{"gene":"WIPI1","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":2004,"finding":"WIPI1 (WIPI49/ATG18) is a member of the WIPI family of WD-repeat proteins that binds 3-phosphorylated phosphoinositides (PI3P and PI(3,5)P2) via its WD40 domain, and this PI-binding activity is required for its function in endosomal organization and mannose-6-phosphate receptor (MPR) trafficking. A double point mutant (R221,222A) unable to bind phosphoinositides does not disrupt MPR pathway function, while wild-type WIPI49 overexpression disrupts it. RNAi knockdown of WIPI49 disrupts normal endosomal organization and CI-MPR distribution.","method":"Phosphoinositide binding assays, immunofluorescence, live-cell imaging, RNAi knockdown, point mutagenesis","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal functional rescue with PI-binding mutant plus RNAi knockdown phenotype, two orthogonal methods in one study","pmids":["15020712"],"is_preprint":false},{"year":2004,"finding":"Human WIPI-1alpha (WIPI49/ATG18) colocalizes with the autophagosomal marker LC3 at punctate cytoplasmic structures in human melanoma cells and accumulates in large vesicular and cup-shaped structures upon amino-acid deprivation-induced autophagy. These structures are blocked by wortmannin, implicating PI3-kinase activity upstream. WIPI-1 also binds androgen and estrogen receptors in vitro via LXXLL motifs.","method":"Immunofluorescence colocalization, wortmannin inhibition, in vitro receptor binding assay","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — colocalization and inhibitor studies in single lab, two orthogonal methods","pmids":["15602573"],"is_preprint":false},{"year":2007,"finding":"WIPI-1 (ATG18) functions as a PI(3)P scaffold at the onset of autophagy in human cells. WIPI-1 puncta formation at LC3-positive autophagosomal membranes is induced by rapamycin, gleevec, thapsigargin, and amino acid deprivation, and is inhibited by wortmannin and LY294002 (PI3-kinase inhibitors). A PI(3)P-binding-deficient WIPI-1 mutant is unable to form puncta, establishing that PI(3)P binding is required for WIPI-1 membrane recruitment.","method":"Fluorescence microscopy, pharmacological inhibition, PI(3)P-binding mutant expression","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function mutant with defined phenotype plus pharmacological validation, single lab","pmids":["17618624"],"is_preprint":false},{"year":2011,"finding":"WIPI-1 and WIPI-2 are integral membrane proteins of autophagosomes and also present in plasma membrane, ER (WIPI-1), and Golgi-area membranes (WIPI-2), as established by freeze-fracture replica immunolabelling.","method":"Freeze-fracture replica immunolabelling electron microscopy","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct ultrastructural localization method, single lab","pmids":["21564513"],"is_preprint":false},{"year":2011,"finding":"WIPI1 inhibits TORC1 (mTORC1) signaling in melanocytes, leading to GSK3β inhibition, β-Catenin stabilization, increased MITF transcription and expression of melanogenic enzymes, and formation of mature (stage III-IV) melanosomes. WIPI1-depleted cells accumulate stage I melanosomes but lack stage III-IV melanosomes. This TORC1-dependent melanosome maturation role is distinct from starvation-induced autophagy.","method":"siRNA knockdown, rapamycin treatment, melanosome staging by electron microscopy, signaling pathway analysis","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined cellular phenotype plus pathway dissection, single lab","pmids":["21317285"],"is_preprint":false},{"year":2011,"finding":"Starvation- and pharmacological compound-induced WIPI-1 puncta formation (autophagosomal membrane recruitment) requires Ca2+-dependent signaling through CaMKI. siRNA-mediated knockdown of CaMKI (but not CaMKIV) reduces WIPI-1 puncta formation. AMPKα1/α2 deficiency reduces basal autophagy (WIPI-1 puncta) but starvation-induced autophagy remains CaMKK/CaMKI-dependent.","method":"siRNA knockdown, pharmacological inhibitors (STO-609, KN-93, BAPTA-AM), automated high-throughput WIPI-1 puncta analysis, LC3 lipidation assays","journal":"Molecular pharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA knockdown with quantitative phenotypic readout, multiple inhibitors, single lab","pmids":["21896713"],"is_preprint":false},{"year":2012,"finding":"Alanine scanning mutagenesis of conserved residues in the human WIPI-1 β-propeller identified the critical PtdIns(3)P/PtdIns(3,5)P2 binding site as S203, S205, G208, T209, R212, R226, R227, G228, S251, T255, H257. WIPI-1 mutants unable to bind these phosphoinositides fail to localize to autophagosomal membranes. Regulatory residues R110, R112, and H185 influence membrane recruitment independently of phosphoinositide binding. PIKfyve inhibition by YM201636 (elevating PtdIns(3)P) increases WIPI-1 autophagosomal localization.","method":"Alanine scanning mutagenesis, phosphoinositide binding assays, fluorescence microscopy, siRNA, pharmacological inhibition","journal":"Journal of molecular signaling","confidence":"High","confidence_rationale":"Tier 1 / Moderate — systematic mutagenesis with binding and localization readouts, multiple orthogonal methods, single lab","pmids":["23088497"],"is_preprint":false},{"year":2012,"finding":"WIPI1 and WIPI2 are required for rVP1-induced, BECN1-independent autophagosome formation in macrophages. Knockdown of WIPI1 (or WIPI2) attenuates rVP1-mediated increases in MAPK1/3 phosphorylation and MMP9 activity; combined depletion of both abolishes macrophage migration. This places WIPI1 upstream of MAPK1/3 and MMP9 in this autophagy-dependent migration pathway.","method":"siRNA knockdown, LC3 autophagosome formation assay, MAPK phosphorylation assay, MMP9 activity assay, migration assay","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA knockdown with multiple downstream readouts, single lab","pmids":["23051912"],"is_preprint":false},{"year":2012,"finding":"WIPI-1 positive vesicles entrap pathogenic Staphylococcus aureus for lysosomal degradation (xenophagy). Lysosomal inhibition by bafilomycin A1 or PIKfyve inhibition by YM201636 (blocking PtdIns(3,5)P2 generation) increases the number of WIPI-1 positive autophagosome-like vesicles entrapping staphylococci, demonstrating that the PI(3)P effector function of WIPI-1 is utilized during xenophagy.","method":"High-content fluorescence analysis, confocal microscopy, electron microscopy, pharmacological