{"gene":"VPS26B","run_date":"2026-04-28T23:00:23","timeline":{"discoveries":[{"year":2007,"finding":"Crystal structure of mouse VPS26B was determined, revealing an arrestin-like fold. Structure-based mutagenesis showed that both VPS26A and VPS26B bind VPS35 through a highly conserved surface patch in the C-terminal subdomain, and this interaction is required for endosomal recruitment. VPS26A and VPS26B compete for a single VPS35/VPS29 binding site with nanomolar affinity, defining distinct retromer complexes in vitro and in vivo.","method":"X-ray crystallography, isothermal titration calorimetry, structure-based mutagenesis, co-immunoprecipitation","journal":"Traffic","confidence":"High","confidence_rationale":"Tier 1 — crystal structure with functional mutagenesis and quantitative binding assays","pmids":["18088321"],"is_preprint":false},{"year":2005,"finding":"VPS26B is a peripheral membrane protein that co-precipitates with VPS35 and interacts directly with VPS35 by yeast two-hybrid analysis, establishing it as a subunit of the retromer complex. In HeLa cells, VPS26B localizes to the cytoplasm with low levels at the plasma membrane, while in A549 cells it co-localizes with actin-rich lamellipodia at the cell surface along with VPS35. TIRF microscopy confirmed VPS26B association with the plasma membrane.","method":"Co-immunoprecipitation, yeast two-hybrid, subcellular fractionation, immunofluorescence, TIRF microscopy","journal":"Traffic","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (CoIP, Y2H, live imaging) in the discovery paper","pmids":["16190980"],"is_preprint":false},{"year":2011,"finding":"VPS26B-retromer associates with TBC1D5 and GOLPH3 but, unlike VPS26A-retromer, does not interact with the cation-independent mannose 6-phosphate receptor (CI-M6PR), leading to CI-M6PR degradation and increased cathepsin D secretion. The VPS26B C-terminal region is directly responsible for this differential cargo selectivity, as its deletion restores CI-M6PR cycling. VPS26B-retromer shows prolonged association with maturing endosomes relative to VPS26A-retromer.","method":"Stable cell lines (HEK293), co-immunoprecipitation, Western blot, immunofluorescence/colocalization with Rab proteins, deletion mutagenesis, cathepsin D secretion assay","journal":"Traffic","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods with functional readouts and domain mapping","pmids":["21920005"],"is_preprint":false},{"year":2010,"finding":"Vps26b knockout mice lack the Vps26b-Vps29-Vps35 retromer complex despite normal Vps26a-retromer, and show a ~20% increase in sortilin protein levels, implicating Vps26b-retromer in retrograde transport of sortilin from endosomes to the TGN. Loss of Vps26b also results in a severe reduction of Vps35 protein at the cellular level.","method":"Vps26b knockout mouse generation, co-immunoprecipitation, Western blot, behavioral/histological analysis","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined molecular phenotype and cargo identification","pmids":["21040701"],"is_preprint":false},{"year":2015,"finding":"VPS26B-retromer negatively regulates plasma membrane repopulation of the protease-activated GPCR PAR-2 following stimulation. Overexpression of VPS26B causes a significant delay in PAR-2 plasma membrane resensitization without affecting initial receptor activation, endocytosis, ERK1/2 signaling, or calcium release.","method":"Stable HEK293 cell overexpression model, calcium flux assay, ERK1/2 signaling assay, flow cytometry/receptor internalization assay","journal":"Cell biology international","confidence":"Medium","confidence_rationale":"Tier 3 — single lab, overexpression model with functional readout but no direct binding demonstrated","pmids":["26113136"],"is_preprint":false},{"year":2019,"finding":"The murine cytomegalovirus M45 protein recruits VPS26B (retromer component) and the LC3-interacting adaptor TBC1D5 to facilitate selective autophagy (aggrephagy) of NEMO and RIPK1 protein aggregates as a viral immune-evasion mechanism.","method":"Co-immunoprecipitation, proximity ligation assay, autophagy flux assays, siRNA knockdown","journal":"Nature microbiology","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal CoIP and functional knockdown but role is in context of viral infection","pmids":["31844296"],"is_preprint":false},{"year":2021,"finding":"NEK1 kinase phosphorylates VPS26B to regulate retromer-mediated endosomal trafficking. NEK1 deficiency disrupts endosomal trafficking of plasma membrane proteins and leads to lysosomal degradation of A20, promoting RIPK1-dependent cell death in cerebrovascular endothelial cells.","method":"In vitro phosphorylation assay, NEK1 knockout mice, genetic epistasis (RIPK1 inactivation rescue), proteomics, Western blot","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro kinase assay demonstrating direct phosphorylation of VPS26B, plus in vivo genetic rescue","pmids":["34376696"],"is_preprint":false},{"year":2021,"finding":"Neurons are enriched with a VPS26B-organized retromer core that is differentially