{"gene":"VPS37B","run_date":"2026-04-28T23:00:23","timeline":{"discoveries":[{"year":2004,"finding":"VPS37B is a component of the human ESCRT-I complex (~350 kDa), binding TSG101 at multiple sites including a putative coiled-coil region and a PTAP motif, and co-immunoprecipitating with TSG101 and VPS28. VPS37B recruits TSG101/ESCRT-I activity and can rescue budding of mutant HIV-1 Gag particles lacking native late domains.","method":"Co-immunoprecipitation, yeast two-hybrid, gel filtration, functional rescue assay of HIV-1 budding, dominant-negative VPS4A trapping","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (Co-IP, size exclusion, functional rescue, dominant-negative trapping) in a single study; foundational paper with 138 citations","pmids":["15218037"],"is_preprint":false},{"year":2004,"finding":"VPS37B is recruited to aberrant endosomal compartments when ATPase-deficient VPS4A is overexpressed, consistent with its function in the class E VPS/ESCRT pathway at endosomes.","method":"Confocal microscopy of dominant-negative VPS4A-expressing cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — direct localization experiment with functional context, replicated independently in VPS37C paper (PMID:15509564)","pmids":["15218037","15509564"],"is_preprint":false},{"year":2004,"finding":"VPS37B depletion, when combined with VPS37C depletion, inhibits ESCRT-I-dependent viral budding, demonstrating a redundant but essential role of VPS37B within ESCRT-I for retroviral release.","method":"siRNA knockdown, virus-like particle release assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — clean knockdown with specific phenotypic readout, but redundancy required co-depletion with VPS37C","pmids":["15509564"],"is_preprint":false},{"year":2007,"finding":"Ebola virus VP40 can redirect VPS37B from endosomes to the cell surface independently of TSG101 interaction, implicating VPS37B in EBOV budding via the VPS pathway.","method":"VP40 deletion analysis, VLP release assay, confocal microscopy","journal":"The Journal of infectious diseases","confidence":"Medium","confidence_rationale":"Tier 2 — direct localization experiment with functional consequence (VP40-dependent redistribution), single study","pmids":["17940959"],"is_preprint":false},{"year":2013,"finding":"VPS37B-containing ESCRT-I complexes interact with ALG-2 more strongly than TSG101 does; ALG-2 functions as a Ca2+-dependent adaptor bridging ALIX and ESCRT-I containing VPS37B to form a ternary ESCRT-I/ALIX/ALG-2 complex.","method":"Far-Western blot, pulldown assay with recombinant proteins co-expressed in HEK293T cells, in vitro binding assays with purified proteins","journal":"Bioscience, biotechnology, and biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro binding with purified proteins plus cell-based pulldown; single lab but multiple orthogonal methods","pmids":["23924735"],"is_preprint":false},{"year":2019,"finding":"SH3YL1 interacts with VPS37B through its C-terminal SH3 domain, and this interaction is required for SH3YL1-mediated EGFR sorting into multivesicular bodies and subsequent EGFR degradation.","method":"Co-immunoprecipitation, siRNA knockdown, EGF trafficking assay, EGFR degradation assay","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP plus loss-of-function with defined cargo trafficking phenotype; single lab","pmids":["31492760"],"is_preprint":false},{"year":2020,"finding":"Crystal structure of the human ESCRT-I headpiece comprising TSG101-VPS28-VPS37B-MVB12A was determined, revealing a helical assembly with a 12-molecule repeat. ESCRT-I forms helical filaments in solution (confirmed by EM), and VPS28 helical interface mutations block filament formation in vitro and autophagosome closure and HIV-1 release in cells.","method":"X-ray crystallography, electron microscopy, in vitro mutagenesis, autophagosome closure assay, HIV-1 release assay, coarse-grained MD simulation","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 — crystal structure plus mutagenesis plus orthogonal EM and functional cell-based assays in a single rigorous study","pmids":["32424346"],"is_preprint":false},{"year":2021,"finding":"CDIP1, a pro-apoptotic protein, preferentially associates with ESCRT-I containing VPS37B (or VPS37C) partly through the adaptor function of ALG-2, and this association promotes