inhibition","journal":"International journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct imaging plus pharmacological perturbation, single lab, two orthogonal methods","pmids":["22829830"],"is_preprint":false},{"year":2021,"finding":"WIPI1 specifically acts in the formation and fission of tubulo-vesicular endosomal transport carriers, supporting PtdIns(3,5)P2-dependent transport of endosomal cargo toward the plasma membrane, Golgi, and lysosomes. Three molecular features differentiate WIPI1's endosomal and autophagic activities: phosphoinositide binding site II, requirement for PtdIns(3,5)P2, and bilayer deformation via a conserved amphipathic α-helix. Inactivation of these features preserves autophagy but causes strong enlargement of endosomes with micrometer-long membrane tubules. Thus, WIPI1 uses different modes of action for autophagy (PtdIns3P-dependent) versus endosomal protein exit (PtdIns(3,5)P2 and amphipathic helix-dependent).","method":"Knockdown/knockout, site-directed mutagenesis, live-cell imaging, electron microscopy, cargo trafficking assays","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 1 / Moderate — mutagenesis dissecting two functional activities with multiple cellular readouts, single lab but multiple orthogonal methods","pmids":["33685363"],"is_preprint":false},{"year":2019,"finding":"Wipi1 regulates mitochondrial oxidative signaling and non-canonical autophagy in cardiac myocytes. siRNA silencing of Wipi1 in neonatal rat ventricular myocytes limits non-canonical autophagy and blunts aldosterone-induced mitochondrial superoxide levels.","method":"siRNA silencing, mitochondrial superoxide measurement, autophagy flux assays","journal":"JCI insight","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — siRNA with defined functional phenotype, single lab, single study","pmids":["31021818"],"is_preprint":false},{"year":2023,"finding":"The ABL-ERK-MYC signalling axis controls WIPI1 gene expression: MYC binds to the WIPI1 promoter and represses WIPI1 transcription. When ABL-ERK-MYC signalling is counteracted, increased WIPI1 expression enhances autophagic membrane formation. WIPI1 assists WIPI2 in recruiting the ATG16L1 complex at the nascent autophagosome, promoting LC3/GABARAP lipidation and autophagosome maturation.","method":"ChIP (MYC-WIPI1 promoter binding), siRNA/kinase inhibitor perturbation, autophagy flux assays, live-cell imaging","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP plus functional perturbation with defined phenotype, single lab, two orthogonal methods","pmids":["37620393"],"is_preprint":false},{"year":2022,"finding":"WIPI1 rings (omegasome structures) serve as docking sites for lysosomes during DNAJB12- and GABARAP-dependent selective ER-associated autophagy (ERAA) of misfolded P23H-rhodopsin. ER tubules containing P23H-R thread through WIPI1 ring walls; GABARAP is required for transfer of P23H-R from phagophores to lysosomes but not for lysosome docking to WIPI1 rings.","method":"Fluorescence microscopy, live-cell imaging, loss-of-function (DNAJB12, GABARAP knockdown/KO), colocalization analysis","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic dissection of pathway steps with defined spatial-temporal phenotypes, single lab","pmids":["35704470"],"is_preprint":false},{"year":2025,"finding":"WIPI1 forms a CROP complex with Retromer (via Vps35 interaction), while WIPI2 forms a distinct CROP2 complex with Retriever (via CCDC93 and SNX17). CROP and CROP2 are mutually exclusive in their associations and pathway-selective for distinct endosomal cargos (EGFR/GLUT1 for CROP; β1-Integrin for CROP2). Both WIPI1 and WIPI2 require an FSSS motif for integration into their respective coat complexes and an amphipathic α-helix for membrane fission activity.","method":"Co-immunoprecipitation, cargo trafficking assays, mutagenesis (FSSS motif, amphipathic helix)","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP plus mutagenesis with functional cargo readouts, preprint single lab","pmids":["bio_10.1101_2025.10.08.681146"],"is_preprint":true},{"year":2025,"finding":"WIPI1 knockdown in cardiomyocytes leads to mitochondrial dysfunction (loss of membrane potential, reduced respiratory capacity), implicating WIPI1 as essential for proper mitophagy; overexpression via AAV9-cTNT-WIPI1 in a diabetic rat/mouse model preserves autophagosome formation/maturation markers (LC3b-II, SQSTM1) and mitophagy-related proteins (PINK, Parkin).","method":"siRNA knockdown, AAV9 overexpression, JC-1 mitochondrial membrane potential assay, high-resolution respirometry, echocardiography","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss- and gain-of-function with multiple mitochondrial readouts, single lab","pmids":["39961409"],"is_preprint":false},{"year":2021,"finding":"WIPI-1 directly interacts with TRIM21 in NPC cells, and this interaction enhances starvation-induced autophagy. WIPI-1 overexpression or knockdown respectively inhibits or facilitates NPC cell migration, colony formation, proliferation, and in vivo tumour growth/metastasis.","method":"Co-immunoprecipitation (WIPI-1/TRIM21 interaction), overexpression/knockdown, in vitro migration and proliferation assays, xenograft mouse models","journal":"Oral oncology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP plus functional assays, single lab, limited mechanistic follow-up","pmids":["34689010"],"is_preprint":false}],"current_model":"WIPI1 (ATG18/WIPI49) is a PI(3)P- and PI(3,5)P2-binding seven-bladed β-propeller protein that acts as a PI3P effector at nascent autophagosomal membranes downstream of mTORC1 inhibition and PI3K class III activity, where it assists WIPI2 in recruiting the ATG16L1 complex to promote LC3/GABARAP lipidation and autophagosome maturation; it also uses its PI(3,5)P2-binding site II and an amphipathic α-helix to drive fission of endosomal tubulo-vesicular carriers as part of a Retromer-WIPI1 (CROP) complex, and it additionally regulates TORC1 signalling to control melanosome maturation, mitophagy in cardiomyocytes, and gene expression through an ABL-ERK-MYC axis that represses WIPI1 transcription via MYC binding to the WIPI1 promoter."