dedicated to endosomal recycling. VPS26B depletion impairs glutamate receptor and SORL1 recycling, selectively causing synaptic dysfunction in the trans-entorhinal cortex, a region most vulnerable in Alzheimer's disease.","method":"Mouse model imaging, VPS26B depletion (siRNA/shRNA), electrophysiology, immunocytochemistry, behavioral assays, human brain tissue analysis","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (electrophysiology, ICC, behavior, human tissue) establishing VPS26B-specific function in endosomal recycling","pmids":["34965419"],"is_preprint":false},{"year":2024,"finding":"VPS26B acts as a novel Rab14 effector and forms a complex with SHIP164 and the ATPase RhoBTB3 at Golgi-early endosome contacts to promote early endosome bud formation. Rab14 activity regulates SHIP164 association with early endosomes. Depletion of VPS26B leads to enlarged Rab14+ early endosomes without buds, phenocopying loss of SHIP164 or RhoBTB3.","method":"Co-immunoprecipitation, siRNA knockdown, live-cell imaging, confocal microscopy, proximity ligation assay, domain mutagenesis","journal":"Cell discovery","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods demonstrating complex formation and functional rescue experiments","pmids":["38565878"],"is_preprint":false},{"year":2008,"finding":"Vps26b forms a distinct Vps26b-Vps29-Vps35 retromer complex in mouse testis, with the Vps26b-Vps35 interaction confirmed by immunoprecipitation and pull-down assay.","method":"Co-immunoprecipitation, pull-down assay, Western blot, RT-PCR","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 — direct interaction confirmed by pulldown but limited functional follow-up","pmids":["18656452"],"is_preprint":false},{"year":2020,"finding":"Acute retromer inactivation by knocksideways technology (which requires VPS26A or VPS26B for retromer function) reveals that retromer is required for cell-surface recycling of GLUT1 but not for CI-MPR retrograde sorting in HeLa and H4 cells.","method":"Knocksideways (acute inactivation), flow cytometry, immunofluorescence, quantitative microscopy","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 — acute inactivation method with quantitative cargo sorting readouts, though VPS26B not individually distinguished from VPS26A","pmids":["32747499"],"is_preprint":false},{"year":2022,"finding":"Retromer (containing VPS26A or VPS26B) co-immunoprecipitates with the centriolar protein CP110 and is required for CP110 removal from the mother centriole, establishing a role for retromer in primary ciliogenesis in mammalian cells. VPS35 localizes to the primary cilium.","method":"Co-immunoprecipitation, siRNA knockdown, immunofluorescence, ciliogenesis assay, CRISPR knockout in C. elegans","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 — CoIP plus depletion phenotype, but VPS26B not individually distinguished from VPS26A in most experiments","pmids":["35510502"],"is_preprint":false}],"current_model":"VPS26B is a subunit of a distinct mammalian retromer complex (VPS26B-VPS29-VPS35), defined by its arrestin-like structure and binding to VPS35 through a conserved C-terminal surface patch; it acts as a Rab14 effector within a RhoBTB3-SHIP164-VPS26B complex at Golgi-endosome contacts to drive early endosome bud formation, mediates endosomal recycling of cargoes including GLUT1, glutamate receptors, and SORL1 (but not CI-M6PR or PAR-2 resensitization), is phosphorylated by NEK1 to regulate its trafficking function, and can be recruited by viral proteins to facilitate aggrephagy-based immune evasion."},"narrative":{"teleology":[{"year":2005,"claim":"Establishing VPS26B as a bona fide retromer subunit resolved whether VPS26 existed as a single gene or a family with distinct complex-forming capacity.","evidence":"Co-immunoprecipitation, yeast two-hybrid, subcellular fractionation, and TIRF microscopy in HeLa and A549 cells","pmids":["16190980"],"confidence":"High","gaps":["No functional cargo sorting readout was performed","Distinction from VPS26A in vivo was not addressed"]},{"year":2007,"claim":"Structural determination of VPS26B revealed an arrestin-like fold and identified the C-terminal surface patch mediating VPS35 binding, showing that VPS26A and VPS26B compete for a single retromer binding site with nanomolar affinity.","evidence":"X-ray crystallography, ITC, structure-based mutagenesis, co-immunoprecipitation","pmids":["18088321"],"confidence":"High","gaps":["Structural basis for cargo selectivity differences between VPS26A and VPS26B was not resolved","No in vivo confirmation of competitive binding"]},{"year":2010,"claim":"Knockout mice demonstrated that VPS26B-retromer is non-redundant with VPS26A-retromer in vivo, with loss of VPS26B leading to elevated sortilin levels and reduced VPS35 stability.","evidence":"Vps26b knockout mouse, co-immunoprecipitation, Western blot","pmids":["21040701"],"confidence":"High","gaps":["Mechanism by which VPS26B loss destabilizes VPS35 was not determined","Sortilin trafficking was inferred from steady-state levels, not directly