{"gene":"WDR45B","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":2017,"finding":"WIPI3 (WDR45B) scaffolds LKB1-AMPK-TSC signalling upstream of PtdIns3P production: WIPI3 associates with AMPK-activated TSC complex at lysosomes to regulate mTOR, and forms a complex with FIP200 at nascent autophagosomes to control their size.","method":"WIPI interactome analysis (co-immunoprecipitation/mass spectrometry), functional kinase screen, localization studies","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — interactome/Co-IP plus functional kinase screen in single lab, multiple orthogonal methods but no structural or in vitro reconstitution","pmids":["28561066"],"is_preprint":false},{"year":2021,"finding":"WDR45B is specifically required for autophagosome maturation into autolysosomes in neural cells: WDR45B interacts with the tether protein EPG5 and targets it to late endosomes/lysosomes to promote autophagosome-lysosome fusion; disease-related mutations of WDR45B fail to rescue autophagy defects due to impaired EPG5 binding. In Wdr45/45b-depleted cells, formation of the SNARE-EPG5 fusion machinery is dampened.","method":"Co-immunoprecipitation (WDR45B–EPG5 interaction), Wdr45/Wdr45b double knockout mouse neural cells, autophagosome maturation assays, rescue with ATG2A overexpression, SNARE complex analysis, O-GlcNAcylation inhibition rescue","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, genetic KO with defined cellular phenotype, multiple orthogonal assays (lipid transfer rescue, SNARE complex, pharmacological rescue), replicated in companion paper PMID:34105435","pmids":["33636118","34105435"],"is_preprint":false},{"year":2019,"finding":"WDR45B is critical for neural autophagy and acts cooperatively with WDR45: Wdr45b knockout mice accumulate SQSTM1- and ubiquitin-positive aggregates in brain regions and exhibit swollen axons; Wdr45b/Wdr45 double KO mice die within one day of birth with more severe autophagy defects than either single KO, establishing cooperative function in autophagy.","method":"Wdr45b knockout mouse model (histology, immunohistochemistry for autophagy substrates, behavioral tests), double KO genetic epistasis","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with defined cellular and molecular phenotype, genetic epistasis via double KO, single lab","pmids":["31238825"],"is_preprint":false},{"year":2020,"finding":"Wipi3 (WDR45B) is essential for alternative (Atg5/Atg7-independent) autophagy: Wipi3 binds to Golgi membranes and is required for generation of isolation membranes in alternative autophagy. Neuron-specific Wipi3-deficient mice show cerebellar neuronal loss and iron/ceruloplasmin accumulation suppressed by Dram1 expression. Atg7/Wipi3 double-deficient mice are mostly embryonic lethal, indicating Wipi3 maintains neuronal cells via mechanisms distinct from canonical autophagy.","method":"Neuron-specific Wipi3-knockout mice, electron microscopy, subcellular fractionation/localization to Golgi membranes, genetic epistasis (Atg7/Wipi3 double KO), rescue by Dram1 expression","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean tissue-specific KO with defined phenotype, Golgi localization by direct experiment, genetic epistasis with double KO lethality, multiple orthogonal methods","pmids":["33082312"],"is_preprint":false},{"year":2024,"finding":"Cryo-EM structure of the complete human TSC in complex with WIPI3 (WDR45B) at 2.8 Å resolution: WIPI3 serves as a lysosomal recruitment factor for TSC; a previously undetected amino-terminal TSC1 HEAT repeat dimer forms a PIP-binding pocket that specifically binds monophosphorylated PIPs, providing a structural model by which WIPI3 and PIP-signaling networks coordinate to recruit TSC to the lysosomal membrane to inhibit mTORC1.","method":"Cryo-electron microscopy (2.8-Å structure), biochemical reconstitution of TSC:WIPI3 complex","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution cryo-EM structure with biochemical reconstitution, single rigorous study with multiple orthogonal methods","pmids":["39565846"],"is_preprint":false},{"year":2025,"finding":"WIPI3 (WDR45B) forms a tight complex with the ATG13:ATG101 HORMA domain heterodimer; bound to WIPI3 (or WIPI2), ATG13:ATG101 aligns with the membrane to insert its WF finger. WIPI3:ATG13 engagement is required for ATG16L1 phosphorylation by ULK1, ATG13 puncta formation, and bulk autophagic flux, establishing WIPI3 as a PI3P-dependent membrane anchor that recruits the ULK1 kinase domain to the membrane surface.","method":"Biochemical reconstitution (in vitro complex assembly), molecular dynamics simulations, cell-based phosphorylation assay (ATG16L1 phosphorylation), ATG13 puncta formation assay, autophagic flux measurement","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — biochemical reconstitution and cell-based assays in single preprint lab, not yet peer-reviewed","pmids":["bio_10.1101_2025.11.07.687251"],"is_preprint":true}],"current_model":"WDR45B (WIPI3) is a PI(3)P-binding β-propeller scaffold that functions at multiple steps of autophagy: it recruits TSC to lysosomes via a direct interaction (cryo-EM structure resolved) to inhibit mTORC1; it scaffolds LKB1-AMPK-TSC signalling upstream of autophagosome formation in complex with FIP200; it bridges the ATG13:ATG101 HORMA dimer to PI3P-enriched membranes to recruit and activate ULK1; it is essential for alternative (Atg5/Atg7-independent) autophagy through binding to Golgi membranes; and it promotes autophagosome-lysosome fusion by targeting the tether protein EPG5 to late endosomes/lysosomes, facilitating SNARE-dependent fusion—a function disrupted by disease-causing mutations."},"narrative":{"mechanistic_narrative":"WDR45B (WIPI3) is a PI3P-binding β-propeller scaffold that operates at multiple steps of autophagy and lysosomal mTOR signalling, and is essential for neuronal homeostasis [PMID:28561066, PMID:31238825]. It acts as a lysosomal recruitment factor for the TSC complex: a cryo-EM structure of human TSC bound to WIPI3 resolves an amino-terminal TSC1 HEAT-repeat dimer forming a monophosphoinositide-binding pocket, showing how WIPI3 and PIP signalling cooperate to dock TSC at the lysosomal membrane to inhibit mTORC1 [PMID:39565846], consistent with its earlier identification scaffolding LKB1-AMPK-TSC signalling at lysosomes and forming a complex with FIP200 at nascent autophagosomes [PMID:28561066]. Beyond mTOR regulation, WDR45B is also required for autophagosome maturation: it binds the tether protein EPG5 and targets it to late endosomes/lysosomes to promote SNARE-dependent autophagosome-lysosome fusion, a function abolished by disease-causing mutations that impair EPG5 binding [PMID:33636118, PMID:34105435]. It is additionally essential for alternative, Atg5/Atg7-independent autophagy through binding Golgi membranes to generate isolation membranes [PMID:33082312]. In mice, Wdr45b loss causes accumulation of SQSTM1- and ubiquitin-positive aggregates, swollen axons, and cerebellar neuronal loss, and it functions cooperatively with the paralog WDR45, with double knockouts being neonatally lethal [PMID:31238825, PMID:33082312].","teleology":[{"year":2017,"claim":"Established WIPI3 as a signalling scaffold upstream of PtdIns3P production rather than a purely downstream PI3P effector, linking it to AMPK-TSC-mTOR control and to FIP200 at nascent autophagosomes.","evidence":"WIPI interactome by Co-IP/mass spectrometry, functional kinase screen, and localization in cells","pmids":["28561066"],"confidence":"Medium","gaps":["No structural model of the WIPI3-TSC or WIPI3-FIP200 contacts","Single lab, no in vitro reconstitution","Direct vs indirect nature of the AMPK-TSC association not resolved"]},{"year":2019,"claim":"Demonstrated that WDR45B is required for neural autophagy and acts cooperatively with its paralog WDR45, defining a non-redundant but overlapping role.","evidence":"Wdr45b knockout mice with autophagy-substrate histology and Wdr45b/Wdr45 double-KO genetic epistasis","pmids":["31238825"],"confidence":"Medium","gaps":["Molecular step in autophagy disrupted not pinpointed","Basis of cooperativity with WDR45 unresolved","Single lab"]},{"year":2020,"claim":"Showed WDR45B has an