{"gene":"VIPAS39","run_date":"2026-04-28T23:00:23","timeline":{"discoveries":[{"year":2010,"finding":"VIPAR (VIPAS39/C14ORF133) forms a functional complex with VPS33B that interacts with RAB11A, and this complex has diverse functions in pathways regulating apical-basolateral polarity in liver and kidney, including correct sorting of membrane proteins such as Ceacam5 (mis-sorted toward lysosomal degradation when the complex is absent) and E-cadherin (transcriptionally downregulated).","method":"Co-immunoprecipitation, zebrafish vipar knockdown (biliary/E-cadherin defects), mouse mIMCD-3 Vipar/Vps33b-deficient cells with membrane protein mis-sorting and tight junction defects","journal":"Nature genetics","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, multiple orthogonal in vivo models, replicated across species and cell types","pmids":["20190753"],"is_preprint":false},{"year":2008,"finding":"The human SPE-39 orthologue C14orf133 (VIPAS39) interacts with VPS33 homologues and co-immunoprecipitates and co-sediments with other HOPS complex subunits; SPE-39 knockdown in cultured human cells altered endosome morphology (syntaxin 7-, syntaxin 8-, syntaxin 13-positive) and delayed mannose-6-phosphate receptor-mediated cathepsin D delivery and EGFR degradation, establishing VIPAS39 as a regulator of lysosomal delivery via interaction with the core HOPS complex.","method":"Co-immunoprecipitation, co-sedimentation, in vitro interaction assay, siRNA knockdown with endosome morphology and cargo trafficking readouts in human cells; C. elegans genetics","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (Co-IP, cosedimentation, in vitro binding, KD with functional readouts), replicated across organisms","pmids":["19109425"],"is_preprint":false},{"year":2012,"finding":"VPS16B (encoded by C14orf133/VIPAS39) is identified as a VPS33B-binding protein required for megakaryocyte and platelet α-granule biogenesis; GFP-VPS16B co-localizes with markers of the trans-Golgi network, late endosomes, and α-granules, and patient platelets with VIPAS39 mutations show complete absence of α-granules with loss of both soluble and membrane-bound α-granule proteins.","method":"Yeast two-hybrid, mass spectrometry, co-immunoprecipitation, immunofluorescence microscopy, electron microscopy of patient platelets","journal":"Blood","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (Y2H, MS, Co-IP, EM) plus patient cell phenotyping","pmids":["23002115"],"is_preprint":false},{"year":2013,"finding":"Disease-causing ARC syndrome mutations in VIPAS39/SPE-39 largely preserve its interaction with VPS33B but alter subcellular localization of VPS33B to VIPAS39-positive endosomes; some mutants fragment VIPAS39-positive endosomes, suggesting that the complex mediates endosomal maturation or fusion.","method":"Yeast two-hybrid, co-immunoprecipitation, quantitative fluorescent microscopy of wild-type and mutant VIPAS39/VPS33B","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal Co-IP and quantitative imaging in single lab, moderate evidence","pmids":["23918659"],"is_preprint":false},{"year":2012,"finding":"SPE-39 (VIPAS39) is tyrosine-phosphorylated at Tyr-11 following EGF stimulation, which promotes ubiquitination of its C-terminal region and its degradation; VPS33B binding to SPE-39 inhibits this EGF-induced ubiquitination, stabilizing SPE-39; SPE-39 and VPS33B have an opposing functional relationship in downregulation of the EGF receptor.","method":"Immunoprecipitation, phosphorylation and ubiquitination assays, site-directed mutagenesis (Tyr-11), EGF stimulation in COS-7 cells","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 — biochemical assays with mutagenesis in single lab, single study","pmids":["22677173"],"is_preprint":false},{"year":2019,"finding":"VPS33B and VPS16B (VIPAS39) form a distinct small complex with the same hydrodynamic radius as the recombinant VPS33B-VPS16B heterodimer; in VPS33B-knockout megakaryocyte cells, α-granule cargo is degraded in lysosomes rather than sorted to granules, and VPS16B steady-state levels are significantly reduced, indicating VPS16B is destabilized without its partner; the complex localizes to the recycling endosome as a key intermediate in α-granule biogenesis.","method":"CRISPR/Cas9 knockout, size-exclusion chromatography, immunoblotting, live-cell cargo trafficking assay, GFP-VPS33B reconstitution in KO cells","journal":"Blood advances","confidence":"High","confidence_rationale":"Tier 1–2 — reconstituted complex from bacteria, CRISPR KO with defined trafficking phenotype, multiple orthogonal methods","pmids":["31501156"],"is_preprint":false},{"year":2023,"finding":"Human VPS33B and VPS16B (VIPAS39) form a high-molecular-weight complex (~315 kDa) with a 2:3 VPS33B:VPS16B stoichiometry; the complex has a well-folded α-helical structure and a two-lobed shape by SAXS and negative-staining EM, with each lobe containing one VPS33B molecule oriented in opposite directions, forming the only known bidirectional Sec1/Munc18 complex; truncated VPS16B (aa 143–316) is sufficient for complex