caspase-3/7-mediated cell death.","method":"Co-immunoprecipitation of GFP-CDIP1 with ESCRT-I subunits, caspase activity assay, overexpression in HEK293 cells","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 3 — Co-IP with defined cell death readout; single lab, single method for VPS37B-specific interaction","pmids":["33503978"],"is_preprint":false},{"year":2021,"finding":"Concurrent knockdown of VPS37A and VPS37B in colorectal cancer cells destabilizes the ESCRT-I complex and triggers p21 (CDKN1A)-mediated inhibition of cell proliferation and NF-κB-driven sterile inflammatory response; co-silencing VPS37C further potentiates these effects.","method":"siRNA knockdown, transcriptomic profiling, western blotting for ESCRT-I stability, proliferation assays","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 — clean knockdown with multiple defined cellular phenotypes and transcriptomic validation; single lab","pmids":["33419951"],"is_preprint":false},{"year":2021,"finding":"VPS37A and VPS37B enable endocytosis of the mannose receptor in dendritic cells, facilitating recognition and uptake of the house dust mite allergen Der p 1; CRISPR disruption of VPS37A/B in dendritic cells reduces Th2 cytokine production and alleviates allergic rhinitis symptoms in a mouse model.","method":"CRISPR/Cas9 gene disruption, RNA sequencing, in vitro co-culture assay with allogeneic CD4+ T cells, mouse model of allergic rhinitis with intranasal administration","journal":"Biomaterials","confidence":"Medium","confidence_rationale":"Tier 2 — loss-of-function with specific endocytic and immunological phenotypes in both in vitro and in vivo settings; single lab","pmids":["33895493"],"is_preprint":false}],"current_model":"VPS37B is a core subunit of the human ESCRT-I heterotetrameric complex (with TSG101, VPS28, and MVB12), participating in a helical 12-molecule ESCRT-I scaffold (resolved by crystal structure) that bridges ubiquitinated cargo recognition at endosomes to MVB sorting and membrane scission; it binds TSG101 at multiple sites, interacts with ALG-2 as a Ca2+-dependent bridge to ALIX, cooperates with SH3YL1 for EGFR sorting into MVBs, supports HIV-1 and Ebola virus budding, mediates mannose receptor endocytosis in dendritic cells, and its loss destabilizes ESCRT-I and triggers p21/NF-κB-dependent stress responses."},"narrative":{"teleology":[{"year":2004,"claim":"Identification of VPS37B as a stoichiometric ESCRT-I subunit that binds TSG101 at multiple sites and functions in HIV-1 budding established it as a core component of the class E VPS pathway.","evidence":"Co-IP, yeast two-hybrid, gel filtration, functional rescue of HIV-1 Gag budding, dominant-negative VPS4A trapping in human cells","pmids":["15218037","15509564"],"confidence":"High","gaps":["Structural basis of VPS37B–TSG101 interaction not yet resolved","Redundancy with VPS37A and VPS37C not fully delineated","Endogenous cargo sorting role not demonstrated"]},{"year":2007,"claim":"Demonstration that Ebola VP40 can redirect VPS37B from endosomes to the plasma membrane independently of TSG101 interaction broadened VPS37B's role beyond HIV to filovirus budding.","evidence":"VP40 deletion analysis, VLP release assay, confocal microscopy","pmids":["17940959"],"confidence":"Medium","gaps":["Direct binding interface between VP40 and VPS37B not mapped","No confirmation of requirement for VPS37B specifically (versus other VPS37 paralogs) in Ebola budding"]},{"year":2013,"claim":"Discovery that ALG-2 acts as a Ca²⁺-dependent bridge between VPS37B-containing ESCRT-I and ALIX revealed a regulatory layer linking calcium signaling to ESCRT assembly.","evidence":"Far-Western blot, pulldown with recombinant proteins, in vitro binding with purified components","pmids":["23924735"],"confidence":"Medium","gaps":["Physiological contexts in which Ca²⁺-dependent ESCRT-I/ALIX coupling is rate-limiting remain undefined","No in vivo validation of the ternary complex"]},{"year":2019,"claim":"Showing that SH3YL1 binds VPS37B via its SH3 domain to promote EGFR sorting into MVBs established VPS37B as a direct participant in receptor tyrosine kinase downregulation.","evidence":"Co-IP, siRNA knockdown, EGF trafficking and EGFR degradation assays","pmids":["31492760"],"confidence":"Medium","gaps":["Whether the SH3YL1–VPS37B interaction is