtdIns3P down-regulation during early-to-late endosome conversion. Loss of WDR91 in mouse neurons causes accumulation of giant intermediate endosomes and reduced neurite length/complexity; phenotypes are rescued by wild-type WDR91 but not by Rab7-binding-deficient WDR91 mutants. Global Wdr91 knockout causes neonatal death; brain-specific inactivation impairs brain development and causes postnatal death.","method":"Co-immunoprecipitation with GTP-Rab7, in vitro PI3K activity assay, conditional knockout mouse models (global and brain-specific), rescue experiments with WDR91 mutants, live-cell imaging of endosomal PtdIns3P, neuronal morphology analysis","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — direct GTP-Rab7 interaction, PI3K activity assay, in vivo mouse knockout with defined cellular and organismal phenotype, mutagenesis rescue demonstrating Rab7 binding is required","pmids":["28860274"],"is_preprint":false},{"year":2016,"finding":"WDR81 (partner of WDR91) is required for trafficking and lysosomal degradation of tetherin and EGFR; WDR81 and WDR91 function together as a complex in endolysosomal fusion. Absence of WDR81 results in swollen endolysosomal compartments with enlarged early and late endosomes and reduced delivery of endocytosed dextran to cathepsin-active lysosomes.","method":"Forward genetic haploid cell screen (KBM7), functional complementation, endosomal trafficking and degradation assays, fluorescence microscopy of endolysosomal compartments","journal":"Traffic (Copenhagen, Denmark)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — forward genetic screen identifying the WDR81-WDR91 complex, functional assays in human cells, but WDR91 role inferred from complex membership with WDR81 as primary hit","pmids":["27126989"],"is_preprint":false},{"year":2022,"finding":"WDR91 specifies the endosomal retrieval subdomain required for retromer-dependent recycling. WDR91 interacts with sorting nexins (SNXs) through their PX domain and with VPS35, promoting their interaction with Rab7. WDR91 also interacts with the WASH subunit FAM21. In WDR91-deficient cells, Rab7, SNX-retromer, and FAM21 fail to localize to endosomal subdomains and endosomal actin organization is impaired; re-expression of WDR91 rescues Rab7, SNX-retromer, and FAM21 concentration at WDR91-specific subdomains where retromer-mediated membrane tubulation and release occur.","method":"Co-immunoprecipitation (WDR91–SNX PX domain, WDR91–VPS35, WDR91–FAM21), WDR91 knockout cells, rescue/re-expression experiments, fluorescence live imaging of endosomal subdomains, actin organization assay","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP with multiple partners, KO with defined trafficking phenotype, rescue experiments with endosomal subdomain readout, multiple orthogonal methods in one study","pmids":["36190447"],"is_preprint":false},{"year":2024,"finding":"Crystal structure of the human WDR91 WD40 domain in complex with Rab7 reveals an unusual interface at the C-terminus of the Rab7 switch II region; WDR91 is highly selective for Rab7 among tested GTPases. A LIS1 homology (LisH) motif in the WDR91 N-terminal domain mediates self-association and contributes to augmented full-length WDR91–Rab7 interaction. Both the Rab7-binding site and the LisH motif are indispensable for WDR91 function in endocytic trafficking. The WDR91 ortholog SORF1 lacks the WD40 domain and instead uses a C-terminal amphipathic helix for membrane targeting via interactions with acidic lipids.","method":"X-ray crystallography (WDR91 WD40–Rab7 co-crystal), GTPase selectivity assays, biochemical self-association assay (LisH motif), liposome interaction assay (SORF1 amphipathic helix), structure-guided mutagenesis with endocytic trafficking functional readout","journal":"Structure (London, England : 1993)","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with functional mutagenesis, biochemical assays, and mechanistic comparison with ortholog; single lab but multiple orthogonal methods","pmids":["39426373"],"is_preprint":false},{"year":2023,"finding":"A first-in-class small-molecule ligand for WDR91 was discovered; co-crystal structure confirmed binding to the WDR domain side pocket in proximity to cysteine 487, enabling development of covalent analogues confirmed by intact mass LC-MS. This structural data defines a druggable pocket on