formation, and the ARC-causing L30P variant disrupts complex formation while S243F and H344D do not.","method":"Circular dichroism, size-exclusion chromatography-multiangle light scattering (SEC-MALS), small-angle X-ray scattering (SAXS), negative-staining EM, quantitative immunoblotting, avidin tagging, ARC variant expression","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — structural analysis by multiple biophysical methods with domain mapping and disease variant mutagenesis in a single rigorous study","pmids":["37062417"],"is_preprint":false},{"year":2022,"finding":"VPS16B (VIPAS39) protein levels in platelets and megakaryocytes are dependent on VPS33B expression; a homozygous nonsense VPS33B variant causing loss of VPS33B results in concurrent loss of VPS16B expression, confirming that VPS16B stability requires VPS33B.","method":"Patient primary cell analysis, immunoblotting, electron microscopy","journal":"Journal of thrombosis and haemostasis","confidence":"Medium","confidence_rationale":"Tier 3 — single patient observation with protein expression analysis, supports existing mechanism","pmids":["35325493"],"is_preprint":false},{"year":2018,"finding":"VPS33B and VIPAR (VIPAS39) are essential for epidermal lamellar body biogenesis and function; Vipas39-deficient mouse skin shows abnormal lamellar body morphology, disrupted localization of lamellar body cargo, increased corneocyte thickness, decreased cornified envelope thickness, and reduced stratum corneum lipid deposition, establishing a role for the VPS33B-VIPAR complex in lysosome-related organelle biogenesis in skin.","method":"Mouse Vipas39 knockout, histology, immunofluorescence, electron microscopy of skin biopsies and primary cells","journal":"Biochimica et biophysica acta. Molecular basis of disease","confidence":"Medium","confidence_rationale":"Tier 2 — KO mouse with defined organelle and cargo phenotype, multiple imaging modalities","pmids":["29409756"],"is_preprint":false},{"year":2025,"finding":"VIPAS39 sorts ACSL4 (acyl-CoA synthetase long-chain family member 4) into late endosomes, facilitating its subsequent release via exosomes; VIPAS39 knockdown prevents exosomal expulsion of ACSL4 in ferroptosis-resistant ovarian cancer cells, restoring ACSL4 levels and overcoming ferroptosis resistance.","method":"Live-cell imaging with pH-sensitive CD63-pHuji reporter, immunoprecipitation-mass spectrometry, protein binding assays, xenograft models","journal":"EBioMedicine","confidence":"Medium","confidence_rationale":"Tier 2 — IP-MS identification with live imaging and functional rescue in vivo, single lab","pmids":["40088627"],"is_preprint":false}],"current_model":"VIPAS39 (VPS16B/SPE-39/C14orf133) forms a structurally defined, bidirectional ~315 kDa complex with VPS33B (stoichiometry 2:3) that functions as part of the metazoan HOPS machinery to mediate endosomal maturation/fusion, regulate lysosomal delivery, and ensure correct cargo sorting to lysosome-related organelles including platelet α-granules, epidermal lamellar bodies, and the apical membrane of polarized epithelial cells; VIPAS39 is post-translationally regulated by EGF-induced tyrosine phosphorylation and ubiquitination, and VPS33B binding stabilizes VIPAS39, while VIPAS39 loss destabilizes VPS33B, making the two proteins mutually dependent for stability and function."},"narrative":{"teleology":[{"year":2008,"claim":"Establishing VIPAS39 as a HOPS-associated endolysosomal regulator resolved its molecular identity: the human SPE-39 orthologue interacts with VPS33 and other HOPS subunits, and its depletion delays cathepsin D delivery and EGFR degradation, placing it in the lysosomal delivery pathway.","evidence":"Co-IP, co-sedimentation, in vitro binding, siRNA knockdown with endosome morphology and cargo trafficking readouts in human cells and C. elegans genetics","pmids":["19109425"],"confidence":"High","gaps":["Whether VIPAS39 is a stoichiometric HOPS subunit or an accessory factor was unclear","Direct membrane fusion activity not tested","No structural information on the VIPAS39–VPS33B interaction"]},{"year":2010,"claim":"Demonstrating that VIPAS39–VPS33B interacts with RAB11A and controls apical–basolateral polarity broadened its role beyond lysosomal delivery to include epithelial membrane protein sorting (Ceacam5, E-cadherin) and tissue morphogenesis in liver and kidney.","evidence":"Co-IP, zebrafish vipar knockdown, mouse mIMCD-3 Vipas39/Vps33b-deficient cells with membrane protein mis-sorting and tight junction defects","pmids":["20190753"],"confidence":"High","gaps":["How RAB11A interaction is regulated was unknown","Whether the polarity defect is cell-autonomous in all tissues was untested"]},{"year":2012,"claim":"Identifying VIPAS39 as essential for platelet α-granule biogenesis and showing it localizes to TGN, late endosomes, and α-granules linked the complex to lysosome-related organelle formation and explained bleeding phenotypes in ARC syndrome patients.","evidence":"Yeast two-hybrid, mass spectrometry, Co-IP, immunofluorescence, electron microscopy of patient