{"gene":"PIK3C3","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":1993,"finding":"Yeast VPS34 encodes a phosphatidylinositol 3-kinase (PI3K) required for vacuolar protein sorting; vps34 deletion strains lack detectable PI3K activity and exhibit severe vacuolar protein sorting defects, and overexpression of Vps34p increases PI3K activity specifically precipitated with anti-Vps34p antisera.","method":"Gene deletion, overexpression, in vitro PI3K assay, immunoprecipitation","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro kinase assay with direct immunoprecipitation, replicated by multiple subsequent labs","pmids":["8385367"],"is_preprint":false},{"year":1990,"finding":"VPS34 protein (875 aa, ~95 kDa) lacks signal sequence or transmembrane domains; it is found partly in a particulate fraction solubilized by urea but not Triton X-100, indicating membrane association via protein–protein interactions; Vps34p-null cells show defects in vacuolar protein sorting and vacuole segregation to daughter cells.","method":"Gene cloning/sequencing, immunoprecipitation, cell fractionation, fluorescence microscopy of vacuoles","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (fractionation, IP, imaging) in founding paper, replicated by subsequent work","pmids":["2247081"],"is_preprint":false},{"year":2001,"finding":"Two distinct yeast Vps34 PI3K complexes exist: Complex I (Vps15p/Vps30p/Apg14p/Vps34p) required for autophagy, and Complex II (Vps15p/Vps30p/Vps38p/Vps34p) required for CPY vacuolar protein sorting; Vps30p functions as a shared subunit of both.","method":"Co-immunoprecipitation, pull-down, mass spectrometry identification of subunits, phenotypic analysis of deletion mutants","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — reciprocal Co-IP, pulldown, and genetic phenotyping in single rigorous study; foundational finding replicated extensively","pmids":["11157979"],"is_preprint":false},{"year":2005,"finding":"hVps34 is a nutrient-regulated lipid kinase required for activation of S6K1 and mTOR signaling; hVps34 is inhibited by amino acid or glucose starvation and by AMPK activation; it acts upstream of mTOR, as hVps34 knockdown inhibits phosphorylation of both S6K1 and 4EBP1.","method":"siRNA knockdown, anti-hVps34 antibody microinjection, FYVE-domain PI3P sequestration, overexpression, kinase activity assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal loss-of-function approaches (siRNA, inhibitory antibody, dominant-negative lipid sequestration) converging on same phenotype","pmids":["16049009"],"is_preprint":false},{"year":2006,"finding":"Beclin 1 co-immunoprecipitates with hVps34 in glioblastoma cells; siRNA depletion of Beclin 1 specifically blunts the autophagic response to nutrient deprivation or ceramide without affecting EGF receptor post-endocytic sorting, cathepsin D TGN-to-lysosome trafficking, or early endosomal EEA1 association, demonstrating that Beclin 1 selectively directs hVps34 into the autophagic rather than general trafficking pathway.","method":"Co-immunoprecipitation, siRNA knockdown, autophagy assays, EGFR degradation assay, fluid-phase endocytosis","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP plus multiple functional assays in a single study","pmids":["16390869"],"is_preprint":false},{"year":2006,"finding":"hVps34 siRNA knockdown causes accumulation of enlarged LAMP1-positive late endosomes depleted of PI(3)P, impairs inward vesiculation of multivesicular bodies, slows cathepsin D maturation, and delays EGFR degradation, but does not block early endocytic uptake or TGN-to-late-endosome cathepsin D traffic, identifying hVps34 as specifically required for PI(3)P generation in late endosomes/MVBs.","method":"siRNA knockdown, electron microscopy, GFP-2×FYVE PI(3)P probe, EGFR degradation assay, cathepsin D processing assay","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Moderate — siRNA knockdown with multiple orthogonal readouts (EM, lipid probe, receptor trafficking) in single study","pmids":["16522686"],"is_preprint":false},{"year":2006,"finding":"Gpa1 (Gα subunit) is present at endosomes and directly interacts with both Vps34 and Vps15 to stimulate PI3P production; Vps15 resembles a Gβ subunit (seven-WD repeat) and binds GDP-Gpa1, revealing a preformed effector–Gβ-like assembly at the endosome.","method":"Genetic epistasis screen (~5000 deletion