the WDR91 WD40 domain.","method":"DNA-encoded chemical library selection, machine learning virtual screening, surface plasmon resonance (KD ~6 μM), X-ray co-crystallography, intact mass LC-MS for covalent adduct confirmation","journal":"Journal of medicinal chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — co-crystal structure plus SPR binding quantification plus MS-confirmed covalent adduct; single lab with multiple orthogonal biophysical methods","pmids":["37996079"],"is_preprint":false},{"year":2025,"finding":"WDR91 depletion significantly inhibits productive ASO (antisense oligonucleotide) activity in melanoma cells, establishing WDR91-dependent endosomal maturation as required for productive intracellular ASO trafficking and escape from the endosomal compartment.","method":"Genome-wide CRISPR-Cas9 screen in melanoma cells with ASO activity readout, validation by WDR91 depletion with functional ASO potency assay","journal":"Molecular therapy. Nucleic acids","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — CRISPR screen with functional validation in a specific cell context; single lab, single method for validation","pmids":["40529297"],"is_preprint":false},{"year":2022,"finding":"WDR91 (along with WDR81, RAB7, and CCZ1) was identified as a required host factor for late-penetrating virus (reovirus and VSV-EBO GP) infection in a CRISPR-Cas9 screen; loss of WDR81 (WDR91 complex partner) caused accumulation of viral particles in dead-end endosomal compartments, consistent with a role for the WDR81-WDR91 complex in late endosome maturation required for viral penetration.","method":"Genome-wide CRISPR-Cas9 knockout screen, complementation with human WDR81, viral infection assays (reovirus, VSV, VSV-EBO GP), fluorescence microscopy of viral particles in endosomes","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide CRISPR screen with complementation; WDR91 role inferred from screen hit and complex membership; multiple viral infection assays","pmids":["35320319"],"is_preprint":false},{"year":2021,"finding":"C5orf51 (a MON1-CCZ1 complex component) was identified as an interactor of GDP-locked RAB7A and of MON1/CCZ1 (the RAB7A GEF complex); in the absence of C5orf51, RAB7A fails to localize to depolarized mitochondria during mitophagy and is degraded by the proteasome. WDR91 is noted as part of the RAB7A regulatory network but is not a direct subject of mechanistic study in this paper.","method":"Proximity-dependent biotinylation (miniTurbo), co-immunoprecipitation, KO cell lines, fluorescence microscopy of RAB7A on depolarized mitochondria, proteasome inhibitor experiments","journal":"Autophagy","confidence":"Low","confidence_rationale":"Tier 3 / Weak — WDR91 is mentioned only as an abbreviation in the glossary; no direct mechanistic experiment performed on WDR91 in this paper","pmids":["34432599"],"is_preprint":false}],"current_model":"WDR91 is a WD40-repeat Rab7 effector that is recruited to endosomes via a direct interaction with GTP-Rab7 (through the WD40 domain switch II interface) and a LisH-mediated self-association, where it inhibits Beclin1-associated PI3-kinase activity to reduce PtdIns3P levels, thereby coupling Rab5→Rab7 switching with PtdIns3P turnover to drive early-to-late endosome conversion; WDR91 also specifies endosomal retrieval subdomains by bridging Rab7 with SNX-retromer and the WASH complex subunit FAM21 to enable retromer-mediated receptor recycling, and is essential for neuronal development and brain function in vivo."},"narrative":{"mechanistic_narrative":"WDR91 is a WD40-repeat Rab7 effector that couples Rab5-to-Rab7 switching with PtdIns3P turnover to drive early-to-late endosome conversion [PMID:28860274, PMID:26783301]. Together with its partner WDR81, WDR91 associates with Beclin1 and inhibits Beclin1-associated PI3-kinase activity, preventing excessive PtdIns3P accumulation on early endosomes; loss of this function causes Beclin1-dependent enlargement of PtdIns3P-enriched endosomes, defective EGFR degradation, and blocked endosome maturation [PMID:26783301]. Recruitment to endosomes depends on a direct, highly selective interaction between the WDR91 WD40 domain and GTP-Rab7, which a crystal structure localizes to an unusual interface at the C-terminus of the Rab7 switch II region, and on an N-terminal LisH motif that mediates self-association and