measured"]},{"year":2011,"claim":"Mapping differential cargo selectivity showed that VPS26B-retromer fails to interact with CI-M6PR—an effect dependent on the VPS26B C-terminal region—explaining why VPS26B expression promotes CI-M6PR degradation and cathepsin D secretion.","evidence":"Stable HEK293 cell lines, co-immunoprecipitation, deletion mutagenesis, cathepsin D secretion assay","pmids":["21920005"],"confidence":"High","gaps":["Direct structural basis for C-terminal domain–mediated cargo exclusion was not resolved","Whether VPS26B-retromer has unique positive cargoes beyond CI-M6PR exclusion was unclear"]},{"year":2019,"claim":"Discovery that the viral protein M45 recruits VPS26B and TBC1D5 to target NEMO and RIPK1 aggregates for aggrephagy revealed an unexpected link between retromer and selective autophagy during immune evasion.","evidence":"Co-immunoprecipitation, proximity ligation assay, autophagy flux assays, siRNA knockdown in MCMV-infected cells","pmids":["31844296"],"confidence":"Medium","gaps":["Whether VPS26B participates in aggrephagy in non-viral contexts is unknown","Mechanism of VPS26B recruitment by M45 was not structurally defined"]},{"year":2020,"claim":"Acute retromer inactivation using knocksideways technology confirmed that retromer (requiring VPS26A or VPS26B) is essential for GLUT1 cell-surface recycling but dispensable for CI-M6PR retrograde sorting, reframing the core cargo repertoire of mammalian retromer.","evidence":"Knocksideways acute inactivation, flow cytometry, quantitative microscopy in HeLa and H4 cells","pmids":["32747499"],"confidence":"Medium","gaps":["VPS26B was not individually distinguished from VPS26A in this system","Mechanism of GLUT1 recognition by retromer was not identified"]},{"year":2021,"claim":"Two studies established that VPS26B-retromer is neuronally enriched and regulated by NEK1 phosphorylation: NEK1 directly phosphorylates VPS26B to maintain endosomal trafficking, while VPS26B depletion in neurons selectively impairs glutamate receptor and SORL1 recycling, causing synaptic dysfunction in the trans-entorhinal cortex.","evidence":"In vitro kinase assay, NEK1 knockout mice with RIPK1 genetic rescue; VPS26B depletion with electrophysiology, immunocytochemistry, and human brain tissue analysis","pmids":["34376696","34965419"],"confidence":"High","gaps":["Specific phosphorylation site(s) on VPS26B and their structural consequences are not fully defined","Whether NEK1 regulation is neuron-specific or general is unknown","Causal link between VPS26B-retromer dysfunction and Alzheimer's disease pathogenesis remains correlative"]},{"year":2024,"claim":"Identification of VPS26B as a Rab14 effector within a RhoBTB3–SHIP164–VPS26B complex at Golgi–endosome contacts revealed a retromer-independent function in driving early endosome bud formation.","evidence":"Co-immunoprecipitation, siRNA knockdown, live-cell imaging, proximity ligation assay, domain mutagenesis","pmids":["38565878"],"confidence":"High","gaps":["How VPS26B coordinates its retromer-dependent and Rab14-dependent functions is unknown","Whether VPS26B binds SHIP164 and VPS35 simultaneously or in mutually exclusive pools is unresolved","Lipid transfer activity of SHIP164 in this complex has not been functionally dissected"]},{"year":null,"claim":"Key unresolved questions include how VPS26B partitions between retromer-dependent and Rab14/SHIP164-dependent complexes, the structural basis for its distinct cargo selectivity versus VPS26A, and whether VPS26B dysfunction is causally linked to neurodegeneration.","evidence":"","pmids":[],"confidence":"Low","gaps":["No cryo-EM or crystal structure of a full VPS26B-retromer with cargo","No disease-causing mutations in VPS26B have been reported in human genetic studies","Dual complex membership (retromer vs. RhoBTB3–SHIP164) has not been quantified in physiological conditions"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,2,8]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[2,7,8]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[1]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[2,3,7,8,10]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[5]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[2,3,7]}],"complexes":["retromer (VPS26B-VPS29-VPS35)","RhoBTB3-SHIP164-VPS26B"],"partners":["VPS35","VPS29","SHIP164","RHOBTB3","RAB14","TBC1D5","NEK1","GOLPH3"],"other_free_text":[]},"mechanistic_narrative":"VPS26B is a component of a distinct mammalian retromer complex (VPS26B–VPS29–VPS35) that mediates endosomal cargo sorting and recycling. Its arrestin-like fold binds VPS35 through a conserved C-terminal surface patch with nanomolar affinity, competing with VPS26A for a single binding site to define two mutually exclusive retromer populations [PMID:18088321]. VPS26B-retromer preferentially supports recycling of cargoes including GLUT1, glutamate receptors, and SORL1 rather than CI-M6PR retrieval, with VPS26B depletion in neurons selectively impairing synaptic recycling in Alzheimer-vulnerable brain regions [PMID:21920005, PMID:34965419]. Independent of the canonical retromer, VPS26B acts as a Rab14 effector within a RhoBTB3–SHIP164–VPS26B complex at Golgi–endosome contacts to drive early endosome bud formation, and its trafficking function is regulated by NEK1-mediated phosphorylation [PMID:38565878, PMID:34376696]."