},"narrative":{"mechanistic_narrative":"WIPI1 is a 3-phosphoinositide-binding WD40 β-propeller protein that functions as a phosphoinositide effector at two membrane systems: nascent autophagosomes and the endosomal network [PMID:15020712, PMID:17618624, PMID:33685363]. At the onset of autophagy, WIPI1 binds PI(3)P generated downstream of mTORC1 inhibition and class III PI3K activity, forming puncta on LC3-positive autophagosomal membranes; this recruitment is blocked by PI3-kinase inhibitors (wortmannin, LY294002) and abolished by mutation of its phosphoinositide-binding site, a surface mapped to a defined cluster of β-propeller residues [PMID:17618624, PMID:23088497]. There it assists WIPI2 in recruiting the ATG16L1 complex to drive LC3/GABARAP lipidation and autophagosome maturation [PMID:37620393]. WIPI1 membrane recruitment during starvation- and compound-induced autophagy is gated by Ca2+/CaMKK–CaMKI signaling and modulated by AMPK [PMID:21896713]. WIPI1-positive structures act as omegasome rings serving as lysosome docking sites in selective ER-associated autophagy and entrap intracellular bacteria during xenophagy [PMID:35704470, PMID:22829830]. Separately, through phosphoinositide-binding site II, a requirement for PI(3,5)P2, and a conserved amphipathic α-helix that deforms membranes, WIPI1 drives fission of tubulo-vesicular endosomal transport carriers and, via an FSSS motif and Vps35 interaction, integrates into a Retromer-associated CROP complex that sorts cargo such as EGFR and GLUT1; this endosomal activity is genetically separable from its autophagic role [PMID:33685363, PMID:bio_10.1101_2025.10.08.681146]. WIPI1 additionally restrains TORC1 signaling to permit melanosome maturation and supports mitochondrial quality control and mitophagy in cardiomyocytes [PMID:21317285, PMID:39961409]. WIPI1 transcription is repressed by MYC binding at the WIPI1 promoter downstream of an ABL-ERK-MYC axis [PMID:37620393].","teleology":[{"year":2004,"claim":"Established WIPI1 as a 3-phosphoinositide-binding WD40 protein whose lipid-binding activity is functionally required, first linking it to membrane trafficking rather than to its autophagic role.","evidence":"Phosphoinositide binding assays, RNAi, and PI-binding point mutant (R221,222A) rescue in endosomal/MPR trafficking","pmids":["15020712"],"confidence":"High","gaps":["Did not connect the protein to autophagy","Structural basis of lipid recognition not resolved","Direct membrane partners at endosomes not identified"]},{"year":2004,"claim":"Showed WIPI1 redistributes to LC3-positive and cup-shaped structures upon amino-acid starvation in a PI3-kinase-dependent manner, implicating it in autophagosome biogenesis.","evidence":"Immunofluorescence colocalization with LC3 and wortmannin inhibition in melanoma cells","pmids":["15602573"],"confidence":"Medium","gaps":["Whether colocalization reflects functional requirement not tested","In vitro nuclear receptor binding not validated in cells"]},{"year":2007,"claim":"Demonstrated PI(3)P binding is required for WIPI1 recruitment to autophagosomal membranes, defining it as a PI(3)P scaffold at autophagy onset responsive to mTORC1 inhibition and diverse autophagy inducers.","evidence":"Fluorescence microscopy of puncta under multiple inducers/inhibitors plus PI(3)P-binding-deficient mutant","pmids":["17618624"],"confidence":"Medium","gaps":["Downstream effectors recruited by WIPI1 not identified","Order relative to other ATG proteins unresolved"]},{"year":2011,"claim":"Mapped the upstream signaling and identified non-autophagic roles, showing WIPI1 recruitment depends on Ca2+/CaMKK-CaMKI and that WIPI1 restrains TORC1 to enable melanosome maturation.","evidence":"siRNA knockdown, pharmacological inhibitors, melanosome staging by EM, and signaling pathway dissection","pmids":["21896713","21317285"],"confidence":"Medium","gaps":["Direct molecular link between CaMKI and WIPI1 recruitment unknown","How WIPI1 inhibits TORC1 mechanistically unresolved"]},{"year":2011,"claim":"Ultrastructural localization placed WIPI1 as an integral membrane component of autophagosomes and additional compartments (plasma membrane, ER).","evidence":"Freeze-fracture replica immunolabelling electron microscopy","pmids":["21564513"],"confidence":"Medium","gaps":["Functional significance of ER/plasma membrane pools not defined"]},{"year":2012,"claim":"Systematic mutagenesis defined the precise β-propeller phosphoinositide-binding surface and distinguished it from separate regulatory residues governing membrane recruitment.","evidence":"Alanine scanning, phosphoinositide binding assays, fluorescence microscopy, PIKfyve inhibition","pmids":["23088497"],"confidence":"High","gaps":["No crystal structure of human WIPI1-lipid complex","Roles of two distinct binding sites not yet separated functionally"]},{"year":2012,"claim":"Extended WIPI1 PI(3)P effector function to selective autophagy of pathogens, showing WIPI1-positive vesicles entrap intracellular bacteria for lysosomal degradation.","evidence":"High-content imaging, EM, and PIKfyve/lysosomal inhibition during S. aureus xenophagy","pmids":["22829830"],"confidence":"Medium","gaps":["Cargo recognition mechanism not defined","WIPI1-specific contribution versus other WIPIs unclear"]},{"year":2012,"claim":"Showed WIPI1 acts with WIPI2 in BECN1-independent autophagy that drives macrophage migration via MAPK1/3 and MMP9.","evidence":"siRNA knockdown with MAPK phosphorylation, MMP9 activity, and migration assays","pmids":["23051912"],"confidence":"Medium","gaps":["Whether WIPI1 acts on MAPK directly or via autophagy is unresolved","Redundancy with WIPI2 not dissected"]},{"year":2019,"claim":"Linked WIPI1 to non-canonical autophagy and mitochondrial oxidative signaling in cardiomyocytes.","evidence":"siRNA silencing with mitochondrial superoxide and autophagy flux measurements in neonatal rat ventricular myocytes","pmids":["31021818"],"confidence":"Medium","gaps":["Molecular pathway connecting WIPI1 to mitochondrial ROS unknown"]},{"year":2021,"claim":"Mechanistically separated WIPI1's autophagic and endosomal functions, showing endosomal carrier fission requires PI(3,5)P2, binding site II, and an amphipathic α-helix that deforms membranes, while autophagy uses PI(3)P.","evidence":"Knockdown/knockout, site-directed mutagenesis, live imaging, EM, and cargo trafficking assays","pmids":["33685363"],"confidence":"High","gaps":["Structural mechanism of helix-driven fission not resolved","Endosomal partner proteins not yet identified in this study"]},{"year":2021,"claim":"Reported a WIPI1-TRIM21 interaction enhancing starvation autophagy with tumor-suppressive consequences in nasopharyngeal