augments Rab7 binding; both elements are indispensable for endocytic trafficking [PMID:28860274, PMID:39426373]. Beyond regulating PtdIns3P, WDR91 specifies endosomal retrieval subdomains by bridging Rab7 with the SNX-retromer (binding sorting nexin PX domains and VPS35) and the WASH complex subunit FAM21, organizing endosomal actin and enabling retromer-mediated membrane tubulation and receptor recycling [PMID:36190447]. In vivo, WDR91 is essential for neuronal development and brain function: its loss in mouse neurons produces giant intermediate endosomes and reduced neurite complexity, and organismal knockout is lethal [PMID:28860274]. A druggable side pocket near cysteine 487 on the WD40 domain has been defined with a first-in-class covalent ligand [PMID:37996079].","teleology":[{"year":2016,"claim":"Established that WDR91 acts as a negative regulator of PtdIns3P synthesis, answering how early endosomes limit PtdIns3P to permit maturation rather than fuse uncontrollably.","evidence":"C. elegans loss-of-function with Rab-switching epistasis, reciprocal Co-IP with Beclin1, PI3K activity assay, and mammalian EGFR degradation readout","pmids":["26783301"],"confidence":"High","gaps":["Did not define how WDR91 is recruited to endosomes","Structural basis of PI3K inhibition not resolved"]},{"year":2016,"claim":"Showed WDR81 (the WDR91 partner) is required for endolysosomal fusion and degradation of EGFR and tetherin, framing the WDR81–WDR91 complex as a unit acting in endolysosomal maturation.","evidence":"Forward genetic haploid cell screen, complementation, and endosomal trafficking/degradation assays in human cells","pmids":["27126989"],"confidence":"Medium","gaps":["WDR91 role inferred from complex membership rather than direct assay","Stoichiometry and architecture of the WDR81–WDR91 complex not defined"]},{"year":2017,"claim":"Defined WDR91 as a GTP-Rab7 effector, explaining how PtdIns3P down-regulation is spatially coupled to Rab switching, and demonstrated its requirement for neuronal development in vivo.","evidence":"Co-IP with GTP-Rab7, in vitro PI3K activity assay, conditional and global mouse knockouts, and mutant rescue with neuronal morphology readouts","pmids":["28860274"],"confidence":"High","gaps":["Atomic-level Rab7-binding interface not resolved at this stage","Mechanism linking endosomal defects to reduced neurite complexity not detailed"]},{"year":2022,"claim":"Extended WDR91 function beyond PtdIns3P control to organizing endosomal retrieval subdomains, answering how Rab7, retromer, and WASH are spatially concentrated for receptor recycling.","evidence":"Reciprocal Co-IP with SNX PX domains, VPS35, and FAM21, knockout/rescue, and live imaging of endosomal subdomains and actin","pmids":["36190447"],"confidence":"High","gaps":["How a single effector coordinates PI3K inhibition and retromer scaffolding simultaneously is unclear","Direct versus bridged nature of WDR91–FAM21 contact not fully separated"]},{"year":2024,"claim":"Resolved the structural basis of WDR91 recruitment, showing the WD40 domain engages an unusual Rab7 switch II interface and that a LisH motif drives self-association, both required for trafficking.","evidence":"X-ray crystallography of WDR91 WD40–Rab7, GTPase selectivity assays, self-association assay, and structure-guided mutagenesis with functional readout","pmids":["39426373"],"confidence":"High","gaps":["Oligomeric state of full-length WDR91 on membranes not determined","Structure does not capture WDR91 in complex with retromer or Beclin1"]},{"year":2023,"claim":"Identified a druggable pocket on the WDR91 WD40 domain, providing chemical tools to probe and potentially inhibit its function.","evidence":"DNA-encoded library selection, ML virtual screening, SPR binding, X-ray co-crystallography, and covalent adduct confirmation by intact mass LC-MS","pmids":["37996079"],"confidence":"High","gaps":["Cellular consequences of ligand binding not characterized","Selectivity against other WD40 proteins not established"]},{"year":2022,"claim":"Implicated the WDR81–WDR91 complex in host endosomal maturation required for late-penetrating virus entry, connecting its trafficking role to infection.","evidence":"Genome-wide CRISPR-Cas9 screen with WDR81 complementation and viral infection assays (reovirus, VSV-EBO GP)","pmids":["35320319"],"confidence":"Medium","gaps":["WDR91 