},"prefetch_data":{"uniprot":{"accession":"Q4G0F5","full_name":"Vacuolar protein sorting-associated protein 26B","aliases":["Vesicle protein sorting 26B"],"length_aa":336,"mass_kda":39.2,"function":"Acts as a component of the retromer cargo-selective complex (CSC). The CSC is believed to be the core functional component of retromer or respective retromer complex variants acting to prevent missorting of selected transmembrane cargo proteins into the lysosomal degradation pathway. The recruitment of the CSC to the endosomal membrane involves RAB7A and SNX3. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX3-retromer mediates the retrograde transport of WLS distinct from the SNX-BAR retromer pathway. The SNX27-retromer is believed to be involved in endosome-to-plasma membrane trafficking and recycling of a broad spectrum of cargo proteins. The CSC seems to act as recruitment hub for other proteins, such as the WASH complex and TBC1D5. May be involved in retrograde transport of SORT1 but not of IGF2R. Acts redundantly with VSP26A in SNX-27 mediated endocytic recycling of SLC2A1/GLUT1 (By similarity)","subcellular_location":"Cytoplasm; Membrane; Early endosome; Late endosome","url":"https://www.uniprot.org/uniprotkb/Q4G0F5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/VPS26B","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"VPS35","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/search/VPS26B","total_profiled":1310},"omim":[{"mim_id":"610027","title":"VPS26 RETROMER COMPLEX COMPONENT B; VPS26B","url":"https://www.omim.org/entry/610027"}],"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/VPS26B"},"hgnc":{"alias_symbol":["MGC10485","Pep8b"],"prev_symbol":[]},"alphafold":{"accession":"Q4G0F5","domains":[{"cath_id":"2.60.40.640","chopping":"9-148","consensus_level":"high","plddt":95.9483,"start":9,"end":148},{"cath_id":"2.60.40.640","chopping":"161-292","consensus_level":"high","plddt":93.4893,"start":161,"end":292}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q4G0F5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q4G0F5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q4G0F5-F1-predicted_aligned_error_v6.png","plddt_mean":86.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=VPS26B","jax_strain_url":"https://www.jax.org/strain/search?query=VPS26B"},"sequence":{"accession":"Q4G0F5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q4G0F5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q4G0F5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q4G0F5"}},"corpus_meta":[{"pmid":"18088321","id":"PMC_18088321","title":"Structure of Vps26B and mapping of its interaction with the retromer protein complex.","date":"2007","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/18088321","citation_count":98,"is_preprint":false},{"pmid":"21920005","id":"PMC_21920005","title":"Vps26A and Vps26B subunits define distinct retromer complexes.","date":"2011","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/21920005","citation_count":84,"is_preprint":false},{"pmid":"16190980","id":"PMC_16190980","title":"A novel mammalian retromer component, Vps26B.","date":"2005","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/16190980","citation_count":76,"is_preprint":false},{"pmid":"31844296","id":"PMC_31844296","title":"Herpesviruses induce aggregation and selective autophagy of host signalling proteins NEMO and RIPK1 as an immune-evasion mechanism.","date":"2019","source":"Nature microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/31844296","citation_count":54,"is_preprint":false},{"pmid":"34965419","id":"PMC_34965419","title":"Alzheimer's vulnerable brain region relies on a distinct retromer core dedicated to endosomal recycling.","date":"2021","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/34965419","citation_count":51,"is_preprint":false},{"pmid":"21040701","id":"PMC_21040701","title":"Implication of mouse Vps26b-Vps29-Vps35 retromer complex in sortilin trafficking.","date":"2010","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/21040701","citation_count":50,"is_preprint":false},{"pmid":"34376696","id":"PMC_34376696","title":"NEK1-mediated retromer trafficking promotes blood-brain barrier integrity by regulating glucose metabolism and RIPK1 activation.