direct or bridged through other ESCRT-I subunits not fully resolved","Generalizability to other receptor cargoes unknown"]},{"year":2020,"claim":"Solving the crystal structure of the ESCRT-I headpiece (TSG101–VPS28–VPS37B–MVB12A) revealed a helical filament architecture required for membrane scission in autophagosome closure and HIV-1 release, providing the first structural framework for VPS37B within the complex.","evidence":"X-ray crystallography, electron microscopy, mutagenesis, autophagosome closure and HIV-1 release functional assays","pmids":["32424346"],"confidence":"High","gaps":["Specific contacts contributed by VPS37B to helical assembly versus those from other subunits not individually dissected","How helical ESCRT-I filaments coordinate with downstream ESCRT-III in vivo remains unclear"]},{"year":2021,"claim":"Multiple studies in 2021 expanded VPS37B's functional repertoire: its loss (with paralogs) destabilizes ESCRT-I triggering p21/NF-κB stress responses, it enables mannose receptor endocytosis in dendritic cells affecting Th2 immunity, and it selectively associates with the pro-apoptotic factor CDIP1 via ALG-2.","evidence":"siRNA/CRISPR knockdown, transcriptomics, western blotting, Co-IP with CDIP1, caspase activity assays, dendritic cell co-culture and mouse allergic rhinitis model","pmids":["33419951","33895493","33503978"],"confidence":"Medium","gaps":["Whether VPS37B has non-redundant roles distinct from VPS37A/C in any physiological context is not established","Mechanism by which ESCRT-I destabilization activates NF-κB is indirect and not molecularly defined","CDIP1–VPS37B association demonstrated by single Co-IP approach without reciprocal or endogenous validation"]},{"year":null,"claim":"It remains unknown whether VPS37B has non-redundant, paralog-specific functions in vivo, what structural determinants within VPS37B specify its preferential interactions with ALG-2/CDIP1, and how VPS37B contributes to ESCRT-I filament assembly at the residue level.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No single-gene VPS37B knockout phenotype characterized in animal models","No mutagenesis of VPS37B-specific residues within the helical ESCRT-I filament","Post-translational regulation of VPS37B is uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,6]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[1,3,5]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,1,5,6,9]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[6]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[9]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[0,2,3]}],"complexes":["ESCRT-I"],"partners":["TSG101","VPS28","MVB12A","ALG-2","SH3YL1","ALIX","CDIP1"],"other_free_text":[]},"mechanistic_narrative":"VPS37B is a core subunit of the heterotetrameric ESCRT-I complex (with TSG101, VPS28, and MVB12A/B), functioning in endosomal sorting, multivesicular body biogenesis, autophagosome closure, and enveloped virus budding. The crystal structure of the ESCRT-I headpiece containing VPS37B reveals a helical filament with a 12-molecule repeat that is essential for membrane scission events including autophagosome closure and HIV-1 release [PMID:32424346]. VPS37B binds TSG101 at multiple sites, recruits ESCRT-I activity to endosomes, interacts with the Ca²⁺-dependent adaptor ALG-2 to bridge ALIX to ESCRT-I, and cooperates with SH3YL1 to direct EGFR sorting into multivesicular bodies for lysosomal degradation [PMID:15218037, PMID:23924735, PMID:31492760]. Loss of VPS37B, together with paralogs VPS37A/C, destabilizes the ESCRT-I complex and activates p21/NF-κB-dependent growth arrest and sterile inflammation, and disruption of VPS37A/B in dendritic cells impairs mannose receptor endocytosis and downstream Th2 immune responses [PMID:33419951, PMID:33895493]."