role inferred from screen hit and complex membership","No direct WDR91 perturbation in the viral assays"]},{"year":2025,"claim":"Linked WDR91-dependent endosomal maturation to productive antisense oligonucleotide escape, identifying it as a determinant of oligonucleotide therapeutic efficacy.","evidence":"Genome-wide CRISPR-Cas9 screen in melanoma cells with ASO activity readout and WDR91 depletion validation","pmids":["40529297"],"confidence":"Medium","gaps":["Single cell context and single validation method","Mechanism of ASO endosomal escape relative to WDR91 not dissected"]},{"year":null,"claim":"How WDR91 mechanically integrates PI3K inhibition, Rab7 effector function, and retromer/WASH scaffolding into a single coordinated maturation program remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No structure of full-length membrane-bound WDR91 with its multiple partners","Temporal ordering of PtdIns3P down-regulation versus retrieval-subdomain assembly unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[3]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[3]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[1,3]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1,3]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[3]}],"complexes":["WDR81-WDR91 complex"],"partners":["RAB7A","BECN1","WDR81","VPS35","FAM21"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"A4D1P6","full_name":"WD repeat-containing protein 91","aliases":[],"length_aa":747,"mass_kda":83.3,"function":"Functions as a negative regulator of the PI3 kinase/PI3K activity associated with endosomal membranes via BECN1, a core subunit of the PI3K complex. By modifying the phosphatidylinositol 3-phosphate/PtdInsP3 content of endosomal membranes may regulate endosome fusion, recycling, sorting and early to late endosome transport (PubMed:26783301). It is for instance, required for the delivery of cargos like BST2/tetherin from early to late endosome and thereby participates indirectly to their degradation by the lysosome (PubMed:27126989). May play a role in meiosis (By similarity)","subcellular_location":"Early endosome membrane; Late endosome membrane","url":"https://www.uniprot.org/uniprotkb/A4D1P6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/WDR91","classification":"Not Classified","n_dependent_lines":20,"n_total_lines":1208,"dependency_fraction":0.016556291390728478},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/WDR91","total_profiled":1310},"omim":[{"mim_id":"616303","title":"WD REPEAT-CONTAINING PROTEIN 91; WDR91","url":"https://www.omim.org/entry/616303"},{"mim_id":"614235","title":"PDZ DOMAIN-CONTAINING PROTEIN 8; PDZD8","url":"https://www.omim.org/entry/614235"},{"mim_id":"614218","title":"WD REPEAT-CONTAINING PROTEIN 81; WDR81","url":"https://www.omim.org/entry/614218"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"choroid plexus","ntpm":17.5}],"url":"https://www.proteinatlas.org/search/WDR91"},"hgnc":{"alias_symbol":["HSPC049","SORF-1"],"prev_symbol":[]},"alphafold":{"accession":"A4D1P6","domains":[{"cath_id":"-","chopping":"37-175","consensus_level":"high","plddt":86.4752,"start":37,"end":175},{"cath_id":"2.130.10.10","chopping":"397-518_538-745","consensus_level":"medium","plddt":92.3518,"start":397,"end":745}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/A4D1P6","model_url":"https://alphafold.ebi.ac.uk/files/AF-A4D1P6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-A4D1P6-F1-predicted_aligned_error_v6.png","plddt_mean":74.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=WDR91","jax_strain_url":"https://www.jax.org/strain/search?query=WDR91"},"sequence":{"accession":"A4D1P6","fasta_url":"https://rest.uniprot.org/uniprotkb/A4D1P6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/A4D1P6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/A4D1P6"}},"corpus_meta":[{"pmid":"26783301","id":"PMC_26783301","title":"Negative regulation of phosphatidylinositol 3-phosphate levels in early-to-late endosome conversion.","date":"2016","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/26783301","citation_count":66,"is_preprint":false},{"pmid":"27346680","id":"PMC_27346680","title":"Retinoic Acid Is Sufficient for the In Vitro Induction of Mouse Spermatocytes.","date":"2016","source":"Stem cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/27346680","citation_count":58,"is_preprint":false},{"pmid":"20043197","id":"PMC_20043197","title":"Molecular and biological characterization of a Marek's disease virus field strain with reticuloendotheliosis virus LTR insert.","date":"2009","source":"Virus genes","url":"https://pubmed.ncbi.nlm.nih.gov/20043197","citation_count":47,"is_preprint":false},{"pmid":"28860274","id":"PMC_28860274","title":"WDR91 is a Rab7 effector required for neuronal development.","date":"2017","source":"The Journal of cell 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Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/27126989","citation_count":23,"is_preprint":false},{"pmid":"36190447","id":"PMC_36190447","title":"WDR91 specifies the endosomal retrieval subdomain for retromer-dependent recycling.","date":"2022","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/36190447","citation_count":14,"is_preprint":false},{"pmid":"28928133","id":"PMC_28928133","title":"A new Rab7 effector controls phosphoinositide conversion in endosome maturation.","date":"2017","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/28928133","citation_count":14,"is_preprint":false},{"pmid":"37996079","id":"PMC_37996079","title":"Discovery of a First-in-Class Small-Molecule Ligand for WDR91 Using DNA-Encoded Chemical Library Selection Followed by Machine Learning.","date":"2023","source":"Journal of medicinal 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In mammalian cells, WDR91 and WDR81 physically interact with Beclin1 and inhibit PI3K complex activity; their inactivation causes Beclin1-dependent enlargement of PtdIns3P-enriched endosomes and defective EGFR degradation.\",\n      \"method\": \"Genetic loss-of-function in C. elegans, epistasis with Rab switching genes, co-immunoprecipitation (complex with Beclin1), PI3K activity assay, mammalian cell inactivation with EGFR degradation readout, live imaging of endosomal PtdIns3P\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, in vivo genetic epistasis in C. elegans, enzymatic activity assay, validated in mammalian cells with orthogonal functional readouts; independently replicated in subsequent papers\",\n      \"pmids\": [\"26783301\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"WDR91 is a Rab7 effector: it is recruited to endosomes by interacting with GTP-Rab7, and once there it inhibits Rab7-associated PI3-kinase activity to reduce PtdIns3P levels, coupling Rab switching with PtdIns3P down-regulation during early-to-late endosome conversion. Loss of WDR91 in mouse neurons causes accumulation of giant intermediate endosomes and reduced neurite length/complexity; phenotypes are rescued by wild-type WDR91 but not by Rab7-binding-deficient WDR91 mutants. Global Wdr91 knockout causes neonatal death; brain-specific inactivation impairs brain development and causes postnatal death.\",\n      \"method\": \"Co-immunoprecipitation with GTP-Rab7, in vitro PI3K activity assay, conditional knockout mouse models (global and brain-specific), rescue experiments with WDR91 mutants, live-cell imaging of endosomal PtdIns3P, neuronal morphology analysis\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — direct GTP-Rab7 interaction, PI3K activity assay, in vivo mouse knockout with defined cellular and organismal phenotype, mutagenesis rescue demonstrating Rab7 binding is required\",\n      \"pmids\": [\"28860274\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"WDR81 (partner of WDR91) is required for trafficking and lysosomal degradation of tetherin and EGFR; WDR81 and WDR91 function together as a complex in endolysosomal fusion. Absence of WDR81 results in swollen endolysosomal compartments with enlarged early and late endosomes and reduced delivery of endocytosed dextran to cathepsin-active lysosomes.\",\n      \"method\": \"Forward genetic haploid cell screen (KBM7), functional complementation, endosomal trafficking and degradation assays, fluorescence microscopy of endolysosomal compartments\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — forward genetic screen identifying the WDR81-WDR91 complex, functional assays in human cells, but WDR91 role inferred from complex membership with WDR81 as primary hit\",\n      \"pmids\": [\"27126989\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"WDR91 specifies the endosomal retrieval subdomain required for retromer-dependent recycling. WDR91 interacts with sorting nexins (SNXs) through their PX domain and with VPS35, promoting their interaction with Rab7. WDR91 also interacts with the WASH subunit FAM21. In WDR91-deficient cells, Rab7, SNX-retromer, and FAM21 fail to localize to endosomal subdomains and endosomal actin organization is impaired; re-expression of WDR91 rescues Rab7, SNX-retromer, and FAM21 concentration at WDR91-specific subdomains where retromer-mediated membrane tubulation and release occur.