platelets lacking α-granules","pmids":["23002115"],"confidence":"High","gaps":["The trafficking step at which cargo is diverted remained unresolved","Whether VIPAS39 acts at the recycling endosome versus late endosome was unclear"]},{"year":2012,"claim":"Revealing EGF-induced Tyr-11 phosphorylation and C-terminal ubiquitination of VIPAS39, counteracted by VPS33B binding, established post-translational regulation of the complex and a functional interplay with EGFR downregulation.","evidence":"IP, phosphorylation/ubiquitination assays, Tyr-11 mutagenesis, EGF stimulation in COS-7 cells","pmids":["22677173"],"confidence":"Medium","gaps":["The kinase responsible for Tyr-11 phosphorylation was not identified","The E3 ligase mediating ubiquitination was not identified","Findings from a single cell type and single lab"]},{"year":2013,"claim":"Mapping ARC-causing VIPAS39 mutations showed most preserve VPS33B binding but alter endosomal localization or fragment VIPAS39-positive endosomes, separating the interaction interface from the membrane-targeting mechanism.","evidence":"Y2H, Co-IP, quantitative fluorescent microscopy of WT and mutant VIPAS39/VPS33B","pmids":["23918659"],"confidence":"Medium","gaps":["Whether endosome fragmentation reflects a fusion defect or maturation arrest was not distinguished","No in vivo validation of individual mutant phenotypes"]},{"year":2018,"claim":"Extending the complex's role to epidermal lamellar body biogenesis in Vipas39-knockout mice showed it is a general regulator of lysosome-related organelle formation, not restricted to hematopoietic or epithelial polarity contexts.","evidence":"Mouse Vipas39 knockout with histology, immunofluorescence, and electron microscopy of skin","pmids":["29409756"],"confidence":"Medium","gaps":["Molecular cargo sorted by the complex in keratinocytes was not fully defined","Whether VIPAS39 acts at the same endosomal compartment in skin as in megakaryocytes was not resolved"]},{"year":2019,"claim":"CRISPR knockout of VPS33B in megakaryocytes demonstrated that VIPAS39 protein is destabilized in the absence of VPS33B and that the complex acts at recycling endosomes to prevent lysosomal degradation of α-granule cargo, pinpointing the trafficking step.","evidence":"CRISPR/Cas9 KO, SEC, immunoblotting, live-cell cargo trafficking, GFP-VPS33B reconstitution","pmids":["31501156"],"confidence":"High","gaps":["Whether VIPAS39 loss reciprocally destabilizes VPS33B to the same extent was not shown in this system","The SNARE partners or membrane fusion mechanism at the recycling endosome were not identified"]},{"year":2023,"claim":"Structural characterization revealed the VPS33B–VIPAS39 complex has a unique bidirectional Sec1/Munc18 architecture with 2:3 stoichiometry and a two-lobed shape, and that the ARC variant L30P disrupts complex formation while S243F and H344D do not, defining the structural basis for pathogenic versus benign variants.","evidence":"SEC-MALS, SAXS, negative-staining EM, circular dichroism, domain truncation, ARC variant expression","pmids":["37062417"],"confidence":"High","gaps":["High-resolution atomic structure is lacking","How the bidirectional arrangement relates to SNARE engagement is unknown","No membrane fusion reconstitution with the purified complex"]},{"year":2025,"claim":"Identification of ACSL4 as a VIPAS39-sorted cargo destined for exosomal release via late endosomes extended the complex's function to ferroptosis resistance, showing that VIPAS39 knockdown restores ACSL4 and sensitizes ovarian cancer cells to ferroptosis.","evidence":"IP-MS, live-cell CD63-pHuji imaging, protein binding assays, xenograft models","pmids":["40088627"],"confidence":"Medium","gaps":["Whether ACSL4 sorting is direct or mediated by an adaptor is unresolved","Generalizability to other cancer types not tested","Single-lab finding"]},{"year":null,"claim":"Key open questions include the atomic structure of the VPS33B–VIPAS39 complex, the identity of its SNARE partners and the mechanism by which the bidirectional SM architecture promotes membrane fusion, and whether the complex directly participates in tethering or acts as an effector recruited by Rab GTPases.","evidence":"","pmids":[],"confidence":"High","gaps":["No high-resolution structure of the complex","SNARE partners and membrane fusion mechanism unknown","Direct tethering versus Rab-effector role not distinguished"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,5]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[1,2,3,9]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[2]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[5]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,1,2,5,9]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[0,2,5,9]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[2,5,8]}],"complexes":["VPS33B–VIPAS39 complex"],"partners":["VPS33B","RAB11A","ACSL4"],"other_free_text":[]},"mechanistic_narrative":"VIPAS39 is a core subunit of the VPS33B–VIPAS39 complex that functions in endosomal maturation, cargo sorting, and delivery to lysosomes and lysosome-related