},"prefetch_data":{"uniprot":{"accession":"Q9H9H4","full_name":"Vacuolar protein sorting-associated protein 37B","aliases":["ESCRT-I complex subunit VPS37B"],"length_aa":285,"mass_kda":31.3,"function":"Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Required for the sorting of endocytic ubiquitinated cargos into multivesicular bodies. May be involved in cell growth and differentiation","subcellular_location":"Late endosome membrane","url":"https://www.uniprot.org/uniprotkb/Q9H9H4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/VPS37B","classification":"Not Classified","n_dependent_lines":4,"n_total_lines":1208,"dependency_fraction":0.0033112582781456954},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000139722","cell_line_id":"CID000791","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"vesicles","grade":2}],"interactors":[{"gene":"MVB12A","stoichiometry":10.0},{"gene":"TSG101","stoichiometry":10.0},{"gene":"VPS28","stoichiometry":10.0},{"gene":"MVB12B","stoichiometry":10.0},{"gene":"UMAD1","stoichiometry":4.0},{"gene":"GOLGA2","stoichiometry":0.2},{"gene":"VPS25","stoichiometry":0.2},{"gene":"CEP55","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000791","total_profiled":1310},"omim":[{"mim_id":"610038","title":"VPS37C SUBUNIT OF ESCRT-I; VPS37C","url":"https://www.omim.org/entry/610038"},{"mim_id":"610037","title":"VPS37B SUBUNIT OF ESCRT-I; VPS37B","url":"https://www.omim.org/entry/610037"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Uncertain","locations":[{"location":"Cytosol","reliability":"Uncertain"},{"location":"Primary cilium","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/VPS37B"},"hgnc":{"alias_symbol":["FLJ12750"],"prev_symbol":[]},"alphafold":{"accession":"Q9H9H4","domains":[{"cath_id":"1.20.5","chopping":"14-83","consensus_level":"medium","plddt":93.9389,"start":14,"end":83},{"cath_id":"1.10.287","chopping":"102-164","consensus_level":"medium","plddt":95.5694,"start":102,"end":164}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H9H4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H9H4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H9H4-F1-predicted_aligned_error_v6.png","plddt_mean":75.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=VPS37B","jax_strain_url":"https://www.jax.org/strain/search?query=VPS37B"},"sequence":{"accession":"Q9H9H4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H9H4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H9H4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H9H4"}},"corpus_meta":[{"pmid":"15218037","id":"PMC_15218037","title":"The human endosomal sorting complex required for transport (ESCRT-I) and its role in HIV-1 budding.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15218037","citation_count":138,"is_preprint":false},{"pmid":"29180230","id":"PMC_29180230","title":"Glucocorticoids, genes and brain function.","date":"2017","source":"Progress in neuro-psychopharmacology & biological psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/29180230","citation_count":105,"is_preprint":false},{"pmid":"31377428","id":"PMC_31377428","title":"Identification of molecular signatures and pathways to identify novel therapeutic targets in Alzheimer's disease: Insights from a systems biomedicine perspective.","date":"2019","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/31377428","citation_count":90,"is_preprint":false},{"pmid":"15509564","id":"PMC_15509564","title":"Identification of human VPS37C, a component of endosomal sorting complex required for transport-I important for viral budding.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15509564","citation_count":76,"is_preprint":false},{"pmid":"27922854","id":"PMC_27922854","title":"Identification of HIV infection-related DNA methylation sites and advanced epigenetic aging in HIV-positive, treatment-naive U.S. veterans.","date":"2017","source":"AIDS (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/27922854","citation_count":50,"is_preprint":false},{"pmid":"32424346","id":"PMC_32424346","title":"A helical assembly of human ESCRT-I scaffolds reverse-topology membrane scission.","date":"2020","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/32424346","citation_count":47,"is_preprint":false},{"pmid":"21733561","id":"PMC_21733561","title":"Frameshift mutations of vacuolar protein sorting genes in gastric and colorectal cancers with microsatellite instability.","date":"2011","source":"Human pathology","url":"https://pubmed.ncbi.nlm.nih.gov/21733561","citation_count":41,"is_preprint":false},{"pmid":"17940959","id":"PMC_17940959","title":"Involvement of vacuolar protein sorting pathway in Ebola virus release independent of TSG101 interaction.","date":"2007","source":"The Journal of infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/17940959","citation_count":38,"is_preprint":false},{"pmid":"23924735","id":"PMC_23924735","title":"VPS37 