carcinoma.","evidence":"Co-immunoprecipitation, overexpression/knockdown, and xenograft assays","pmids":["34689010"],"confidence":"Low","gaps":["Single Co-IP without reciprocal/structural validation","Direct binding versus complex co-precipitation unresolved","Mechanistic link to autophagy enhancement not defined"]},{"year":2022,"claim":"Defined WIPI1 rings as omegasome docking sites for lysosomes during selective ER-associated autophagy of misfolded rhodopsin.","evidence":"Live-cell imaging and loss-of-function of DNAJB12/GABARAP with colocalization analysis","pmids":["35704470"],"confidence":"Medium","gaps":["Molecular basis of lysosome docking at WIPI1 rings unknown","Whether docking requires WIPI1 lipid binding not tested"]},{"year":2023,"claim":"Placed WIPI1 in an ABL-ERK-MYC transcriptional circuit where MYC directly represses WIPI1, and showed WIPI1 assists WIPI2 in recruiting ATG16L1 for LC3/GABARAP lipidation.","evidence":"ChIP of MYC at the WIPI1 promoter, kinase/siRNA perturbation, autophagy flux, and live imaging","pmids":["37620393"],"confidence":"Medium","gaps":["Direct biochemical contact of WIPI1 with ATG16L1 not shown","Physiological contexts of MYC repression not mapped"]},{"year":2025,"claim":"Identified WIPI1 as a stable subunit of a Retromer-associated CROP coat complex distinct from a WIPI2-Retriever CROP2 complex, with each selective for different endosomal cargos.","evidence":"Reciprocal co-IP (Vps35), cargo trafficking assays, and FSSS-motif/amphipathic-helix mutagenesis (preprint)","pmids":["bio_10.1101_2025.10.08.681146"],"confidence":"Medium","gaps":["Preprint not peer-reviewed","Structure of the CROP coat unresolved","How cargo selectivity is encoded not defined"]},{"year":2025,"claim":"Established WIPI1 as essential for cardiomyocyte mitophagy and mitochondrial integrity, with overexpression preserving mitophagy markers in diabetic models.","evidence":"siRNA knockdown, AAV9 overexpression, JC-1 potential, respirometry, and echocardiography","pmids":["39961409"],"confidence":"Medium","gaps":["Whether WIPI1 acts directly in PINK/Parkin mitophagy or upstream is unclear","Cargo-receptor interactions in mitophagy not defined"]},{"year":null,"claim":"How WIPI1 mechanistically partitions between its PI(3)P-dependent autophagic scaffold role and its PI(3,5)P2/amphipathic-helix-dependent endosomal fission role within a cell, and the structural basis of its coat and ATG16L1 engagements, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No high-resolution structure of WIPI1 bound to lipid or coat partners","Regulatory switch directing WIPI1 to autophagy versus endosomes unknown","Quantitative contribution of WIPI1 versus WIPI2 across pathways not delineated"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[0,2,6,9]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[11,13]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[9,13]}],"localization":[{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[1,8,9]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0,9,13]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[3,12]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[3]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[10,14]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[2,6,11,12]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,9,13]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[4,5,11]}],"complexes":["CROP (WIPI1-Retromer) complex"],"partners":["WIPI2","ATG16L1","VPS35","TRIM21","MYC"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5MNZ9","full_name":"WD repeat domain phosphoinositide-interacting protein 1","aliases":["Atg18 protein homolog","WD40 repeat protein interacting with phosphoinositides of 49 kDa","WIPI 49 kDa"],"length_aa":446,"mass_kda":48.7,"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:15602573, PubMed:20114074, PubMed:20484055, PubMed:20639694, PubMed:23088497, PubMed:28561066, PubMed:31271352). Plays an important role in starvation- and calcium-mediated autophagy, as well as in mitophagy (PubMed:28561066). Functions downstream of the ULK1 and PI3-kinases that produce phosphatidylinositol 3-phosphate (PtdIns3P) on membranes of the endoplasmic reticulum once activated (PubMed:28561066). Binds phosphatidylinositol 3-phosphate (PtdIns3P), and maybe other phosphoinositides including PtdIns3,5P2 and PtdIns5P, and is recruited to phagophore assembly sites at the endoplasmic reticulum membranes (PubMed:28561066, PubMed:31271352, PubMed:33499712). There, it assists WIPI2 in the recruitment of ATG12-ATG5-ATG16L1, a complex that directly controls the elongation of the nascent autophagosomal membrane (PubMed:28561066). Together with WDR45/WIPI4, promotes ATG2 (ATG2A or ATG2B)-mediated lipid transfer by enhancing ATG2-association with phosphatidylinositol 3-monophosphate (PI3P)-containing membranes (PubMed:31271352). Involved in xenophagy of Staphylococcus aureus (PubMed:22829830). Invading S.aureus cells become entrapped in autophagosome-like WIPI1 positive vesicles targeted for lysosomal degradation (PubMed:22829830). Also plays a distinct role in controlling the transcription of melanogenic enzymes and melanosome maturation, a process that is distinct from starvation-induced autophagy (PubMed:21317285). May also regulate the trafficking of proteins involved in the mannose-6-phosphate receptor (MPR) recycling pathway (PubMed:15020712)","subcellular_location":"Golgi apparatus, trans-Golgi network; Endosome; Cytoplasmic vesicle, clathrin-coated vesicle; Preautophagosomal structure membrane; Cytoplasm, cytoskeleton","url":"https://www.uniprot.org/uniprotkb/Q5MNZ9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/WIPI1","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/WIPI1","total_profiled":1310},"omim":[{"mim_id":"609226","title":"WD REPEAT-CONTAINING PROTEIN 45B; WDR45B","url":"https://www.omim.org/entry/609226"},{"mim_id":"609225","title":"WD40 REPEAT PROTEIN INTERACTING WITH PHOSPHOINOSITIDES 2; WIPI2","url":"https://www.omim.org/entry/609225"},{"mim_id":"609224","title":"WD40 REPEAT PROTEIN INTERACTING WITH PHOSPHOINOSITIDES 1; WIPI1","url":"https://www.omim.org/entry/609224"},{"mim_id":"608309","title":"PTEN-INDUCED KINASE 1; PINK1","url":"https://www.omim.org/entry/608309"},{"mim_id":"604587","title":"CALCIUM BINDING AND COILED-COIL DOMAIN PROTEIN 2; CALCOCO2","url":"https://www.omim.org/entry/604587"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Golgi apparatus","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":119.2}],"url":"https://www.proteinatlas.org/search/WIPI1"},"hgnc":{"alias_symbol":["FLJ10055","WIPI49","ATG18","ATG18A"],"prev_symbol":[]},"alphafold":{"accession":"Q5MNZ9","domains":[{"cath_id":"2.40.10,2.40.10","chopping":"236-264_299-361","consensus_level":"medium","plddt":91.8451,"start":236,"end":361}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5MNZ9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5MNZ9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5MNZ9-F1-predicted_aligned_error_v6.png","plddt_mean":77.