autophagy-step function distinct from canonical macroautophagy by being essential for Atg5/Atg7-independent alternative autophagy at the Golgi.","evidence":"Neuron-specific Wipi3-KO mice, EM, Golgi localization by fractionation, Atg7/Wipi3 double-KO lethality, and Dram1 rescue","pmids":["33082312"],"confidence":"High","gaps":["Mechanism of isolation-membrane generation from Golgi not defined","How iron/ceruloplasmin accumulation links to the autophagy defect unclear"]},{"year":2021,"claim":"Identified a discrete maturation-stage role: WDR45B targets the tether EPG5 to late endosomes/lysosomes to promote SNARE-dependent fusion, and connected disease mutations to loss of this interaction.","evidence":"Reciprocal Co-IP, Wdr45/Wdr45b double-KO neural cells, maturation assays, SNARE complex analysis, ATG2A and O-GlcNAcylation-inhibition rescues; replicated in companion paper","pmids":["33636118","34105435"],"confidence":"High","gaps":["Structural basis of WDR45B-EPG5 binding not resolved","How a single scaffold coordinates both early signalling and late fusion roles unclear"]},{"year":2024,"claim":"Provided the structural mechanism for WIPI3 as a lysosomal recruitment factor for TSC, revealing a TSC1 HEAT-repeat PIP-binding pocket that, with WIPI3, docks TSC to inhibit mTORC1.","evidence":"2.8-Å cryo-EM structure of human TSC:WIPI3 with biochemical reconstitution","pmids":["39565846"],"confidence":"High","gaps":["In vivo contribution of WIPI3-dependent TSC recruitment to mTORC1 output not quantified","Interplay with the LKB1-AMPK arm not structurally addressed"]},{"year":2025,"claim":"Defined WIPI3 as a PI3P-dependent membrane anchor that bridges the ATG13:ATG101 HORMA dimer to membranes to recruit and activate ULK1 during autophagosome initiation.","evidence":"In vitro complex reconstitution, molecular dynamics, ATG16L1 phosphorylation assay, ATG13 puncta and autophagic flux measurements (preprint)","pmids":["bio_10.1101_2025.11.07.687251"],"confidence":"Medium","gaps":["Not yet peer-reviewed","Functional redundancy with WIPI2 at this step not delineated","In vivo requirement of the WIPI3:ATG13 contact untested"]},{"year":null,"claim":"How a single β-propeller scaffold is partitioned among its distinct lysosomal mTOR, initiation, alternative-autophagy, and fusion roles in a given cell remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No spatiotemporal map of which complex WDR45B occupies at each autophagy stage","Determinants selecting EPG5 vs TSC vs ATG13 partners unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[4,5]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,4,5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,4]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[0,1,4]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[3]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[1,2,3,5]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,4]}],"complexes":["TSC complex","ATG13:ATG101 HORMA dimer","EPG5-SNARE fusion machinery"],"partners":["EPG5","FIP200","ATG13","ATG101","TSC1","WDR45"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5MNZ6","full_name":"WD repeat domain phosphoinositide-interacting protein 3","aliases":["WD repeat-containing protein 45-like","WDR45-like protein","WD repeat-containing protein 45B","WIPI49-like protein"],"length_aa":344,"mass_kda":38.1,"function":"Component of the autophagy machinery that controls the major intracellular degradation process by which cytoplasmic materials are packaged into autophagosomes and delivered to lysosomes for degradation (PubMed:28561066). Binds phosphatidylinositol 3-phosphate (PtdIns3P), and other phosphoinositides including PtdIns(3,5)P2, forming on membranes of the endoplasmic reticulum upon activation of the upstream ULK1 and PI3 kinases and is recruited at phagophore assembly sites where it regulates the elongation of nascent phagophores downstream of WIPI2 (PubMed:28561066, PubMed:30797857). In the cellular response to starvation, may also function together with the TSC1-TSC2 complex and RB1CC1 in the inhibition of the mTORC1 signaling pathway (PubMed:28503735)","subcellular_location":"Preautophagosomal structure; Lysosome","url":"https://www.uniprot.org/uniprotkb/Q5MNZ6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/WDR45B","classification":"Not Classified","n_dependent_lines":4,"n_total_lines":1208,"dependency_fraction":0.0033112582781456954},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/WDR45B","total_profiled":1310},"omim":[{"mim_id":"617977","title":"NEURODEVELOPMENTAL DISORDER WITH SPASTIC QUADRIPLEGIA AND BRAIN ABNORMALITIES WITH OR WITHOUT SEIZURES; NEDSBAS","url":"https://www.omim.org/entry/617977"},{"mim_id":"609226","title":"WD REPEAT-CONTAINING PROTEIN 45B; WDR45B","url":"https://www.omim.org/entry/609226"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Uncertain","locations":[{"location":"Golgi apparatus","reliability":"Uncertain"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/WDR45B"},"hgnc":{"alias_symbol":["WIPI3"],"prev_symbol":["WDR45L"]},"alphafold":{"accession":"Q5MNZ6","domains":[{"cath_id":"2.40.128","chopping":"241-344","consensus_level":"medium","plddt":90.9985,"start":241,"end":344}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5MNZ6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5MNZ6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5MNZ6-F1-predicted_aligned_error_v6.png","plddt_mean":94.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=WDR45B","jax_strain_url":"https://www.jax.org/strain/search?query=WDR45B"},"sequence":{"accession":"Q5MNZ6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5MNZ6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5MNZ6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5MNZ6"}},"corpus_meta":[{"pmid":"28561066","id":"PMC_28561066","title":"WIPI3 and WIPI4 β-propellers are scaffolds for LKB1-AMPK-TSC signalling circuits in the control of autophagy.","date":"2017","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/28561066","citation_count":173,"is_preprint":false},{"pmid":"33636118","id":"PMC_33636118","title":"β-propeller proteins WDR45 and WDR45B regulate autophagosome maturation into autolysosomes in neural cells.","date":"2021","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/33636118","citation_count":53,"is_preprint":false},{"pmid":"31238825","id":"PMC_31238825","title":"Role of Wdr45b in maintaining neural autophagy and cognitive function.","date":"2019","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/31238825","citation_count":49,"is_preprint":false},{"pmid":"33082312","id":"PMC_33082312","title":"Wipi3 is essential for alternative autophagy and its loss causes neurodegeneration.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33082312","citation_count":44,"is_preprint":false},{"pmid":"28503735","id":"PMC_28503735","title":"WDR45B-related intellectual disability, spastic quadriplegia, epilepsy, and cerebral hypoplasia: A consistent neurodevelopmental syndrome.","date":"2017","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28503735","citation_count":36,"is_preprint":false},{"pmid":"34105435","id":"PMC_34105435","title":"The BPAN and intellectual disability disease proteins WDR45 and WDR45B modulate autophagosome-lysosome fusion.","date":"2021","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/34105435","citation_count":14,"is_preprint":false},{"pmid":"34328055","id":"PMC_34328055","title":"A Dictyostelium model for BPAN disease reveals a functional relationship between the WDR45/WIPI4 homolog Wdr45l and Vmp1 in the regulation of autophagy-associated PtdIns3P and ER stress.","date":"2021","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/34328055","citation_count":13,"is_preprint":false},{"pmid":"39565846","id":"PMC_39565846","title":"Structure of the human TSC:WIPI3 lysosomal recruitment complex.","date":"2024","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/39565846","citation_count":7,"is_preprint":false},{"pmid":"35962600","id":"PMC_35962600","title":"A homozygous variant of WDR45B results in global developmental delay: Additional case and literature review.","date":"2022","source":"Molecular genetics & genomic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35962600","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.11.07.687251","title":"Reconstitution of multistep recruitment of ULK1 to membranes in autophagy","date":"2025-11-09","source":"bioRxiv","url":"https://doi.org/10.1101/2025.11.07.687251","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7257,"output_tokens":1961,"usd":0.025593,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8859,"output_tokens":2744,"usd":0.056447,"stage2_stop_reason":"end_turn"},"total_usd":0.08204,"stage1_batch_id":"msgbatch_01UT1AahFPCAyn2uVweS7A9z","stage2_batch_id":"msgbatch_01HuKWtKNT4Pqj1bc8eEP5RV","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"WIPI3 (WDR45B) scaffolds LKB1-AMPK-TSC signalling upstream of PtdIns3P production: WIPI3 associates with AMPK-activated TSC complex at lysosomes to regulate mTOR, and forms a complex with FIP200 at nascent autophagosomes to control their size.\",\n      \"method\": \"WIPI interactome analysis (co-immunoprecipitation/mass spectrometry), functional kinase screen, localization studies\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — interactome/Co-IP plus functional kinase screen in single lab, multiple orthogonal methods but no structural or in vitro reconstitution\",\n      \"pmids\": [\"28561066\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"WDR45B is specifically required for autophagosome maturation into autolysosomes in neural cells: WDR45B interacts with the tether protein EPG5 and targets it to late endosomes/lysosomes to promote autophagosome-lysosome fusion; disease-related mutations of WDR45B fail to rescue autophagy defects due to impaired EPG5 binding. In Wdr45/45b-depleted cells, formation of the SNARE-EPG5 fusion machinery is dampened.\",\n      \"method\": \"Co-immunoprecipitation (WDR45B–EPG5 interaction), Wdr45/Wdr45b double knockout mouse neural cells, autophagosome maturation assays, rescue with ATG2A overexpression, SNARE complex analysis, O-GlcNAcylation inhibition rescue\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, genetic KO with defined cellular phenotype, multiple orthogonal assays (lipid transfer rescue, SNARE complex, pharmacological rescue), replicated in companion paper PMID:34105435\",\n      \"pmids\": [\"33636118\", \"34105435\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"WDR45B is critical for neural autophagy and acts cooperatively with WDR45: Wdr45b knockout mice accumulate SQSTM1- and ubiquitin-positive aggregates in brain regions and exhibit swollen axons; Wdr45b/Wdr45 double KO mice die within one day of birth with more severe autophagy defects than either single KO, establishing cooperative function in autophagy.\",\n      \"method\": \"Wdr45b knockout mouse model (histology, immunohistochemistry for autophagy substrates, behavioral tests), double KO genetic epistasis\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined cellular and molecular phenotype, genetic epistasis via double KO, single lab\",\n      \"pmids\": [\"31238825\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Wipi3 (WDR45B) is essential for alternative (Atg5/Atg7-independent) autophagy: Wipi3 binds to Golgi membranes and is required for generation of isolation membranes in alternative autophagy. Neuron-specific Wipi3-deficient mice show cerebellar neuronal loss and iron/ceruloplasmin accumulation suppressed by Dram1 expression. Atg7/Wipi3 double-deficient mice are mostly embryonic lethal, indicating Wipi3 maintains neuronal cells via mechanisms distinct from canonical autophagy.\",\n      \"method\": \"Neuron-specific Wipi3-knockout mice, electron microscopy, subcellular fractionation/localization to Golgi membranes, genetic epistasis (Atg7/Wipi3 double KO), rescue by Dram1 expression\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean tissue-specific KO with defined phenotype, Golgi localization by direct experiment, genetic epistasis with double KO lethality, multiple orthogonal methods\",\n      \"pmids\": [\"33082312\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cryo-EM structure of the complete human TSC in complex with WIPI3 (WDR45B) at 2.8 Å resolution: WIPI3 serves as a lysosomal recruitment factor for TSC; a previously undetected amino-terminal TSC1 HEAT repeat dimer forms a PIP-binding pocket that specifically binds monophosphorylated PIPs, providing a structural model by which WIPI3 and PIP-signaling networks coordinate to recruit TSC to the lysosomal membrane to inhibit mTORC1.