isoforms differentially modulate the ternary complex formation of ALIX, ALG-2, and ESCRT-I.","date":"2013","source":"Bioscience, biotechnology, and biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23924735","citation_count":26,"is_preprint":false},{"pmid":"33419951","id":"PMC_33419951","title":"Concurrent depletion of Vps37 proteins evokes ESCRT-I destabilization and profound cellular stress responses.","date":"2021","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/33419951","citation_count":24,"is_preprint":false},{"pmid":"33895493","id":"PMC_33895493","title":"A novel therapeutic modality using CRISPR-engineered dendritic cells to treat allergies.","date":"2021","source":"Biomaterials","url":"https://pubmed.ncbi.nlm.nih.gov/33895493","citation_count":16,"is_preprint":false},{"pmid":"33503978","id":"PMC_33503978","title":"The Novel ALG-2 Target Protein CDIP1 Promotes Cell Death by Interacting with ESCRT-I and VAPA/B.","date":"2021","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/33503978","citation_count":15,"is_preprint":false},{"pmid":"39362218","id":"PMC_39362218","title":"Cross-ancestry analysis of brain QTLs enhances interpretation of schizophrenia genome-wide association studies.","date":"2024","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39362218","citation_count":13,"is_preprint":false},{"pmid":"35923698","id":"PMC_35923698","title":"Transcriptome Analysis Reveals Hub Genes Regulating Autophagy in Patients With Severe COVID-19.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35923698","citation_count":10,"is_preprint":false},{"pmid":"32436959","id":"PMC_32436959","title":"Analysis of putative cis-regulatory elements regulating blood pressure variation.","date":"2020","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/32436959","citation_count":8,"is_preprint":false},{"pmid":"38932209","id":"PMC_38932209","title":"Intrinsic Disorder in the Host Proteins Entrapped in Rabies Virus Particles.","date":"2024","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/38932209","citation_count":5,"is_preprint":false},{"pmid":"31492760","id":"PMC_31492760","title":"SH3YL1 cooperates with ESCRT-I in the sorting and degradation of the EGF receptor.","date":"2019","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/31492760","citation_count":4,"is_preprint":false},{"pmid":"38405973","id":"PMC_38405973","title":"Brain eQTLs of European, African American, and Asian ancestry improve interpretation of schizophrenia GWAS.","date":"2024","source":"medRxiv : the preprint server for health sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38405973","citation_count":2,"is_preprint":false},{"pmid":"40236703","id":"PMC_40236703","title":"PM2.5 exposure reprograms cell cycle dynamics in uterine immune cells at single-cell resolution.","date":"2025","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/40236703","citation_count":1,"is_preprint":false},{"pmid":"41229824","id":"PMC_41229824","title":"Research on the correlation between lung adenocarcinoma and necrosis by sodium overload.","date":"2025","source":"Journal of thoracic disease","url":"https://pubmed.ncbi.nlm.nih.gov/41229824","citation_count":0,"is_preprint":false},{"pmid":"41297598","id":"PMC_41297598","title":"Epigenetic signature of prenatal heat stress: DNA methylation changes in whole blood of dairy calves from birth to weaning.","date":"2025","source":"Journal of dairy science","url":"https://pubmed.ncbi.nlm.nih.gov/41297598","citation_count":0,"is_preprint":false},{"pmid":"40699655","id":"PMC_40699655","title":"Mapping Small Extracellular Vesicle Secretion Potential in Healthy Human Gingiva Using Spatial Transcriptomics.","date":"2025","source":"Current issues in molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/40699655","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13435,"output_tokens":2337,"usd":0.03768},"stage2":{"model":"claude-opus-4-6","input_tokens":5652,"output_tokens":2145,"usd":0.122828},"total_usd":0.160508,"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\": 2004,\n      \"finding\": \"VPS37B is a component of the human ESCRT-I complex (~350 kDa), binding TSG101 at multiple sites including a putative coiled-coil region and a PTAP motif, and co-immunoprecipitating with TSG101 and VPS28. VPS37B recruits TSG101/ESCRT-I activity and can rescue budding of mutant HIV-1 Gag particles lacking native late domains.