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=WIPI1","jax_strain_url":"https://www.jax.org/strain/search?query=WIPI1"},"sequence":{"accession":"Q5MNZ9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5MNZ9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5MNZ9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5MNZ9"}},"corpus_meta":[{"pmid":"20505359","id":"PMC_20505359","title":"Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation.","date":"2010","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/20505359","citation_count":563,"is_preprint":false},{"pmid":"15602573","id":"PMC_15602573","title":"WIPI-1alpha (WIPI49), a member of the novel 7-bladed WIPI protein family, is aberrantly expressed in human cancer and is linked to starvation-induced autophagy.","date":"2004","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/15602573","citation_count":287,"is_preprint":false},{"pmid":"30254161","id":"PMC_30254161","title":"The Atg2-Atg18 complex tethers pre-autophagosomal membranes to the endoplasmic reticulum for autophagosome formation.","date":"2018","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/30254161","citation_count":240,"is_preprint":false},{"pmid":"17618624","id":"PMC_17618624","title":"Human WIPI-1 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A double point mutant (R221,222A) unable to bind phosphoinositides does not disrupt MPR pathway function, while wild-type WIPI49 overexpression disrupts it. RNAi knockdown of WIPI49 disrupts normal endosomal organization and CI-MPR distribution.\",\n      \"method\": \"Phosphoinositide binding assays, immunofluorescence, live-cell imaging, RNAi knockdown, point mutagenesis\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal functional rescue with PI-binding mutant plus RNAi knockdown phenotype, two orthogonal methods in one study\",\n      \"pmids\": [\"15020712\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Human WIPI-1alpha (WIPI49/ATG18) colocalizes with the autophagosomal marker LC3 at punctate cytoplasmic structures in human melanoma cells and accumulates in large vesicular and cup-shaped structures upon amino-acid deprivation-induced autophagy. These structures are blocked by wortmannin, implicating PI3-kinase activity upstream. WIPI-1 also binds androgen and estrogen receptors in vitro via LXXLL motifs.\",\n      \"method\": \"Immunofluorescence colocalization, wortmannin inhibition, in vitro receptor binding assay\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — colocalization and inhibitor studies in single lab, two orthogonal methods\",\n      \"pmids\": [\"15602573\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"WIPI-1 (ATG18) functions as a PI(3)P scaffold at the onset of autophagy in human cells. WIPI-1 puncta formation at LC3-positive autophagosomal membranes is induced by rapamycin, gleevec, thapsigargin, and amino acid deprivation, and is inhibited by wortmannin and LY294002 (PI3-kinase inhibitors). A PI(3)P-binding-deficient WIPI-1 mutant is unable to form puncta, establishing that PI(3)P binding is required for WIPI-1 membrane recruitment.\",\n      \"method\": \"Fluorescence microscopy, pharmacological inhibition, PI(3)P-binding mutant expression\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function mutant with defined phenotype plus pharmacological validation, single lab\",\n      \"pmids\": [\"17618624\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"WIPI-1 and WIPI-2 are integral membrane proteins of autophagosomes and also present in plasma membrane, ER (WIPI-1), and Golgi-area membranes (WIPI-2), as established by freeze-fracture replica immunolabelling.\",\n      \"method\": \"Freeze-fracture replica immunolabelling electron microscopy\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct ultrastructural localization method, single lab\",\n      \"pmids\": [\"21564513\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"WIPI1 inhibits TORC1 (mTORC1) signaling in melanocytes, leading to GSK3β inhibition, β-Catenin stabilization, increased MITF transcription and expression of melanogenic enzymes, and formation of mature (stage III-IV) melanosomes. WIPI1-depleted cells accumulate stage I melanosomes but lack stage III-IV melanosomes. This TORC1-dependent melanosome maturation role is distinct from starvation-induced autophagy.\",\n      \"method\": \"siRNA knockdown, rapamycin treatment, melanosome staging by electron microscopy, signaling pathway analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined cellular phenotype plus pathway dissection, single lab\",\n      \"pmids\": [\"21317285\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Starvation- and pharmacological compound-induced WIPI-1 puncta formation (autophagosomal membrane recruitment) requires Ca2+-dependent signaling through CaMKI. siRNA-mediated knockdown of CaMKI (but not CaMKIV) reduces WIPI-1 puncta formation. AMPKα1/α2 deficiency reduces basal autophagy (WIPI-1 puncta) but starvation-induced autophagy remains CaMKK/CaMKI-dependent.\",\n      \"method\": \"siRNA knockdown, pharmacological inhibitors (STO-609, KN-93, BAPTA-AM), automated high-throughput WIPI-1 puncta analysis, LC3 lipidation assays\",\n      \"journal\": \"Molecular pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA knockdown with quantitative phenotypic readout, multiple inhibitors, single lab\",\n      \"pmids\": [\"21896713\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Alanine scanning mutagenesis of conserved residues in the human WIPI-1 β-propeller identified the critical PtdIns(3)P/PtdIns(3,5)P2 binding site as S203, S205, G208, T209, R212, R226, R227, G228, S251, T255, H257. WIPI-1 mutants unable to bind these phosphoinositides fail to localize to autophagosomal membranes. Regulatory residues R110, R112, and H185 influence membrane recruitment independently of phosphoinositide binding. PIKfyve inhibition by YM201636 (elevating PtdIns(3)P) increases WIPI-1 autophagosomal localization.