organelles. VIPAS39 and VPS33B form a ~315 kDa bidirectional complex with 2:3 stoichiometry—the only known bidirectional Sec1/Munc18 assembly—in which a central VIPAS39 region (aa 143–316) is sufficient for binding, and the two proteins are mutually required for stability [PMID:37062417, PMID:31501156, PMID:35325493]. The complex interacts with RAB11A and HOPS subunits to regulate apical–basolateral polarity in epithelia, platelet α-granule biogenesis, epidermal lamellar body formation, and late-endosomal sorting of cargoes including ACSL4 for exosomal release [PMID:20190753, PMID:19109425, PMID:23002115, PMID:29409756, PMID:40088627]. Loss-of-function mutations in VIPAS39 cause arthrogryposis–renal dysfunction–cholestasis (ARC) syndrome, with disease variants such as L30P disrupting complex formation while others alter endosomal localization [PMID:23918659, PMID:37062417]."},"prefetch_data":{"uniprot":{"accession":"Q9H9C1","full_name":"Spermatogenesis-defective protein 39 homolog","aliases":["VPS33B-interacting protein in apical-basolateral polarity regulator","VPS33B-interacting protein in polarity and apical restriction"],"length_aa":493,"mass_kda":57.0,"function":"Proposed to be involved in endosomal maturation implicating in part VPS33B. In epithelial cells, the VPS33B:VIPAS39 complex may play a role in the apical RAB11A-dependent recycling pathway and in the maintenance of the apical-basolateral polarity (PubMed:20190753). May play a role in lysosomal trafficking, probably via association with the core HOPS complex in a discrete population of endosomes; the functions seems to be independent of VPS33B (PubMed:19109425). May play a role in vesicular trafficking during spermatogenesis (By similarity). May be involved in direct or indirect transcriptional regulation of E-cadherin (By similarity)","subcellular_location":"Cytoplasm; Cytoplasmic vesicle; Early endosome; Recycling endosome; Late endosome","url":"https://www.uniprot.org/uniprotkb/Q9H9C1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/VIPAS39","classification":"Not Classified","n_dependent_lines":6,"n_total_lines":1208,"dependency_fraction":0.004966887417218543},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"WASF2","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/VIPAS39","total_profiled":1310},"omim":[{"mim_id":"616700","title":"COMM DOMAIN-CONTAINING PROTEIN 3; COMMD3","url":"https://www.omim.org/entry/616700"},{"mim_id":"613404","title":"ARTHROGRYPOSIS, RENAL DYSFUNCTION, AND CHOLESTASIS 2; ARCS2","url":"https://www.omim.org/entry/613404"},{"mim_id":"613401","title":"VPS33B-INTERACTING PROTEIN, APICAL-BASOLATERAL POLARITY REGULATOR, SPE39 HOMOLOG; VIPAS39","url":"https://www.omim.org/entry/613401"},{"mim_id":"608552","title":"VPS33B LATE ENDOSOME AND LYSOSOME ASSOCIATED; VPS33B","url":"https://www.omim.org/entry/608552"},{"mim_id":"606892","title":"SYNTAXIN 12; STX12","url":"https://www.omim.org/entry/606892"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/VIPAS39"},"hgnc":{"alias_symbol":["VIPAR","VPS16B","SPE-39","SPE39","hSPE-39"],"prev_symbol":["C14orf133"]},"alphafold":{"accession":"Q9H9C1","domains":[{"cath_id":"-","chopping":"250-338","consensus_level":"medium","plddt":94.33,"start":250,"end":338},{"cath_id":"-","chopping":"382-440","consensus_level":"medium","plddt":95.6241,"start":382,"end":440},{"cath_id":"-","chopping":"446-493","consensus_level":"medium","plddt":95.0413,"start":446,"end":493},{"cath_id":"1.25.10","chopping":"156-248","consensus_level":"high","plddt":93.7766,"start":156,"end":248}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H9C1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H9C1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H9C1-F1-predicted_aligned_error_v6.png","plddt_mean":78.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=VIPAS39","jax_strain_url":"https://www.jax.org/strain/search?query=VIPAS39"},"sequence":{"accession":"Q9H9C1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H9C1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H9C1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H9C1"}},"corpus_meta":[{"pmid":"20190753","id":"PMC_20190753","title":"Mutations in VIPAR cause an arthrogryposis, renal dysfunction and cholestasis syndrome phenotype with defects in epithelial polarization.","date":"2010","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/20190753","citation_count":139,"is_preprint":false},{"pmid":"23002115","id":"PMC_23002115","title":"The VPS33B-binding protein VPS16B is required in megakaryocyte and platelet α-granule biogenesis.","date":"2012","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/23002115","citation_count":65,"is_preprint":false},{"pmid":"19109425","id":"PMC_19109425","title":"SPE-39 family proteins interact with the HOPS complex and function in lysosomal delivery.","date":"2008","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/19109425","citation_count":55,"is_preprint":false},{"pmid":"29409756","id":"PMC_29409756","title":"VPS33B and VIPAR are essential for epidermal lamellar body biogenesis and