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34376696","citation_count":38,"is_preprint":false},{"pmid":"27528657","id":"PMC_27528657","title":"Atypical parkinsonism-associated retromer mutant alters endosomal sorting of specific cargo proteins.","date":"2016","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/27528657","citation_count":38,"is_preprint":false},{"pmid":"25475142","id":"PMC_25475142","title":"Genetic variability of the retromer cargo recognition complex in parkinsonism.","date":"2014","source":"Movement disorders : official journal of the Movement Disorder Society","url":"https://pubmed.ncbi.nlm.nih.gov/25475142","citation_count":23,"is_preprint":false},{"pmid":"32320094","id":"PMC_32320094","title":"Dysregulation of the Retromer Complex System in Down Syndrome.","date":"2020","source":"Annals of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/32320094","citation_count":21,"is_preprint":false},{"pmid":"34502533","id":"PMC_34502533","title":"Viral Induced Protein Aggregation: A Mechanism of Immune Evasion.","date":"2021","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/34502533","citation_count":19,"is_preprint":false},{"pmid":"32747499","id":"PMC_32747499","title":"Acute inactivation of retromer and ESCPE-1 leads to time-resolved defects in endosomal cargo sorting.","date":"2020","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/32747499","citation_count":19,"is_preprint":false},{"pmid":"37949073","id":"PMC_37949073","title":"Pharmacologic enhancement of retromer rescues endosomal pathology induced by defects in the Alzheimer's gene SORL1.","date":"2023","source":"Stem cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/37949073","citation_count":17,"is_preprint":false},{"pmid":"18656452","id":"PMC_18656452","title":"Identification of novel retromer complexes in the mouse testis.","date":"2008","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/18656452","citation_count":15,"is_preprint":false},{"pmid":"37042072","id":"PMC_37042072","title":"Retromer Proteins Reduced in Down Syndrome and the Dp16 Model: Impact of APP Dose and Preclinical Studies of a γ-Secretase Modulator.","date":"2023","source":"Annals of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/37042072","citation_count":9,"is_preprint":false},{"pmid":"35510502","id":"PMC_35510502","title":"The retromer complex regulates C. elegans development and mammalian ciliogenesis.","date":"2022","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/35510502","citation_count":8,"is_preprint":false},{"pmid":"26113136","id":"PMC_26113136","title":"Vps26B-retromer negatively regulates plasma membrane resensitization of PAR-2.","date":"2015","source":"Cell biology international","url":"https://pubmed.ncbi.nlm.nih.gov/26113136","citation_count":7,"is_preprint":false},{"pmid":"35882632","id":"PMC_35882632","title":"Identification of novel rare copy number variants associated with sporadic tetralogy of Fallot and clinical implications.","date":"2022","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35882632","citation_count":7,"is_preprint":false},{"pmid":"38565878","id":"PMC_38565878","title":"Biogenesis of Rab14-positive endosome buds at Golgi-endosome contacts by the RhoBTB3-SHIP164-Vps26B complex.","date":"2024","source":"Cell discovery","url":"https://pubmed.ncbi.nlm.nih.gov/38565878","citation_count":4,"is_preprint":false},{"pmid":"39944650","id":"PMC_39944650","title":"Variations in rumen microbiota and host genome impacted feed efficiency in goat breeds.","date":"2025","source":"Frontiers in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/39944650","citation_count":4,"is_preprint":false},{"pmid":"21359680","id":"PMC_21359680","title":"Quantitative analysis of retromer complex-related genes during embryo development in the mouse.","date":"2011","source":"Molecules and cells","url":"https://pubmed.ncbi.nlm.nih.gov/21359680","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11065,"output_tokens":2940,"usd":0.038648},"stage2":{"model":"claude-opus-4-6","input_tokens":6283,"output_tokens":2497,"usd":0.14076},"total_usd":0.179408,"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\": 2007,\n      \"finding\": \"Crystal structure of mouse VPS26B was determined, revealing an arrestin-like fold. Structure-based mutagenesis showed that both VPS26A and VPS26B bind VPS35 through a highly conserved surface patch in the C-terminal subdomain, and this interaction is required for endosomal recruitment. VPS26A and VPS26B compete for a single VPS35/VPS29 binding site with nanomolar affinity, defining distinct retromer complexes in vitro and in vivo.\",\n      \"method\": \"X-ray crystallography, isothermal titration calorimetry, structure-based mutagenesis, co-immunoprecipitation\",\n      \"journal\": \"Traffic\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure with functional mutagenesis and quantitative binding assays\",\n      \"pmids\": [\"18088321\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"VPS26B is a peripheral membrane protein that co-precipitates with VPS35 and interacts directly with VPS35 by yeast two-hybrid analysis, establishing it as a subunit of the retromer complex. In HeLa cells, VPS26B localizes to the cytoplasm with low levels at the plasma membrane, while in A549 cells it co-localizes with actin-rich lamellipodia at the cell surface along with VPS35. TIRF microscopy confirmed VPS26B association with the plasma membrane.