\",\n      \"method\": \"Alanine scanning mutagenesis, phosphoinositide binding assays, fluorescence microscopy, siRNA, pharmacological inhibition\",\n      \"journal\": \"Journal of molecular signaling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — systematic mutagenesis with binding and localization readouts, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"23088497\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"WIPI1 and WIPI2 are required for rVP1-induced, BECN1-independent autophagosome formation in macrophages. Knockdown of WIPI1 (or WIPI2) attenuates rVP1-mediated increases in MAPK1/3 phosphorylation and MMP9 activity; combined depletion of both abolishes macrophage migration. This places WIPI1 upstream of MAPK1/3 and MMP9 in this autophagy-dependent migration pathway.\",\n      \"method\": \"siRNA knockdown, LC3 autophagosome formation assay, MAPK phosphorylation assay, MMP9 activity assay, migration assay\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA knockdown with multiple downstream readouts, single lab\",\n      \"pmids\": [\"23051912\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"WIPI-1 positive vesicles entrap pathogenic Staphylococcus aureus for lysosomal degradation (xenophagy). Lysosomal inhibition by bafilomycin A1 or PIKfyve inhibition by YM201636 (blocking PtdIns(3,5)P2 generation) increases the number of WIPI-1 positive autophagosome-like vesicles entrapping staphylococci, demonstrating that the PI(3)P effector function of WIPI-1 is utilized during xenophagy.\",\n      \"method\": \"High-content fluorescence analysis, confocal microscopy, electron microscopy, pharmacological inhibition\",\n      \"journal\": \"International journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct imaging plus pharmacological perturbation, single lab, two orthogonal methods\",\n      \"pmids\": [\"22829830\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"WIPI1 specifically acts in the formation and fission of tubulo-vesicular endosomal transport carriers, supporting PtdIns(3,5)P2-dependent transport of endosomal cargo toward the plasma membrane, Golgi, and lysosomes. Three molecular features differentiate WIPI1's endosomal and autophagic activities: phosphoinositide binding site II, requirement for PtdIns(3,5)P2, and bilayer deformation via a conserved amphipathic α-helix. Inactivation of these features preserves autophagy but causes strong enlargement of endosomes with micrometer-long membrane tubules. Thus, WIPI1 uses different modes of action for autophagy (PtdIns3P-dependent) versus endosomal protein exit (PtdIns(3,5)P2 and amphipathic helix-dependent).\",\n      \"method\": \"Knockdown/knockout, site-directed mutagenesis, live-cell imaging, electron microscopy, cargo trafficking assays\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — mutagenesis dissecting two functional activities with multiple cellular readouts, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"33685363\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Wipi1 regulates mitochondrial oxidative signaling and non-canonical autophagy in cardiac myocytes. siRNA silencing of Wipi1 in neonatal rat ventricular myocytes limits non-canonical autophagy and blunts aldosterone-induced mitochondrial superoxide levels.\",\n      \"method\": \"siRNA silencing, mitochondrial superoxide measurement, autophagy flux assays\",\n      \"journal\": \"JCI insight\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — siRNA with defined functional phenotype, single lab, single study\",\n      \"pmids\": [\"31021818\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The ABL-ERK-MYC signalling axis controls WIPI1 gene expression: MYC binds to the WIPI1 promoter and represses WIPI1 transcription. When ABL-ERK-MYC signalling is counteracted, increased WIPI1 expression enhances autophagic membrane formation. WIPI1 assists WIPI2 in recruiting the ATG16L1 complex at the nascent autophagosome, promoting LC3/GABARAP lipidation and autophagosome maturation.\",\n      \"method\": \"ChIP (MYC-WIPI1 promoter binding), siRNA/kinase inhibitor perturbation, autophagy flux assays, live-cell imaging\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP plus functional perturbation with defined phenotype, single lab, two orthogonal methods\",\n      \"pmids\": [\"37620393\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"WIPI1 rings (omegasome structures) serve as docking sites for lysosomes during DNAJB12- and GABARAP-dependent selective ER-associated autophagy (ERAA) of misfolded P23H-rhodopsin. ER tubules containing P23H-R thread through WIPI1 ring walls; GABARAP is required for transfer of P23H-R from phagophores to lysosomes but not for lysosome docking to WIPI1 rings.\",\n      \"method\": \"Fluorescence microscopy, live-cell imaging, loss-of-function (DNAJB12, GABARAP knockdown/KO), colocalization analysis\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic dissection of pathway steps with defined spatial-temporal phenotypes, single lab\",\n      \"pmids\": [\"35704470\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"WIPI1 forms a CROP complex with Retromer (via Vps35 interaction), while WIPI2 forms a distinct CROP2 complex with Retriever (via CCDC93 and SNX17). CROP and CROP2 are mutually exclusive in their associations and pathway-selective for distinct endosomal cargos (EGFR/GLUT1 for CROP; β1-Integrin for CROP2). Both WIPI1 and WIPI2 require an FSSS motif for integration into their respective coat complexes and an amphipathic α-helix for membrane fission activity.\",\n      \"method\": \"Co-immunoprecipitation, cargo trafficking assays, mutagenesis (FSSS motif, amphipathic helix)\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP plus mutagenesis with functional cargo readouts, preprint single lab\",\n      \"pmids\": [\"bio_10.1101_2025.10.08.681146\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"WIPI1 knockdown in cardiomyocytes leads to mitochondrial dysfunction (loss of membrane potential, reduced respiratory capacity), implicating WIPI1 as essential for proper mitophagy; overexpression via AAV9-cTNT-WIPI1 in a diabetic rat/mouse model preserves autophagosome formation/maturation markers (LC3b-II, SQSTM1) and mitophagy-related proteins (PINK, Parkin).