function.","date":"2018","source":"Biochimica et biophysica acta. Molecular basis of disease","url":"https://pubmed.ncbi.nlm.nih.gov/29409756","citation_count":29,"is_preprint":false},{"pmid":"23918659","id":"PMC_23918659","title":"Vps33b pathogenic mutations preferentially affect VIPAS39/SPE-39-positive endosomes.","date":"2013","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23918659","citation_count":23,"is_preprint":false},{"pmid":"14504223","id":"PMC_14504223","title":"The Caenorhabditis elegans spe-39 gene is required for intracellular membrane reorganization during spermatogenesis.","date":"2003","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/14504223","citation_count":22,"is_preprint":false},{"pmid":"31501156","id":"PMC_31501156","title":"Mechanism of platelet α-granule biogenesis: study of cargo transport and the VPS33B-VPS16B complex in a model system.","date":"2019","source":"Blood advances","url":"https://pubmed.ncbi.nlm.nih.gov/31501156","citation_count":20,"is_preprint":false},{"pmid":"37062417","id":"PMC_37062417","title":"The Sec1-Munc18 protein VPS33B forms a uniquely bidirectional complex with VPS16B.","date":"2023","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37062417","citation_count":11,"is_preprint":false},{"pmid":"26808426","id":"PMC_26808426","title":"Novel VIPAS39 mutation in a syndromic patient with arthrogryposis, renal tubular dysfunction and intrahepatic cholestasis.","date":"2016","source":"European journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/26808426","citation_count":10,"is_preprint":false},{"pmid":"35325493","id":"PMC_35325493","title":"Platelet VPS16B is dependent on VPS33B expression, as determined in two siblings with arthrogryposis, renal dysfunction, and cholestasis syndrome.","date":"2022","source":"Journal of thrombosis and haemostasis : JTH","url":"https://pubmed.ncbi.nlm.nih.gov/35325493","citation_count":6,"is_preprint":false},{"pmid":"40088627","id":"PMC_40088627","title":"VIPAS39 confers ferroptosis resistance in epithelial ovarian cancer through exporting ACSL4.","date":"2025","source":"EBioMedicine","url":"https://pubmed.ncbi.nlm.nih.gov/40088627","citation_count":4,"is_preprint":false},{"pmid":"22677173","id":"PMC_22677173","title":"Inhibitory effect of SPE-39 due to tyrosine phosphorylation and ubiquitination on the function of Vps33B in the EGF-stimulated cells.","date":"2012","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/22677173","citation_count":4,"is_preprint":false},{"pmid":"39736737","id":"PMC_39736737","title":"VIPAS39 related arthrogryposis-renal dysfunction-cholestasis syndrome-case report and systematic review.","date":"2024","source":"Orphanet journal of rare diseases","url":"https://pubmed.ncbi.nlm.nih.gov/39736737","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.06.04.657864","title":"Mechanobiological proximal tubular defects in ARC syndrome: A <i>VPS33B</i> CRISPR knockout study","date":"2025-06-04","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.04.657864","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8181,"output_tokens":2827,"usd":0.033474},"stage2":{"model":"claude-opus-4-6","input_tokens":6172,"output_tokens":2638,"usd":0.145215},"total_usd":0.178689,"stage1_batch_id":"msgbatch_01BparvgRZ9S2LMidvaoo86K","stage2_batch_id":"msgbatch_01NkBfv9SVZWthhS7j6mU6G3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"VIPAR (VIPAS39/C14ORF133) forms a functional complex with VPS33B that interacts with RAB11A, and this complex has diverse functions in pathways regulating apical-basolateral polarity in liver and kidney, including correct sorting of membrane proteins such as Ceacam5 (mis-sorted toward lysosomal degradation when the complex is absent) and E-cadherin (transcriptionally downregulated).\",\n      \"method\": \"Co-immunoprecipitation, zebrafish vipar knockdown (biliary/E-cadherin defects), mouse mIMCD-3 Vipar/Vps33b-deficient cells with membrane protein mis-sorting and tight junction defects\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, multiple orthogonal in vivo models, replicated across species and cell types\",\n      \"pmids\": [\"20190753\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"The human SPE-39 orthologue C14orf133 (VIPAS39) interacts with VPS33 homologues and co-immunoprecipitates and co-sediments with other HOPS complex subunits; SPE-39 knockdown in cultured human cells altered endosome morphology (syntaxin 7-, syntaxin 8-, syntaxin 13-positive) and delayed mannose-6-phosphate receptor-mediated cathepsin D delivery and EGFR degradation, establishing VIPAS39 as a regulator of lysosomal delivery via interaction with the core HOPS complex.\",\n      \"method\": \"Co-immunoprecipitation, co-sedimentation, in vitro interaction assay, siRNA knockdown with endosome morphology and cargo trafficking readouts in human cells; C. elegans genetics\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Co-IP, cosedimentation, in vitro binding, KD with functional readouts), replicated across organisms\",\n      \"pmids\": [\"19109425\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"VPS16B (encoded by C14orf133/VIPAS39) is identified as a VPS33B-binding protein required for megakaryocyte and platelet α-granule biogenesis; GFP-VPS16B co-localizes with markers of the trans-Golgi network, late endosomes, and α-granules, and patient platelets with VIPAS39 mutations show complete absence of α-granules with loss of both soluble and membrane-bound α-granule proteins.