strains), direct protein interaction assay, PI3P production measurement at endosomes","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — genome-wide epistasis plus direct interaction and lipid kinase assays in single study","pmids":["16839886"],"is_preprint":false},{"year":2008,"finding":"Amino acids trigger a rise in intracellular Ca2+ that activates hVps34 via direct binding of Ca2+/calmodulin (CaM) to an evolutionarily conserved motif in hVps34; this CaM binding is required for hVps34 lipid kinase activity and for subsequent mTOR Complex 1 activation.","method":"Ca2+ imaging, direct CaM-binding assay, lipid kinase activity assay, CaM-binding motif mutagenesis","journal":"Cell metabolism","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct binding assay with mutagenesis of CaM-binding motif plus in vitro kinase activity measurement","pmids":["18460336"],"is_preprint":false},{"year":2009,"finding":"hVps15 is required for hVps34 lipid kinase activity in mammalian cells; co-expression with hVps15 markedly increases hVps34 activity, and Beclin 1/UVRAG activation of hVps34 requires hVps15 co-expression; hVps34 activity in cells is independent of Ca2+/CaM (chelation of Ca2+ or CaM has no effect on hVps34 activity in vitro or in cells).","method":"In vitro lipid kinase assay, co-expression, BAPTA/AM treatment, EDTA/EGTA wash, W7 CaM inhibitor","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution of kinase activity with and without hVps15, with multiple CaM perturbation approaches","pmids":["18957027"],"is_preprint":false},{"year":2003,"finding":"hVPS34 and its adaptor p150 colocalize with Rab7 on late endosomes; hVPS34 PI3K activity is dependent on nucleotide cycling of Rab7; total cellular PI3P levels are modulated by Rab7 expression, identifying Rab7 as a regulator of late endosomal hVPS34 function.","method":"Co-immunoprecipitation, colocalization imaging, PI3K activity assay, Rab7 nucleotide-state mutants","journal":"Traffic","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and activity assay with Rab7 mutants, single lab","pmids":["14617358"],"is_preprint":false},{"year":2002,"finding":"Rab5-GTP promotes endosomal localization of hVps34/p150; the p150 HEAT and WD40 domains are required for Rab5 binding; p150 is required for EEA1 endosomal targeting (recombinant p150 fragments displace EEA1); however, Rab5 does not significantly recruit hVps34/p150 from cytosol to membrane, indicating Rab5 regulates localization rather than membrane recruitment.","method":"Dominant-active Rab5 expression, recombinant fragment competition, subcellular fractionation, immunofluorescence colocalization","journal":"Traffic","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple methods (fractionation, competition, imaging), single lab","pmids":["12010460"],"is_preprint":false},{"year":2003,"finding":"M. tuberculosis virulence toxin lipoarabinomannan (LAM) blocks phagosome maturation by inhibiting a Ca2+/calmodulin–hVPS34 cascade; Ca2+ and calmodulin are required for hVPS34-mediated PI3P production on phagosomes in vivo, and LAM from virulent (but not avirulent) mycobacteria blocks cytosolic Ca2+ rise to prevent PI3P generation.","method":"In vitro PI3P production assay on liposomes, in vivo phagosomal PI3P imaging, Ca2+ chelation, calmodulin inhibition","journal":"The Journal of experimental medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro and in vivo PI3P assays with Ca2+/CaM perturbation, single lab","pmids":["12925680"],"is_preprint":false},{"year":2013,"finding":"ULK1 phosphorylates Beclin 1 at Ser14 following amino acid starvation or mTOR inhibition, enhancing the lipid kinase activity of the ATG14L-containing VPS34 complex; this phosphorylation is required for full autophagic induction in mammals and C. elegans.","method":"In vitro kinase assay, site-directed mutagenesis (S14A), VPS34 complex immunoprecipitation and lipid kinase assay, C. elegans genetic rescue","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro kinase assay with mutagenesis, complex-specific activity measurement, cross-species validation","pmids":["23685627"],"is_preprint":false},{"year":2013,"finding":"MTORC1 directly phosphorylates ATG14 to inhibit the ATG14-containing PIK3C3 complex specifically; MTORC1 inactivation by nutrient starvation selectively activates the ATG14-containing (autophagy-specific) PIK3C3 