\",\n      \"method\": \"Co-immunoprecipitation, yeast two-hybrid, gel filtration, functional rescue assay of HIV-1 budding, dominant-negative VPS4A trapping\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Co-IP, size exclusion, functional rescue, dominant-negative trapping) in a single study; foundational paper with 138 citations\",\n      \"pmids\": [\"15218037\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"VPS37B is recruited to aberrant endosomal compartments when ATPase-deficient VPS4A is overexpressed, consistent with its function in the class E VPS/ESCRT pathway at endosomes.\",\n      \"method\": \"Confocal microscopy of dominant-negative VPS4A-expressing cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct localization experiment with functional context, replicated independently in VPS37C paper (PMID:15509564)\",\n      \"pmids\": [\"15218037\", \"15509564\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"VPS37B depletion, when combined with VPS37C depletion, inhibits ESCRT-I-dependent viral budding, demonstrating a redundant but essential role of VPS37B within ESCRT-I for retroviral release.\",\n      \"method\": \"siRNA knockdown, virus-like particle release assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean knockdown with specific phenotypic readout, but redundancy required co-depletion with VPS37C\",\n      \"pmids\": [\"15509564\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Ebola virus VP40 can redirect VPS37B from endosomes to the cell surface independently of TSG101 interaction, implicating VPS37B in EBOV budding via the VPS pathway.\",\n      \"method\": \"VP40 deletion analysis, VLP release assay, confocal microscopy\",\n      \"journal\": \"The Journal of infectious diseases\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct localization experiment with functional consequence (VP40-dependent redistribution), single study\",\n      \"pmids\": [\"17940959\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"VPS37B-containing ESCRT-I complexes interact with ALG-2 more strongly than TSG101 does; ALG-2 functions as a Ca2+-dependent adaptor bridging ALIX and ESCRT-I containing VPS37B to form a ternary ESCRT-I/ALIX/ALG-2 complex.\",\n      \"method\": \"Far-Western blot, pulldown assay with recombinant proteins co-expressed in HEK293T cells, in vitro binding assays with purified proteins\",\n      \"journal\": \"Bioscience, biotechnology, and biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro binding with purified proteins plus cell-based pulldown; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"23924735\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SH3YL1 interacts with VPS37B through its C-terminal SH3 domain, and this interaction is required for SH3YL1-mediated EGFR sorting into multivesicular bodies and subsequent EGFR degradation.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, EGF trafficking assay, EGFR degradation assay\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus loss-of-function with defined cargo trafficking phenotype; single lab\",\n      \"pmids\": [\"31492760\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Crystal structure of the human ESCRT-I headpiece comprising TSG101-VPS28-VPS37B-MVB12A was determined, revealing a helical assembly with a 12-molecule repeat. ESCRT-I forms helical filaments in solution (confirmed by EM), and VPS28 helical interface mutations block filament formation in vitro and autophagosome closure and HIV-1 release in cells.\",\n      \"method\": \"X-ray crystallography, electron microscopy, in vitro mutagenesis, autophagosome closure assay, HIV-1 release assay, coarse-grained MD simulation\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure plus mutagenesis plus orthogonal EM and functional cell-based assays in a single rigorous study\",\n      \"pmids\": [\"32424346\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CDIP1, a pro-apoptotic protein, preferentially associates with ESCRT-I containing VPS37B (or VPS37C) partly through the adaptor function of ALG-2, and this association promotes caspase-3/7-mediated cell death.