\",\n      \"method\": \"siRNA knockdown, AAV9 overexpression, JC-1 mitochondrial membrane potential assay, high-resolution respirometry, echocardiography\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss- and gain-of-function with multiple mitochondrial readouts, single lab\",\n      \"pmids\": [\"39961409\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"WIPI-1 directly interacts with TRIM21 in NPC cells, and this interaction enhances starvation-induced autophagy. WIPI-1 overexpression or knockdown respectively inhibits or facilitates NPC cell migration, colony formation, proliferation, and in vivo tumour growth/metastasis.\",\n      \"method\": \"Co-immunoprecipitation (WIPI-1/TRIM21 interaction), overexpression/knockdown, in vitro migration and proliferation assays, xenograft mouse models\",\n      \"journal\": \"Oral oncology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP plus functional assays, single lab, limited mechanistic follow-up\",\n      \"pmids\": [\"34689010\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"WIPI1 (ATG18/WIPI49) is a PI(3)P- and PI(3,5)P2-binding seven-bladed β-propeller protein that acts as a PI3P effector at nascent autophagosomal membranes downstream of mTORC1 inhibition and PI3K class III activity, where it assists WIPI2 in recruiting the ATG16L1 complex to promote LC3/GABARAP lipidation and autophagosome maturation; it also uses its PI(3,5)P2-binding site II and an amphipathic α-helix to drive fission of endosomal tubulo-vesicular carriers as part of a Retromer-WIPI1 (CROP) complex, and it additionally regulates TORC1 signalling to control melanosome maturation, mitophagy in cardiomyocytes, and gene expression through an ABL-ERK-MYC axis that represses WIPI1 transcription via MYC binding to the WIPI1 promoter.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"WIPI1 is a 3-phosphoinositide-binding WD40 β-propeller protein that functions as a phosphoinositide effector at two membrane systems: nascent autophagosomes and the endosomal network [#0, #2, #9]. At the onset of autophagy, WIPI1 binds PI(3)P generated downstream of mTORC1 inhibition and class III PI3K activity, forming puncta on LC3-positive autophagosomal membranes; this recruitment is blocked by PI3-kinase inhibitors (wortmannin, LY294002) and abolished by mutation of its phosphoinositide-binding site, a surface mapped to a defined cluster of β-propeller residues [#2, #6]. There it assists WIPI2 in recruiting the ATG16L1 complex to drive LC3/GABARAP lipidation and autophagosome maturation [#11]. WIPI1 membrane recruitment during starvation- and compound-induced autophagy is gated by Ca2+/CaMKK–CaMKI signaling and modulated by AMPK [#5]. WIPI1-positive structures act as omegasome rings serving as lysosome docking sites in selective ER-associated autophagy and entrap intracellular bacteria during xenophagy [#12, #8]. Separately, through phosphoinositide-binding site II, a requirement for PI(3,5)P2, and a conserved amphipathic α-helix that deforms membranes, WIPI1 drives fission of tubulo-vesicular endosomal transport carriers and, via an FSSS motif and Vps35 interaction, integrates into a Retromer-associated CROP complex that sorts cargo such as EGFR and GLUT1; this endosomal activity is genetically separable from its autophagic role [#9, #13]. WIPI1 additionally restrains TORC1 signaling to permit melanosome maturation and supports mitochondrial quality control and mitophagy in cardiomyocytes [#4, #14]. WIPI1 transcription is repressed by MYC binding at the WIPI1 promoter downstream of an ABL-ERK-MYC axis [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Established WIPI1 as a 3-phosphoinositide-binding WD40 protein whose lipid-binding activity is functionally required, first linking it to membrane trafficking rather than to its autophagic role.\",\n      \"evidence\": \"Phosphoinositide binding assays, RNAi, and PI-binding point mutant (R221,222A) rescue in endosomal/MPR trafficking\",\n      \"pmids\": [\"15020712\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not connect the protein to autophagy\", \"Structural basis of lipid recognition not resolved\", \"Direct membrane partners at endosomes not identified\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Showed WIPI1 redistributes to LC3-positive and cup-shaped structures upon amino-acid starvation in a PI3-kinase-dependent manner, implicating it in autophagosome biogenesis.\",\n      \"evidence\": \"Immunofluorescence colocalization with LC3 and wortmannin inhibition in melanoma cells\",\n      \"pmids\": [\"15602573\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether colocalization reflects functional requirement not tested\", \"In vitro nuclear receptor binding not validated in cells\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Demonstrated PI(3)P binding is required for WIPI1 recruitment to autophagosomal membranes, defining it as a PI(3)P scaffold at autophagy onset responsive to mTORC1 inhibition and diverse autophagy inducers.\",\n      \"evidence\": \"Fluorescence microscopy of puncta under multiple inducers/inhibitors plus PI(3)P-binding-deficient mutant\",\n      \"pmids\": [\"17618624\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream effectors recruited by WIPI1 not identified\", \"Order relative to other ATG proteins unresolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Mapped the upstream signaling and identified non-autophagic roles, showing WIPI1 recruitment depends on Ca2+/CaMKK-CaMKI and that WIPI1 restrains TORC1 to enable melanosome maturation.\",\n      \"evidence\": \"siRNA knockdown, pharmacological inhibitors, melanosome staging by EM, and signaling pathway dissection\",\n      \"pmids\": [\"21896713\", \"21317285\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular link between CaMKI and WIPI1 recruitment unknown\", \"How WIPI1 inhibits TORC1 mechanistically unresolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Ultrastructural localization placed WIPI1 as an integral membrane component of autophagosomes and additional compartments (plasma membrane, ER).\",\n      \"evidence\": \"Freeze-fracture replica immunolabelling electron microscopy\",\n      \"pmids\": [\"21564513\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional significance of ER/plasma membrane pools not defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Systematic mutagenesis defined the precise β-propeller phosphoinositide-binding surface and distinguished it from separate regulatory residues governing membrane recruitment.