\",\n      \"method\": \"Yeast two-hybrid, mass spectrometry, co-immunoprecipitation, immunofluorescence microscopy, electron microscopy of patient platelets\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Y2H, MS, Co-IP, EM) plus patient cell phenotyping\",\n      \"pmids\": [\"23002115\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Disease-causing ARC syndrome mutations in VIPAS39/SPE-39 largely preserve its interaction with VPS33B but alter subcellular localization of VPS33B to VIPAS39-positive endosomes; some mutants fragment VIPAS39-positive endosomes, suggesting that the complex mediates endosomal maturation or fusion.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, quantitative fluorescent microscopy of wild-type and mutant VIPAS39/VPS33B\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP and quantitative imaging in single lab, moderate evidence\",\n      \"pmids\": [\"23918659\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"SPE-39 (VIPAS39) is tyrosine-phosphorylated at Tyr-11 following EGF stimulation, which promotes ubiquitination of its C-terminal region and its degradation; VPS33B binding to SPE-39 inhibits this EGF-induced ubiquitination, stabilizing SPE-39; SPE-39 and VPS33B have an opposing functional relationship in downregulation of the EGF receptor.\",\n      \"method\": \"Immunoprecipitation, phosphorylation and ubiquitination assays, site-directed mutagenesis (Tyr-11), EGF stimulation in COS-7 cells\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — biochemical assays with mutagenesis in single lab, single study\",\n      \"pmids\": [\"22677173\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"VPS33B and VPS16B (VIPAS39) form a distinct small complex with the same hydrodynamic radius as the recombinant VPS33B-VPS16B heterodimer; in VPS33B-knockout megakaryocyte cells, α-granule cargo is degraded in lysosomes rather than sorted to granules, and VPS16B steady-state levels are significantly reduced, indicating VPS16B is destabilized without its partner; the complex localizes to the recycling endosome as a key intermediate in α-granule biogenesis.\",\n      \"method\": \"CRISPR/Cas9 knockout, size-exclusion chromatography, immunoblotting, live-cell cargo trafficking assay, GFP-VPS33B reconstitution in KO cells\",\n      \"journal\": \"Blood advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — reconstituted complex from bacteria, CRISPR KO with defined trafficking phenotype, multiple orthogonal methods\",\n      \"pmids\": [\"31501156\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Human VPS33B and VPS16B (VIPAS39) form a high-molecular-weight complex (~315 kDa) with a 2:3 VPS33B:VPS16B stoichiometry; the complex has a well-folded α-helical structure and a two-lobed shape by SAXS and negative-staining EM, with each lobe containing one VPS33B molecule oriented in opposite directions, forming the only known bidirectional Sec1/Munc18 complex; truncated VPS16B (aa 143–316) is sufficient for complex formation, and the ARC-causing L30P variant disrupts complex formation while S243F and H344D do not.\",\n      \"method\": \"Circular dichroism, size-exclusion chromatography-multiangle light scattering (SEC-MALS), small-angle X-ray scattering (SAXS), negative-staining EM, quantitative immunoblotting, avidin tagging, ARC variant expression\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — structural analysis by multiple biophysical methods with domain mapping and disease variant mutagenesis in a single rigorous study\",\n      \"pmids\": [\"37062417\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"VPS16B (VIPAS39) protein levels in platelets and megakaryocytes are dependent on VPS33B expression; a homozygous nonsense VPS33B variant causing loss of VPS33B results in concurrent loss of VPS16B expression, confirming that VPS16B stability requires VPS33B.\",\n      \"method\": \"Patient primary cell analysis, immunoblotting, electron microscopy\",\n      \"journal\": \"Journal of thrombosis and haemostasis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single patient observation with protein expression analysis, supports existing mechanism\",\n      \"pmids\": [\"35325493\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"VPS33B and VIPAR (VIPAS39) are essential for epidermal lamellar body biogenesis and function; Vipas39-deficient mouse skin shows abnormal lamellar body morphology, disrupted localization of lamellar body cargo, increased corneocyte thickness, decreased cornified envelope thickness, and reduced stratum corneum lipid deposition, establishing a role for the VPS33B-VIPAR complex in lysosome-related organelle biogenesis in skin.