\",\n      \"method\": \"Co-immunoprecipitation of GFP-CDIP1 with ESCRT-I subunits, caspase activity assay, overexpression in HEK293 cells\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — Co-IP with defined cell death readout; single lab, single method for VPS37B-specific interaction\",\n      \"pmids\": [\"33503978\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Concurrent knockdown of VPS37A and VPS37B in colorectal cancer cells destabilizes the ESCRT-I complex and triggers p21 (CDKN1A)-mediated inhibition of cell proliferation and NF-κB-driven sterile inflammatory response; co-silencing VPS37C further potentiates these effects.\",\n      \"method\": \"siRNA knockdown, transcriptomic profiling, western blotting for ESCRT-I stability, proliferation assays\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean knockdown with multiple defined cellular phenotypes and transcriptomic validation; single lab\",\n      \"pmids\": [\"33419951\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"VPS37A and VPS37B enable endocytosis of the mannose receptor in dendritic cells, facilitating recognition and uptake of the house dust mite allergen Der p 1; CRISPR disruption of VPS37A/B in dendritic cells reduces Th2 cytokine production and alleviates allergic rhinitis symptoms in a mouse model.\",\n      \"method\": \"CRISPR/Cas9 gene disruption, RNA sequencing, in vitro co-culture assay with allogeneic CD4+ T cells, mouse model of allergic rhinitis with intranasal administration\",\n      \"journal\": \"Biomaterials\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function with specific endocytic and immunological phenotypes in both in vitro and in vivo settings; single lab\",\n      \"pmids\": [\"33895493\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"VPS37B is a core subunit of the human ESCRT-I heterotetrameric complex (with TSG101, VPS28, and MVB12), participating in a helical 12-molecule ESCRT-I scaffold (resolved by crystal structure) that bridges ubiquitinated cargo recognition at endosomes to MVB sorting and membrane scission; it binds TSG101 at multiple sites, interacts with ALG-2 as a Ca2+-dependent bridge to ALIX, cooperates with SH3YL1 for EGFR sorting into MVBs, supports HIV-1 and Ebola virus budding, mediates mannose receptor endocytosis in dendritic cells, and its loss destabilizes ESCRT-I and triggers p21/NF-κB-dependent stress responses.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"VPS37B is a core subunit of the heterotetrameric ESCRT-I complex (with TSG101, VPS28, and MVB12A/B), functioning in endosomal sorting, multivesicular body biogenesis, autophagosome closure, and enveloped virus budding. The crystal structure of the ESCRT-I headpiece containing VPS37B reveals a helical filament with a 12-molecule repeat that is essential for membrane scission events including autophagosome closure and HIV-1 release [PMID:32424346]. VPS37B binds TSG101 at multiple sites, recruits ESCRT-I activity to endosomes, interacts with the Ca²⁺-dependent adaptor ALG-2 to bridge ALIX to ESCRT-I, and cooperates with SH3YL1 to direct EGFR sorting into multivesicular bodies for lysosomal degradation [PMID:15218037, PMID:23924735, PMID:31492760]. Loss of VPS37B, together with paralogs VPS37A/C, destabilizes the ESCRT-I complex and activates p21/NF-κB-dependent growth arrest and sterile inflammation, and disruption of VPS37A/B in dendritic cells impairs mannose receptor endocytosis and downstream Th2 immune responses [PMID:33419951, PMID:33895493].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Identification of VPS37B as a stoichiometric ESCRT-I subunit that binds TSG101 at multiple sites and functions in HIV-1 budding established it as a core component of the class E VPS pathway.\",\n      \"evidence\": \"Co-IP, yeast two-hybrid, gel filtration, functional rescue of HIV-1 Gag budding, dominant-negative VPS4A trapping in human cells\",\n      \"pmids\": [\"15218037\", \"15509564\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of VPS37B–TSG101 interaction not yet resolved\",\n        \"Redundancy with VPS37A and VPS37C not fully delineated\",\n        \"Endogenous cargo sorting role not demonstrated\"\n      ]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Demonstration that Ebola VP40 can redirect VPS37B from endosomes to the plasma membrane independently of TSG101 interaction broadened VPS37B's role beyond HIV to filovirus budding.