\",\n      \"evidence\": \"Alanine scanning, phosphoinositide binding assays, fluorescence microscopy, PIKfyve inhibition\",\n      \"pmids\": [\"23088497\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No crystal structure of human WIPI1-lipid complex\", \"Roles of two distinct binding sites not yet separated functionally\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Extended WIPI1 PI(3)P effector function to selective autophagy of pathogens, showing WIPI1-positive vesicles entrap intracellular bacteria for lysosomal degradation.\",\n      \"evidence\": \"High-content imaging, EM, and PIKfyve/lysosomal inhibition during S. aureus xenophagy\",\n      \"pmids\": [\"22829830\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cargo recognition mechanism not defined\", \"WIPI1-specific contribution versus other WIPIs unclear\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Showed WIPI1 acts with WIPI2 in BECN1-independent autophagy that drives macrophage migration via MAPK1/3 and MMP9.\",\n      \"evidence\": \"siRNA knockdown with MAPK phosphorylation, MMP9 activity, and migration assays\",\n      \"pmids\": [\"23051912\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether WIPI1 acts on MAPK directly or via autophagy is unresolved\", \"Redundancy with WIPI2 not dissected\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Linked WIPI1 to non-canonical autophagy and mitochondrial oxidative signaling in cardiomyocytes.\",\n      \"evidence\": \"siRNA silencing with mitochondrial superoxide and autophagy flux measurements in neonatal rat ventricular myocytes\",\n      \"pmids\": [\"31021818\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular pathway connecting WIPI1 to mitochondrial ROS unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Mechanistically separated WIPI1's autophagic and endosomal functions, showing endosomal carrier fission requires PI(3,5)P2, binding site II, and an amphipathic α-helix that deforms membranes, while autophagy uses PI(3)P.\",\n      \"evidence\": \"Knockdown/knockout, site-directed mutagenesis, live imaging, EM, and cargo trafficking assays\",\n      \"pmids\": [\"33685363\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural mechanism of helix-driven fission not resolved\", \"Endosomal partner proteins not yet identified in this study\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Reported a WIPI1-TRIM21 interaction enhancing starvation autophagy with tumor-suppressive consequences in nasopharyngeal carcinoma.\",\n      \"evidence\": \"Co-immunoprecipitation, overexpression/knockdown, and xenograft assays\",\n      \"pmids\": [\"34689010\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single Co-IP without reciprocal/structural validation\", \"Direct binding versus complex co-precipitation unresolved\", \"Mechanistic link to autophagy enhancement not defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined WIPI1 rings as omegasome docking sites for lysosomes during selective ER-associated autophagy of misfolded rhodopsin.\",\n      \"evidence\": \"Live-cell imaging and loss-of-function of DNAJB12/GABARAP with colocalization analysis\",\n      \"pmids\": [\"35704470\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis of lysosome docking at WIPI1 rings unknown\", \"Whether docking requires WIPI1 lipid binding not tested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Placed WIPI1 in an ABL-ERK-MYC transcriptional circuit where MYC directly represses WIPI1, and showed WIPI1 assists WIPI2 in recruiting ATG16L1 for LC3/GABARAP lipidation.\",\n      \"evidence\": \"ChIP of MYC at the WIPI1 promoter, kinase/siRNA perturbation, autophagy flux, and live imaging\",\n      \"pmids\": [\"37620393\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical contact of WIPI1 with ATG16L1 not shown\", \"Physiological contexts of MYC repression not mapped\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified WIPI1 as a stable subunit of a Retromer-associated CROP coat complex distinct from a WIPI2-Retriever CROP2 complex, with each selective for different endosomal cargos.\",\n      \"evidence\": \"Reciprocal co-IP (Vps35), cargo trafficking assays, and FSSS-motif/amphipathic-helix mutagenesis (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.10.08.681146\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint not peer-reviewed\", \"Structure of the CROP coat unresolved\", \"How cargo selectivity is encoded not defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established WIPI1 as essential for cardiomyocyte mitophagy and mitochondrial integrity, with overexpression preserving mitophagy markers in diabetic models.\",\n      \"evidence\": \"siRNA knockdown, AAV9 overexpression, JC-1 potential, respirometry, and echocardiography\",\n      \"pmids\": [\"39961409\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether WIPI1 acts directly in PINK/Parkin mitophagy or upstream is unclear\", \"Cargo-receptor interactions in mitophagy not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How WIPI1 mechanistically partitions between its PI(3)P-dependent autophagic scaffold role and its PI(3,5)P2/amphipathic-helix-dependent endosomal fission role within a cell, and the structural basis of its coat and ATG16L1 engagements, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No high-resolution structure of WIPI1 bound to lipid or coat partners\", \"Regulatory switch directing WIPI1 to autophagy versus endosomes unknown\", \"Quantitative contribution of WIPI1 versus WIPI2 across pathways not delineated\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [0, 2, 6, 9]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [11, 13]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [9, 13]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [1, 8, 9]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0, 9, 13]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [3, 12]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [10, 14]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [2, 6, 11, 12]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 9, 13]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [4, 5, 11]}\n    ],\n    \"complexes\": [\n      \"CROP (WIPI1-Retromer) complex\"\n    ],\n    \"partners\": [\n      \"WIPI2\",\n      \"ATG16L1\",\n      \"Vps35\",\n      \"TRIM21\",\n      \"MYC\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}