complex without affecting UVRAG-containing PIK3C3 complexes.","method":"In vitro kinase assay (MTORC1 phosphorylation of ATG14), lipid kinase assay of immunopurified complexes, starvation/rapamycin treatment","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution of MTORC1→ATG14→PIK3C3 inhibition with complex-selective activity assays","pmids":["24013218"],"is_preprint":false},{"year":2013,"finding":"AMPK directly phosphorylates PIK3C3/VPS34 and BECN1 to differentially regulate PIK3C3 complexes in response to energy starvation: AMPK inhibits non-autophagic PIK3C3 complexes while activating pro-autophagic (ATG14-containing) complexes via Beclin 1 phosphorylation.","method":"In vitro kinase assay, complex-specific lipid kinase assay, phosphorylation site mapping","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro kinase assay described in review/commentary, single lab, details compressed in abstract","pmids":["23669030"],"is_preprint":false},{"year":2013,"finding":"Acetylated Hsp70 binds the Beclin 1–Vps34 complex upon autophagy-inducing stress and recruits the E3 SUMO ligase KAP1, which SUMOylates Vps34 at Lys840, increasing Vps34 lipid kinase activity; Hsp70 knockdown abolishes Beclin 1–Vps34 complex formation and prevents autophagosome formation.","method":"Co-immunoprecipitation, Vps34 SUMO modification assay, lipid kinase assay, siRNA knockdown, autophagosome formation assay in Hsp70 KO MEFs","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus SUMO modification plus functional KO MEF experiments, single lab","pmids":["23569248"],"is_preprint":false},{"year":2014,"finding":"VPS34-IN1 (25 nM IC50 in vitro) is a highly selective Vps34 inhibitor; its administration rapidly disperses PI(3)P from endosomal membranes within 1 minute; Vps34-produced PI(3)P at endosomes controls SGK3 activation by enabling PDK1-site and hydrophobic-motif phosphorylation via SGK3's PX domain; a second pool of PI(3)P from class I PI3K→PI(3,4,5)P3→PI(3)P conversion also contributes to SGK3 activity.","method":"In vitro kinase selectivity panel (340 protein kinases, 25 lipid kinases), PI(3)P probe imaging, SGK3 phosphorylation assays, PX-domain mutation","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — highly selective inhibitor characterized against broad kinase panel, multiple orthogonal methods (lipid imaging, kinase assays, domain mutants)","pmids":["25177796"],"is_preprint":false},{"year":2014,"finding":"SAR405 (KD 1.5 nM) selectively inhibits Vps34 kinase activity; its unique binding mode within the ATP-binding cleft explains selectivity; Vps34 inhibition by SAR405 disrupts late endosome–lysosome compartments and prevents autophagy.","method":"Biophysical binding assay (KD measurement), crystal structure of inhibitor-Vps34 complex, cell-based autophagy and vesicle trafficking assays","journal":"Nature chemical biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus in vitro binding plus functional cellular assays in a single study","pmids":["25326666"],"is_preprint":false},{"year":2015,"finding":"Crystal structure of the 385-kDa endosomal Vps34 complex II (PIK3C3-CII: Vps34/Vps15/Beclin1/UVRAG) at 4.4 Å reveals a Y-shaped assembly centered on the Vps34 C2 domain; Vps15 kinase domain engages the Vps34 activation loop to regulate its activity; HDX-MS identifies a Vps30/Beclin1 loop critical for complex II activity on giant liposomes but not for complex I.","method":"X-ray crystallography (4.4 Å), hydrogen-deuterium exchange mass spectrometry, liposome-based lipid kinase assay","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional HDX-MS and membrane activity assays in single rigorous study","pmids":["26450213"],"is_preprint":false},{"year":2015,"finding":"mTOR directly phosphorylates UVRAG at Ser550 and Ser571 to activate the VPS34-UVRAG complex; this activation generates a lysosomal PI(3)P pool required for autolysosomal tubulation and lysosome reformation (ALR); loss of these phosphorylation sites reduces VPS34 lipid kinase activity and causes massive cell death due to impaired ALR.","method":"In vitro mTOR kinase assay, phosphomutant UVRAG constructs, VPS34 lipid kinase assay, lysosomal tubulation imaging, cell survival assays","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro kinase assay with defined phosphosites, complex-specific activity measurement, and functional tubulation/cell death