\",\n      \"method\": \"Cryo-electron microscopy (2.8-Å structure), biochemical reconstitution of TSC:WIPI3 complex\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution cryo-EM structure with biochemical reconstitution, single rigorous study with multiple orthogonal methods\",\n      \"pmids\": [\"39565846\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"WIPI3 (WDR45B) forms a tight complex with the ATG13:ATG101 HORMA domain heterodimer; bound to WIPI3 (or WIPI2), ATG13:ATG101 aligns with the membrane to insert its WF finger. WIPI3:ATG13 engagement is required for ATG16L1 phosphorylation by ULK1, ATG13 puncta formation, and bulk autophagic flux, establishing WIPI3 as a PI3P-dependent membrane anchor that recruits the ULK1 kinase domain to the membrane surface.\",\n      \"method\": \"Biochemical reconstitution (in vitro complex assembly), molecular dynamics simulations, cell-based phosphorylation assay (ATG16L1 phosphorylation), ATG13 puncta formation assay, autophagic flux measurement\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — biochemical reconstitution and cell-based assays in single preprint lab, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.11.07.687251\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"WDR45B (WIPI3) is a PI(3)P-binding β-propeller scaffold that functions at multiple steps of autophagy: it recruits TSC to lysosomes via a direct interaction (cryo-EM structure resolved) to inhibit mTORC1; it scaffolds LKB1-AMPK-TSC signalling upstream of autophagosome formation in complex with FIP200; it bridges the ATG13:ATG101 HORMA dimer to PI3P-enriched membranes to recruit and activate ULK1; it is essential for alternative (Atg5/Atg7-independent) autophagy through binding to Golgi membranes; and it promotes autophagosome-lysosome fusion by targeting the tether protein EPG5 to late endosomes/lysosomes, facilitating SNARE-dependent fusion—a function disrupted by disease-causing mutations.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"WDR45B (WIPI3) is a PI3P-binding β-propeller scaffold that operates at multiple steps of autophagy and lysosomal mTOR signalling, and is essential for neuronal homeostasis [#0, #2]. It acts as a lysosomal recruitment factor for the TSC complex: a cryo-EM structure of human TSC bound to WIPI3 resolves an amino-terminal TSC1 HEAT-repeat dimer forming a monophosphoinositide-binding pocket, showing how WIPI3 and PIP signalling cooperate to dock TSC at the lysosomal membrane to inhibit mTORC1 [#4], consistent with its earlier identification scaffolding LKB1-AMPK-TSC signalling at lysosomes and forming a complex with FIP200 at nascent autophagosomes [#0]. Beyond mTOR regulation, WDR45B is also required for autophagosome maturation: it binds the tether protein EPG5 and targets it to late endosomes/lysosomes to promote SNARE-dependent autophagosome-lysosome fusion, a function abolished by disease-causing mutations that impair EPG5 binding [#1]. It is additionally essential for alternative, Atg5/Atg7-independent autophagy through binding Golgi membranes to generate isolation membranes [#3]. In mice, Wdr45b loss causes accumulation of SQSTM1- and ubiquitin-positive aggregates, swollen axons, and cerebellar neuronal loss, and it functions cooperatively with the paralog WDR45, with double knockouts being neonatally lethal [#2, #3].\"\n,\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Established WIPI3 as a signalling scaffold upstream of PtdIns3P production rather than a purely downstream PI3P effector, linking it to AMPK-TSC-mTOR control and to FIP200 at nascent autophagosomes.