\",\n      \"method\": \"Mouse Vipas39 knockout, histology, immunofluorescence, electron microscopy of skin biopsies and primary cells\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular basis of disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with defined organelle and cargo phenotype, multiple imaging modalities\",\n      \"pmids\": [\"29409756\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"VIPAS39 sorts ACSL4 (acyl-CoA synthetase long-chain family member 4) into late endosomes, facilitating its subsequent release via exosomes; VIPAS39 knockdown prevents exosomal expulsion of ACSL4 in ferroptosis-resistant ovarian cancer cells, restoring ACSL4 levels and overcoming ferroptosis resistance.\",\n      \"method\": \"Live-cell imaging with pH-sensitive CD63-pHuji reporter, immunoprecipitation-mass spectrometry, protein binding assays, xenograft models\",\n      \"journal\": \"EBioMedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — IP-MS identification with live imaging and functional rescue in vivo, single lab\",\n      \"pmids\": [\"40088627\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"VIPAS39 (VPS16B/SPE-39/C14orf133) forms a structurally defined, bidirectional ~315 kDa complex with VPS33B (stoichiometry 2:3) that functions as part of the metazoan HOPS machinery to mediate endosomal maturation/fusion, regulate lysosomal delivery, and ensure correct cargo sorting to lysosome-related organelles including platelet α-granules, epidermal lamellar bodies, and the apical membrane of polarized epithelial cells; VIPAS39 is post-translationally regulated by EGF-induced tyrosine phosphorylation and ubiquitination, and VPS33B binding stabilizes VIPAS39, while VIPAS39 loss destabilizes VPS33B, making the two proteins mutually dependent for stability and function.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"VIPAS39 is a core subunit of the VPS33B–VIPAS39 complex that functions in endosomal maturation, cargo sorting, and delivery to lysosomes and lysosome-related organelles. VIPAS39 and VPS33B form a ~315 kDa bidirectional complex with 2:3 stoichiometry—the only known bidirectional Sec1/Munc18 assembly—in which a central VIPAS39 region (aa 143–316) is sufficient for binding, and the two proteins are mutually required for stability [PMID:37062417, PMID:31501156, PMID:35325493]. The complex interacts with RAB11A and HOPS subunits to regulate apical–basolateral polarity in epithelia, platelet α-granule biogenesis, epidermal lamellar body formation, and late-endosomal sorting of cargoes including ACSL4 for exosomal release [PMID:20190753, PMID:19109425, PMID:23002115, PMID:29409756, PMID:40088627]. Loss-of-function mutations in VIPAS39 cause arthrogryposis–renal dysfunction–cholestasis (ARC) syndrome, with disease variants such as L30P disrupting complex formation while others alter endosomal localization [PMID:23918659, PMID:37062417].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Establishing VIPAS39 as a HOPS-associated endolysosomal regulator resolved its molecular identity: the human SPE-39 orthologue interacts with VPS33 and other HOPS subunits, and its depletion delays cathepsin D delivery and EGFR degradation, placing it in the lysosomal delivery pathway.\",\n      \"evidence\": \"Co-IP, co-sedimentation, in vitro binding, siRNA knockdown with endosome morphology and cargo trafficking readouts in human cells and C. elegans genetics\",\n      \"pmids\": [\"19109425\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether VIPAS39 is a stoichiometric HOPS subunit or an accessory factor was unclear\", \"Direct membrane fusion activity not tested\", \"No structural information on the VIPAS39–VPS33B interaction\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Demonstrating that VIPAS39–VPS33B interacts with RAB11A and controls apical–basolateral polarity broadened its role beyond lysosomal delivery to include epithelial membrane protein sorting (Ceacam5, E-cadherin) and tissue morphogenesis in liver and kidney.\",\n      \"evidence\": \"Co-IP, zebrafish vipar knockdown, mouse mIMCD-3 Vipas39/Vps33b-deficient cells with membrane protein mis-sorting and tight junction defects\",\n      \"pmids\": [\"20190753\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How RAB11A interaction is regulated was unknown\", \"Whether the polarity defect is cell-autonomous in all tissues was untested\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identifying VIPAS39 as essential for platelet α-granule biogenesis and showing it localizes to TGN, late endosomes, and α-granules linked the complex to lysosome-related organelle formation and explained bleeding phenotypes in ARC syndrome patients.\",\n      \"evidence\": \"Yeast two-hybrid, mass spectrometry, Co-IP, immunofluorescence, electron microscopy of patient platelets lacking α-granules\",\n      \"pmids\": [\"23002115\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The trafficking step at which cargo is diverted remained unresolved\", \"Whether VIPAS39 acts at the recycling endosome versus late endosome was unclear\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Revealing EGF-induced Tyr-11 phosphorylation and C-terminal ubiquitination of VIPAS39, counteracted by VPS33B binding, established post-translational regulation of the complex and a functional interplay with EGFR downregulation.