\",\n      \"method\": \"Co-immunoprecipitation (WDR91–SNX PX domain, WDR91–VPS35, WDR91–FAM21), WDR91 knockout cells, rescue/re-expression experiments, fluorescence live imaging of endosomal subdomains, actin organization assay\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP with multiple partners, KO with defined trafficking phenotype, rescue experiments with endosomal subdomain readout, multiple orthogonal methods in one study\",\n      \"pmids\": [\"36190447\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Crystal structure of the human WDR91 WD40 domain in complex with Rab7 reveals an unusual interface at the C-terminus of the Rab7 switch II region; WDR91 is highly selective for Rab7 among tested GTPases. A LIS1 homology (LisH) motif in the WDR91 N-terminal domain mediates self-association and contributes to augmented full-length WDR91–Rab7 interaction. Both the Rab7-binding site and the LisH motif are indispensable for WDR91 function in endocytic trafficking. The WDR91 ortholog SORF1 lacks the WD40 domain and instead uses a C-terminal amphipathic helix for membrane targeting via interactions with acidic lipids.\",\n      \"method\": \"X-ray crystallography (WDR91 WD40–Rab7 co-crystal), GTPase selectivity assays, biochemical self-association assay (LisH motif), liposome interaction assay (SORF1 amphipathic helix), structure-guided mutagenesis with endocytic trafficking functional readout\",\n      \"journal\": \"Structure (London, England : 1993)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with functional mutagenesis, biochemical assays, and mechanistic comparison with ortholog; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"39426373\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"A first-in-class small-molecule ligand for WDR91 was discovered; co-crystal structure confirmed binding to the WDR domain side pocket in proximity to cysteine 487, enabling development of covalent analogues confirmed by intact mass LC-MS. This structural data defines a druggable pocket on the WDR91 WD40 domain.\",\n      \"method\": \"DNA-encoded chemical library selection, machine learning virtual screening, surface plasmon resonance (KD ~6 μM), X-ray co-crystallography, intact mass LC-MS for covalent adduct confirmation\",\n      \"journal\": \"Journal of medicinal chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — co-crystal structure plus SPR binding quantification plus MS-confirmed covalent adduct; single lab with multiple orthogonal biophysical methods\",\n      \"pmids\": [\"37996079\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"WDR91 depletion significantly inhibits productive ASO (antisense oligonucleotide) activity in melanoma cells, establishing WDR91-dependent endosomal maturation as required for productive intracellular ASO trafficking and escape from the endosomal compartment.\",\n      \"method\": \"Genome-wide CRISPR-Cas9 screen in melanoma cells with ASO activity readout, validation by WDR91 depletion with functional ASO potency assay\",\n      \"journal\": \"Molecular therapy. Nucleic acids\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — CRISPR screen with functional validation in a specific cell context; single lab, single method for validation\",\n      \"pmids\": [\"40529297\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"WDR91 (along with WDR81, RAB7, and CCZ1) was identified as a required host factor for late-penetrating virus (reovirus and VSV-EBO GP) infection in a CRISPR-Cas9 screen; loss of WDR81 (WDR91 complex partner) caused accumulation of viral particles in dead-end endosomal compartments, consistent with a role for the WDR81-WDR91 complex in late endosome maturation required for viral penetration.