\",\n      \"evidence\": \"VP40 deletion analysis, VLP release assay, confocal microscopy\",\n      \"pmids\": [\"17940959\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct binding interface between VP40 and VPS37B not mapped\",\n        \"No confirmation of requirement for VPS37B specifically (versus other VPS37 paralogs) in Ebola budding\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Discovery that ALG-2 acts as a Ca²⁺-dependent bridge between VPS37B-containing ESCRT-I and ALIX revealed a regulatory layer linking calcium signaling to ESCRT assembly.\",\n      \"evidence\": \"Far-Western blot, pulldown with recombinant proteins, in vitro binding with purified components\",\n      \"pmids\": [\"23924735\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Physiological contexts in which Ca²⁺-dependent ESCRT-I/ALIX coupling is rate-limiting remain undefined\",\n        \"No in vivo validation of the ternary complex\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Showing that SH3YL1 binds VPS37B via its SH3 domain to promote EGFR sorting into MVBs established VPS37B as a direct participant in receptor tyrosine kinase downregulation.\",\n      \"evidence\": \"Co-IP, siRNA knockdown, EGF trafficking and EGFR degradation assays\",\n      \"pmids\": [\"31492760\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether the SH3YL1–VPS37B interaction is direct or bridged through other ESCRT-I subunits not fully resolved\",\n        \"Generalizability to other receptor cargoes unknown\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Solving the crystal structure of the ESCRT-I headpiece (TSG101–VPS28–VPS37B–MVB12A) revealed a helical filament architecture required for membrane scission in autophagosome closure and HIV-1 release, providing the first structural framework for VPS37B within the complex.\",\n      \"evidence\": \"X-ray crystallography, electron microscopy, mutagenesis, autophagosome closure and HIV-1 release functional assays\",\n      \"pmids\": [\"32424346\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Specific contacts contributed by VPS37B to helical assembly versus those from other subunits not individually dissected\",\n        \"How helical ESCRT-I filaments coordinate with downstream ESCRT-III in vivo remains unclear\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Multiple studies in 2021 expanded VPS37B's functional repertoire: its loss (with paralogs) destabilizes ESCRT-I triggering p21/NF-κB stress responses, it enables mannose receptor endocytosis in dendritic cells affecting Th2 immunity, and it selectively associates with the pro-apoptotic factor CDIP1 via ALG-2.\",\n      \"evidence\": \"siRNA/CRISPR knockdown, transcriptomics, western blotting, Co-IP with CDIP1, caspase activity assays, dendritic cell co-culture and mouse allergic rhinitis model\",\n      \"pmids\": [\"33419951\", \"33895493\", \"33503978\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether VPS37B has non-redundant roles distinct from VPS37A/C in any physiological context is not established\",\n        \"Mechanism by which ESCRT-I destabilization activates NF-κB is indirect and not molecularly defined\",\n        \"CDIP1–VPS37B association demonstrated by single Co-IP approach without reciprocal or endogenous validation\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown whether VPS37B has non-redundant, paralog-specific functions in vivo, what structural determinants within VPS37B specify its preferential interactions with ALG-2/CDIP1, and how VPS37B contributes to ESCRT-I filament assembly at the residue level.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No single-gene VPS37B knockout phenotype characterized in animal models\",\n        \"No mutagenesis of VPS37B-specific residues within the helical ESCRT-I filament\",\n        \"Post-translational regulation of VPS37B is uncharacterized\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [1, 3, 5]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 1, 5, 6, 9]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [0, 2, 3]}\n    ],\n    \"complexes\": [\n      \"ESCRT-I\"\n    ],\n    \"partners\": [\n      \"TSG101\",\n      \"VPS28\",\n      \"MVB12A\",\n      \"ALG-2\",\n      \"SH3YL1\",\n      \"ALIX\",\n      \"CDIP1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}