\",\n      \"method\": \"Co-immunoprecipitation, yeast two-hybrid, subcellular fractionation, immunofluorescence, TIRF microscopy\",\n      \"journal\": \"Traffic\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (CoIP, Y2H, live imaging) in the discovery paper\",\n      \"pmids\": [\"16190980\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"VPS26B-retromer associates with TBC1D5 and GOLPH3 but, unlike VPS26A-retromer, does not interact with the cation-independent mannose 6-phosphate receptor (CI-M6PR), leading to CI-M6PR degradation and increased cathepsin D secretion. The VPS26B C-terminal region is directly responsible for this differential cargo selectivity, as its deletion restores CI-M6PR cycling. VPS26B-retromer shows prolonged association with maturing endosomes relative to VPS26A-retromer.\",\n      \"method\": \"Stable cell lines (HEK293), co-immunoprecipitation, Western blot, immunofluorescence/colocalization with Rab proteins, deletion mutagenesis, cathepsin D secretion assay\",\n      \"journal\": \"Traffic\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods with functional readouts and domain mapping\",\n      \"pmids\": [\"21920005\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Vps26b knockout mice lack the Vps26b-Vps29-Vps35 retromer complex despite normal Vps26a-retromer, and show a ~20% increase in sortilin protein levels, implicating Vps26b-retromer in retrograde transport of sortilin from endosomes to the TGN. Loss of Vps26b also results in a severe reduction of Vps35 protein at the cellular level.\",\n      \"method\": \"Vps26b knockout mouse generation, co-immunoprecipitation, Western blot, behavioral/histological analysis\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined molecular phenotype and cargo identification\",\n      \"pmids\": [\"21040701\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"VPS26B-retromer negatively regulates plasma membrane repopulation of the protease-activated GPCR PAR-2 following stimulation. Overexpression of VPS26B causes a significant delay in PAR-2 plasma membrane resensitization without affecting initial receptor activation, endocytosis, ERK1/2 signaling, or calcium release.\",\n      \"method\": \"Stable HEK293 cell overexpression model, calcium flux assay, ERK1/2 signaling assay, flow cytometry/receptor internalization assay\",\n      \"journal\": \"Cell biology international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single lab, overexpression model with functional readout but no direct binding demonstrated\",\n      \"pmids\": [\"26113136\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The murine cytomegalovirus M45 protein recruits VPS26B (retromer component) and the LC3-interacting adaptor TBC1D5 to facilitate selective autophagy (aggrephagy) of NEMO and RIPK1 protein aggregates as a viral immune-evasion mechanism.\",\n      \"method\": \"Co-immunoprecipitation, proximity ligation assay, autophagy flux assays, siRNA knockdown\",\n      \"journal\": \"Nature microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal CoIP and functional knockdown but role is in context of viral infection\",\n      \"pmids\": [\"31844296\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NEK1 kinase phosphorylates VPS26B to regulate retromer-mediated endosomal trafficking. NEK1 deficiency disrupts endosomal trafficking of plasma membrane proteins and leads to lysosomal degradation of A20, promoting RIPK1-dependent cell death in cerebrovascular endothelial cells.\",\n      \"method\": \"In vitro phosphorylation assay, NEK1 knockout mice, genetic epistasis (RIPK1 inactivation rescue), proteomics, Western blot\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro kinase assay demonstrating direct phosphorylation of VPS26B, plus in vivo genetic rescue\",\n      \"pmids\": [\"34376696\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Neurons are enriched with a VPS26B-organized retromer core that is differentially dedicated to endosomal recycling. VPS26B depletion impairs glutamate receptor and SORL1 recycling, selectively causing synaptic dysfunction in the trans-entorhinal cortex, a region most vulnerable in Alzheimer's disease.\",\n      \"method\": \"Mouse model imaging, VPS26B depletion (siRNA/shRNA), electrophysiology, immunocytochemistry, behavioral assays, human brain tissue analysis\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (electrophysiology, ICC, behavior, human tissue) establishing VPS26B-specific function in endosomal recycling\",\n      \"pmids\": [\"34965419\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"VPS26B acts as a novel Rab14 effector and forms a complex with SHIP164 and the ATPase RhoBTB3 at Golgi-early endosome contacts to promote early endosome bud formation. Rab14 activity regulates SHIP164 association with early endosomes. Depletion of VPS26B leads to enlarged Rab14+ early endosomes without buds, phenocopying loss of SHIP164 or RhoBTB3.