\",\n      \"method\": \"Genome-wide CRISPR-Cas9 knockout screen, complementation with human WDR81, viral infection assays (reovirus, VSV, VSV-EBO GP), fluorescence microscopy of viral particles in endosomes\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide CRISPR screen with complementation; WDR91 role inferred from screen hit and complex membership; multiple viral infection assays\",\n      \"pmids\": [\"35320319\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"C5orf51 (a MON1-CCZ1 complex component) was identified as an interactor of GDP-locked RAB7A and of MON1/CCZ1 (the RAB7A GEF complex); in the absence of C5orf51, RAB7A fails to localize to depolarized mitochondria during mitophagy and is degraded by the proteasome. WDR91 is noted as part of the RAB7A regulatory network but is not a direct subject of mechanistic study in this paper.\",\n      \"method\": \"Proximity-dependent biotinylation (miniTurbo), co-immunoprecipitation, KO cell lines, fluorescence microscopy of RAB7A on depolarized mitochondria, proteasome inhibitor experiments\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — WDR91 is mentioned only as an abbreviation in the glossary; no direct mechanistic experiment performed on WDR91 in this paper\",\n      \"pmids\": [\"34432599\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"WDR91 is a WD40-repeat Rab7 effector that is recruited to endosomes via a direct interaction with GTP-Rab7 (through the WD40 domain switch II interface) and a LisH-mediated self-association, where it inhibits Beclin1-associated PI3-kinase activity to reduce PtdIns3P levels, thereby coupling Rab5→Rab7 switching with PtdIns3P turnover to drive early-to-late endosome conversion; WDR91 also specifies endosomal retrieval subdomains by bridging Rab7 with SNX-retromer and the WASH complex subunit FAM21 to enable retromer-mediated receptor recycling, and is essential for neuronal development and brain function in vivo.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"WDR91 is a WD40-repeat Rab7 effector that couples Rab5-to-Rab7 switching with PtdIns3P turnover to drive early-to-late endosome conversion [#1, #0]. Together with its partner WDR81, WDR91 associates with Beclin1 and inhibits Beclin1-associated PI3-kinase activity, preventing excessive PtdIns3P accumulation on early endosomes; loss of this function causes Beclin1-dependent enlargement of PtdIns3P-enriched endosomes, defective EGFR degradation, and blocked endosome maturation [#0]. Recruitment to endosomes depends on a direct, highly selective interaction between the WDR91 WD40 domain and GTP-Rab7, which a crystal structure localizes to an unusual interface at the C-terminus of the Rab7 switch II region, and on an N-terminal LisH motif that mediates self-association and augments Rab7 binding; both elements are indispensable for endocytic trafficking [#1, #4]. Beyond regulating PtdIns3P, WDR91 specifies endosomal retrieval subdomains by bridging Rab7 with the SNX-retromer (binding sorting nexin PX domains and VPS35) and the WASH complex subunit FAM21, organizing endosomal actin and enabling retromer-mediated membrane tubulation and receptor recycling [#3]. In vivo, WDR91 is essential for neuronal development and brain function: its loss in mouse neurons produces giant intermediate endosomes and reduced neurite complexity, and organismal knockout is lethal [#1]. A druggable side pocket near cysteine 487 on the WD40 domain has been defined with a first-in-class covalent ligand [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Established that WDR91 acts as a negative regulator of PtdIns3P synthesis, answering how early endosomes limit PtdIns3P to permit maturation rather than fuse uncontrollably.\",\n      \"evidence\": \"C. elegans loss-of-function with Rab-switching epistasis, reciprocal Co-IP with Beclin1, PI3K activity assay, and mammalian EGFR degradation readout\",\n      \"pmids\": [\"26783301\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define how WDR91 is recruited to endosomes\", \"Structural basis of PI3K inhibition not resolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed WDR81 (the WDR91 partner) is required for endolysosomal fusion and degradation of EGFR and tetherin, framing the WDR81–WDR91 complex as a unit acting in endolysosomal maturation.