\",\n      \"evidence\": \"IP, phosphorylation/ubiquitination assays, Tyr-11 mutagenesis, EGF stimulation in COS-7 cells\",\n      \"pmids\": [\"22677173\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The kinase responsible for Tyr-11 phosphorylation was not identified\", \"The E3 ligase mediating ubiquitination was not identified\", \"Findings from a single cell type and single lab\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Mapping ARC-causing VIPAS39 mutations showed most preserve VPS33B binding but alter endosomal localization or fragment VIPAS39-positive endosomes, separating the interaction interface from the membrane-targeting mechanism.\",\n      \"evidence\": \"Y2H, Co-IP, quantitative fluorescent microscopy of WT and mutant VIPAS39/VPS33B\",\n      \"pmids\": [\"23918659\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether endosome fragmentation reflects a fusion defect or maturation arrest was not distinguished\", \"No in vivo validation of individual mutant phenotypes\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extending the complex's role to epidermal lamellar body biogenesis in Vipas39-knockout mice showed it is a general regulator of lysosome-related organelle formation, not restricted to hematopoietic or epithelial polarity contexts.\",\n      \"evidence\": \"Mouse Vipas39 knockout with histology, immunofluorescence, and electron microscopy of skin\",\n      \"pmids\": [\"29409756\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular cargo sorted by the complex in keratinocytes was not fully defined\", \"Whether VIPAS39 acts at the same endosomal compartment in skin as in megakaryocytes was not resolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"CRISPR knockout of VPS33B in megakaryocytes demonstrated that VIPAS39 protein is destabilized in the absence of VPS33B and that the complex acts at recycling endosomes to prevent lysosomal degradation of α-granule cargo, pinpointing the trafficking step.\",\n      \"evidence\": \"CRISPR/Cas9 KO, SEC, immunoblotting, live-cell cargo trafficking, GFP-VPS33B reconstitution\",\n      \"pmids\": [\"31501156\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether VIPAS39 loss reciprocally destabilizes VPS33B to the same extent was not shown in this system\", \"The SNARE partners or membrane fusion mechanism at the recycling endosome were not identified\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Structural characterization revealed the VPS33B–VIPAS39 complex has a unique bidirectional Sec1/Munc18 architecture with 2:3 stoichiometry and a two-lobed shape, and that the ARC variant L30P disrupts complex formation while S243F and H344D do not, defining the structural basis for pathogenic versus benign variants.\",\n      \"evidence\": \"SEC-MALS, SAXS, negative-staining EM, circular dichroism, domain truncation, ARC variant expression\",\n      \"pmids\": [\"37062417\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"High-resolution atomic structure is lacking\", \"How the bidirectional arrangement relates to SNARE engagement is unknown\", \"No membrane fusion reconstitution with the purified complex\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identification of ACSL4 as a VIPAS39-sorted cargo destined for exosomal release via late endosomes extended the complex's function to ferroptosis resistance, showing that VIPAS39 knockdown restores ACSL4 and sensitizes ovarian cancer cells to ferroptosis.\",\n      \"evidence\": \"IP-MS, live-cell CD63-pHuji imaging, protein binding assays, xenograft models\",\n      \"pmids\": [\"40088627\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ACSL4 sorting is direct or mediated by an adaptor is unresolved\", \"Generalizability to other cancer types not tested\", \"Single-lab finding\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include the atomic structure of the VPS33B–VIPAS39 complex, the identity of its SNARE partners and the mechanism by which the bidirectional SM architecture promotes membrane fusion, and whether the complex directly participates in tethering or acts as an effector recruited by Rab GTPases.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No high-resolution structure of the complex\", \"SNARE partners and membrane fusion mechanism unknown\", \"Direct tethering versus Rab-effector role not distinguished\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [1, 2, 3, 9]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 1, 2, 5, 9]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [0, 2, 5, 9]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [2, 5, 8]}\n    ],\n    \"complexes\": [\n      \"VPS33B–VIPAS39 complex\"\n    ],\n    \"partners\": [\n      \"VPS33B\",\n      \"RAB11A\",\n      \"ACSL4\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}