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, live-cell imaging, confocal microscopy, proximity ligation assay, domain mutagenesis\",\n      \"journal\": \"Cell discovery\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods demonstrating complex formation and functional rescue experiments\",\n      \"pmids\": [\"38565878\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Vps26b forms a distinct Vps26b-Vps29-Vps35 retromer complex in mouse testis, with the Vps26b-Vps35 interaction confirmed by immunoprecipitation and pull-down assay.\",\n      \"method\": \"Co-immunoprecipitation, pull-down assay, Western blot, RT-PCR\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — direct interaction confirmed by pulldown but limited functional follow-up\",\n      \"pmids\": [\"18656452\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Acute retromer inactivation by knocksideways technology (which requires VPS26A or VPS26B for retromer function) reveals that retromer is required for cell-surface recycling of GLUT1 but not for CI-MPR retrograde sorting in HeLa and H4 cells.\",\n      \"method\": \"Knocksideways (acute inactivation), flow cytometry, immunofluorescence, quantitative microscopy\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — acute inactivation method with quantitative cargo sorting readouts, though VPS26B not individually distinguished from VPS26A\",\n      \"pmids\": [\"32747499\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Retromer (containing VPS26A or VPS26B) co-immunoprecipitates with the centriolar protein CP110 and is required for CP110 removal from the mother centriole, establishing a role for retromer in primary ciliogenesis in mammalian cells. VPS35 localizes to the primary cilium.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, immunofluorescence, ciliogenesis assay, CRISPR knockout in C. elegans\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — CoIP plus depletion phenotype, but VPS26B not individually distinguished from VPS26A in most experiments\",\n      \"pmids\": [\"35510502\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"VPS26B is a subunit of a distinct mammalian retromer complex (VPS26B-VPS29-VPS35), defined by its arrestin-like structure and binding to VPS35 through a conserved C-terminal surface patch; it acts as a Rab14 effector within a RhoBTB3-SHIP164-VPS26B complex at Golgi-endosome contacts to drive early endosome bud formation, mediates endosomal recycling of cargoes including GLUT1, glutamate receptors, and SORL1 (but not CI-M6PR or PAR-2 resensitization), is phosphorylated by NEK1 to regulate its trafficking function, and can be recruited by viral proteins to facilitate aggrephagy-based immune evasion.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"VPS26B is a component of a distinct mammalian retromer complex (VPS26B–VPS29–VPS35) that mediates endosomal cargo sorting and recycling. Its arrestin-like fold binds VPS35 through a conserved C-terminal surface patch with nanomolar affinity, competing with VPS26A for a single binding site to define two mutually exclusive retromer populations [PMID:18088321]. VPS26B-retromer preferentially supports recycling of cargoes including GLUT1, glutamate receptors, and SORL1 rather than CI-M6PR retrieval, with VPS26B depletion in neurons selectively impairing synaptic recycling in Alzheimer-vulnerable brain regions [PMID:21920005, PMID:34965419]. Independent of the canonical retromer, VPS26B acts as a Rab14 effector within a RhoBTB3–SHIP164–VPS26B complex at Golgi–endosome contacts to drive early endosome bud formation, and its trafficking function is regulated by NEK1-mediated phosphorylation [PMID:38565878, PMID:34376696].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Establishing VPS26B as a bona fide retromer subunit resolved whether VPS26 existed as a single gene or a family with distinct complex-forming capacity.\",\n      \"evidence\": \"Co-immunoprecipitation, yeast two-hybrid, subcellular fractionation, and TIRF microscopy in HeLa and A549 cells\",\n      \"pmids\": [\"16190980\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No functional cargo sorting readout was performed\",\n        \"Distinction from VPS26A in vivo was not addressed\"\n      ]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Structural determination of VPS26B revealed an arrestin-like fold and identified the C-terminal surface patch mediating VPS35 binding, showing that VPS26A and VPS26B compete for a single retromer binding site with nanomolar affinity.\",\n      \"evidence\": \"X-ray crystallography, ITC, structure-based mutagenesis, co-immunoprecipitation\",\n      \"pmids\": [\"18088321\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis for cargo selectivity differences between VPS26A and VPS26B was not resolved\",\n        \"No in vivo confirmation of competitive binding\"\n      ]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Knockout mice demonstrated that VPS26B-retromer is non-redundant with VPS26A-retromer in vivo, with loss of VPS26B leading to elevated sortilin levels and reduced VPS35 stability.