\",\n      \"evidence\": \"WIPI interactome by Co-IP/mass spectrometry, functional kinase screen, and localization in cells\",\n      \"pmids\": [\"28561066\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of the WIPI3-TSC or WIPI3-FIP200 contacts\", \"Single lab, no in vitro reconstitution\", \"Direct vs indirect nature of the AMPK-TSC association not resolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrated that WDR45B is required for neural autophagy and acts cooperatively with its paralog WDR45, defining a non-redundant but overlapping role.\",\n      \"evidence\": \"Wdr45b knockout mice with autophagy-substrate histology and Wdr45b/Wdr45 double-KO genetic epistasis\",\n      \"pmids\": [\"31238825\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular step in autophagy disrupted not pinpointed\", \"Basis of cooperativity with WDR45 unresolved\", \"Single lab\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Showed WDR45B has an autophagy-step function distinct from canonical macroautophagy by being essential for Atg5/Atg7-independent alternative autophagy at the Golgi.\",\n      \"evidence\": \"Neuron-specific Wipi3-KO mice, EM, Golgi localization by fractionation, Atg7/Wipi3 double-KO lethality, and Dram1 rescue\",\n      \"pmids\": [\"33082312\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of isolation-membrane generation from Golgi not defined\", \"How iron/ceruloplasmin accumulation links to the autophagy defect unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified a discrete maturation-stage role: WDR45B targets the tether EPG5 to late endosomes/lysosomes to promote SNARE-dependent fusion, and connected disease mutations to loss of this interaction.\",\n      \"evidence\": \"Reciprocal Co-IP, Wdr45/Wdr45b double-KO neural cells, maturation assays, SNARE complex analysis, ATG2A and O-GlcNAcylation-inhibition rescues; replicated in companion paper\",\n      \"pmids\": [\"33636118\", \"34105435\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of WDR45B-EPG5 binding not resolved\", \"How a single scaffold coordinates both early signalling and late fusion roles unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Provided the structural mechanism for WIPI3 as a lysosomal recruitment factor for TSC, revealing a TSC1 HEAT-repeat PIP-binding pocket that, with WIPI3, docks TSC to inhibit mTORC1.\",\n      \"evidence\": \"2.8-Å cryo-EM structure of human TSC:WIPI3 with biochemical reconstitution\",\n      \"pmids\": [\"39565846\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo contribution of WIPI3-dependent TSC recruitment to mTORC1 output not quantified\", \"Interplay with the LKB1-AMPK arm not structurally addressed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined WIPI3 as a PI3P-dependent membrane anchor that bridges the ATG13:ATG101 HORMA dimer to membranes to recruit and activate ULK1 during autophagosome initiation.\",\n      \"evidence\": \"In vitro complex reconstitution, molecular dynamics, ATG16L1 phosphorylation assay, ATG13 puncta and autophagic flux measurements (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.11.07.687251\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Not yet peer-reviewed\", \"Functional redundancy with WIPI2 at this step not delineated\", \"In vivo requirement of the WIPI3:ATG13 contact untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single β-propeller scaffold is partitioned among its distinct lysosomal mTOR, initiation, alternative-autophagy, and fusion roles in a given cell remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No spatiotemporal map of which complex WDR45B occupies at each autophagy stage\", \"Determinants selecting EPG5 vs TSC vs ATG13 partners unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [4, 5]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 4, 5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [0, 1, 4]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [1, 2, 3, 5]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"complexes\": [\"TSC complex\", \"ATG13:ATG101 HORMA dimer\", \"EPG5-SNARE fusion machinery\"],\n    \"partners\": [\"EPG5\", \"FIP200\", \"ATG13\", \"ATG101\", \"TSC1\", \"WDR45\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}