\",\n      \"evidence\": \"Forward genetic haploid cell screen, complementation, and endosomal trafficking/degradation assays in human cells\",\n      \"pmids\": [\"27126989\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"WDR91 role inferred from complex membership rather than direct assay\", \"Stoichiometry and architecture of the WDR81–WDR91 complex not defined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined WDR91 as a GTP-Rab7 effector, explaining how PtdIns3P down-regulation is spatially coupled to Rab switching, and demonstrated its requirement for neuronal development in vivo.\",\n      \"evidence\": \"Co-IP with GTP-Rab7, in vitro PI3K activity assay, conditional and global mouse knockouts, and mutant rescue with neuronal morphology readouts\",\n      \"pmids\": [\"28860274\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic-level Rab7-binding interface not resolved at this stage\", \"Mechanism linking endosomal defects to reduced neurite complexity not detailed\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Extended WDR91 function beyond PtdIns3P control to organizing endosomal retrieval subdomains, answering how Rab7, retromer, and WASH are spatially concentrated for receptor recycling.\",\n      \"evidence\": \"Reciprocal Co-IP with SNX PX domains, VPS35, and FAM21, knockout/rescue, and live imaging of endosomal subdomains and actin\",\n      \"pmids\": [\"36190447\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How a single effector coordinates PI3K inhibition and retromer scaffolding simultaneously is unclear\", \"Direct versus bridged nature of WDR91–FAM21 contact not fully separated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Resolved the structural basis of WDR91 recruitment, showing the WD40 domain engages an unusual Rab7 switch II interface and that a LisH motif drives self-association, both required for trafficking.\",\n      \"evidence\": \"X-ray crystallography of WDR91 WD40–Rab7, GTPase selectivity assays, self-association assay, and structure-guided mutagenesis with functional readout\",\n      \"pmids\": [\"39426373\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Oligomeric state of full-length WDR91 on membranes not determined\", \"Structure does not capture WDR91 in complex with retromer or Beclin1\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified a druggable pocket on the WDR91 WD40 domain, providing chemical tools to probe and potentially inhibit its function.\",\n      \"evidence\": \"DNA-encoded library selection, ML virtual screening, SPR binding, X-ray co-crystallography, and covalent adduct confirmation by intact mass LC-MS\",\n      \"pmids\": [\"37996079\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cellular consequences of ligand binding not characterized\", \"Selectivity against other WD40 proteins not established\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Implicated the WDR81–WDR91 complex in host endosomal maturation required for late-penetrating virus entry, connecting its trafficking role to infection.\",\n      \"evidence\": \"Genome-wide CRISPR-Cas9 screen with WDR81 complementation and viral infection assays (reovirus, VSV-EBO GP)\",\n      \"pmids\": [\"35320319\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"WDR91 role inferred from screen hit and complex membership\", \"No direct WDR91 perturbation in the viral assays\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Linked WDR91-dependent endosomal maturation to productive antisense oligonucleotide escape, identifying it as a determinant of oligonucleotide therapeutic efficacy.\",\n      \"evidence\": \"Genome-wide CRISPR-Cas9 screen in melanoma cells with ASO activity readout and WDR91 depletion validation\",\n      \"pmids\": [\"40529297\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single cell context and single validation method\", \"Mechanism of ASO endosomal escape relative to WDR91 not dissected\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How WDR91 mechanically integrates PI3K inhibition, Rab7 effector function, and retromer/WASH scaffolding into a single coordinated maturation program remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structure of full-length membrane-bound WDR91 with its multiple partners\", \"Temporal ordering of PtdIns3P down-regulation versus retrieval-subdomain assembly unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\"WDR81-WDR91 complex\"],\n    \"partners\": [\"RAB7A\", \"BECN1\", \"WDR81\", \"VPS35\", \"FAM21\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}