\",\n      \"evidence\": \"Vps26b knockout mouse, co-immunoprecipitation, Western blot\",\n      \"pmids\": [\"21040701\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Mechanism by which VPS26B loss destabilizes VPS35 was not determined\",\n        \"Sortilin trafficking was inferred from steady-state levels, not directly measured\"\n      ]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Mapping differential cargo selectivity showed that VPS26B-retromer fails to interact with CI-M6PR—an effect dependent on the VPS26B C-terminal region—explaining why VPS26B expression promotes CI-M6PR degradation and cathepsin D secretion.\",\n      \"evidence\": \"Stable HEK293 cell lines, co-immunoprecipitation, deletion mutagenesis, cathepsin D secretion assay\",\n      \"pmids\": [\"21920005\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct structural basis for C-terminal domain–mediated cargo exclusion was not resolved\",\n        \"Whether VPS26B-retromer has unique positive cargoes beyond CI-M6PR exclusion was unclear\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Discovery that the viral protein M45 recruits VPS26B and TBC1D5 to target NEMO and RIPK1 aggregates for aggrephagy revealed an unexpected link between retromer and selective autophagy during immune evasion.\",\n      \"evidence\": \"Co-immunoprecipitation, proximity ligation assay, autophagy flux assays, siRNA knockdown in MCMV-infected cells\",\n      \"pmids\": [\"31844296\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether VPS26B participates in aggrephagy in non-viral contexts is unknown\",\n        \"Mechanism of VPS26B recruitment by M45 was not structurally defined\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Acute retromer inactivation using knocksideways technology confirmed that retromer (requiring VPS26A or VPS26B) is essential for GLUT1 cell-surface recycling but dispensable for CI-M6PR retrograde sorting, reframing the core cargo repertoire of mammalian retromer.\",\n      \"evidence\": \"Knocksideways acute inactivation, flow cytometry, quantitative microscopy in HeLa and H4 cells\",\n      \"pmids\": [\"32747499\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"VPS26B was not individually distinguished from VPS26A in this system\",\n        \"Mechanism of GLUT1 recognition by retromer was not identified\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Two studies established that VPS26B-retromer is neuronally enriched and regulated by NEK1 phosphorylation: NEK1 directly phosphorylates VPS26B to maintain endosomal trafficking, while VPS26B depletion in neurons selectively impairs glutamate receptor and SORL1 recycling, causing synaptic dysfunction in the trans-entorhinal cortex.\",\n      \"evidence\": \"In vitro kinase assay, NEK1 knockout mice with RIPK1 genetic rescue; VPS26B depletion with electrophysiology, immunocytochemistry, and human brain tissue analysis\",\n      \"pmids\": [\"34376696\", \"34965419\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Specific phosphorylation site(s) on VPS26B and their structural consequences are not fully defined\",\n        \"Whether NEK1 regulation is neuron-specific or general is unknown\",\n        \"Causal link between VPS26B-retromer dysfunction and Alzheimer's disease pathogenesis remains correlative\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identification of VPS26B as a Rab14 effector within a RhoBTB3–SHIP164–VPS26B complex at Golgi–endosome contacts revealed a retromer-independent function in driving early endosome bud formation.\",\n      \"evidence\": \"Co-immunoprecipitation, siRNA knockdown, live-cell imaging, proximity ligation assay, domain mutagenesis\",\n      \"pmids\": [\"38565878\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How VPS26B coordinates its retromer-dependent and Rab14-dependent functions is unknown\",\n        \"Whether VPS26B binds SHIP164 and VPS35 simultaneously or in mutually exclusive pools is unresolved\",\n        \"Lipid transfer activity of SHIP164 in this complex has not been functionally dissected\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include how VPS26B partitions between retromer-dependent and Rab14/SHIP164-dependent complexes, the structural basis for its distinct cargo selectivity versus VPS26A, and whether VPS26B dysfunction is causally linked to neurodegeneration.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No cryo-EM or crystal structure of a full VPS26B-retromer with cargo\",\n        \"No disease-causing mutations in VPS26B have been reported in human genetic studies\",\n        \"Dual complex membership (retromer vs. RhoBTB3–SHIP164) has not been quantified in physiological conditions\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 2, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [2, 7, 8]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [2, 3, 7, 8, 10]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [2, 3, 7]}\n    ],\n    \"complexes\": [\n      \"retromer (VPS26B-VPS29-VPS35)\",\n      \"RhoBTB3-SHIP164-VPS26B\"\n    ],\n    \"partners\": [\n      \"VPS35\",\n      \"VPS29\",\n      \"SHIP164\",\n      \"RHOBTB3\",\n      \"RAB14\",\n      \"TBC1D5\",\n      \"NEK1\",\n      \"GOLPH3\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}