readouts","pmids":["26139536"],"is_preprint":false},{"year":2017,"finding":"VPS34 is specifically acetylated by p300 at K771 (reducing affinity for PI substrate) and K29 (hindering VPS34–Beclin 1 complex formation); p300 inhibition induces VPS34 deacetylation and autophagy even in AMPK−/−, TSC2−/−, or ULK1−/− cells, establishing p300-dependent acetylation as a direct control of VPS34 activity independent of upstream kinases.","method":"Acetyltransferase assay, acetylation site mutagenesis, in vitro lipid kinase assay, autophagy induction in triple-knockout MEFs, liver fasting model","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with mutagenesis, genetic epistasis via KO cells, and physiological validation in vivo","pmids":["28844862"],"is_preprint":false},{"year":2017,"finding":"EM and crosslinking mass spectrometry reveal five conformational substates of PI3KC3-C1; in one substate the VPS34 catalytic domain is dislodged from the complex while remaining tethered by an intrinsically disordered linker; a 'leashed' construct that prevents dislodging blocks enzyme activity in vitro and autophagy induction in yeast, identifying catalytic-domain dislodging as an allosteric switch regulated by VPS15.","method":"Electron microscopy, crosslinking mass spectrometry, in vitro lipid kinase assay, yeast genetic autophagy assay","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — structural analysis combined with mutagenesis and in vitro/in vivo functional assays in single study","pmids":["28757208"],"is_preprint":false},{"year":2021,"finding":"Cryo-electron tomography of complex II on Rab5a-GTP-decorated vesicles shows Rab5a-GTP recruits and activates complex II by binding between the VPS34 C2 domain and VPS15 WD40 domain, releasing the VPS34 kinase domain from VPS15-mediated inhibition into a catalysis-competent position; Rab1a specifically recruits and activates autophagy complex I (not complex II) via the same VPS34 interface but in a distinct manner.","method":"Electron cryotomography, hydrogen-deuterium exchange mass spectrometry, Rab GTPase mutant binding assays, in vitro lipid kinase assay on vesicles","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-ET structural data combined with HDX-MS, GTPase mutants, and activity assays on membranes in a single rigorous study","pmids":["33692360"],"is_preprint":false},{"year":2021,"finding":"ULK1/2 phosphorylates VPS15 at six sites including the major site Ser861; mutation of these sites reduces autophagosome formation in cells and VPS34 lipid kinase activity in vitro, establishing VPS15 as a ULK substrate that links ULK activity to VPS34 complex regulation.","method":"Phosphoproteomics in Ulk1/2 DKO MEFs, in vitro VPS34 lipid kinase assay with phosphomutant VPS15, autophagosome formation assays","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — phosphoproteomics discovery plus in vitro kinase reconstitution with mutagenesis in single study","pmids":["34121209"],"is_preprint":false},{"year":2010,"finding":"The Rubicon RUN domain directly interacts with the hVps34 catalytic subunit and contributes to efficient inhibition of PI3KC3 lipid kinase activity; a RUN domain deletion mutant fails to rescue autophagy deficiency in Rubicon-depleted cells.","method":"Co-immunoprecipitation, in vitro PI3K lipid kinase assay, deletion mutagenesis, siRNA complementation assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding demonstrated with domain-deletion mutants and functional lipid kinase inhibition assay, single lab","pmids":["21062745"],"is_preprint":false},{"year":2007,"finding":"The myotubularin PI3-phosphatase MTM1 directly binds the hVPS15/hVPS34 complex via the WD40 domain of hVPS15; overexpression of catalytically active (but not dead) MTM1 depletes endosomal PI(3)P; the hVPS15/hVPS34 complex forms mutually exclusive complexes with Rab5, Rab7, or MTM1, suggesting Rab GTPases and MTM1 act as molecular switches controlling PI(3)P synthesis and degradation.","method":"Co-immunoprecipitation, PI(3)P level measurement, catalytic-dead mutant controls, domain-mapping pulldown","journal":"Traffic","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP with domain mapping and catalytic-dead controls, single lab","pmids":["17651088"],"is_preprint":false},{"year":2013,"finding":"Conditional deletion of Pik3c3 in differentiated sensory neurons causes rapid neurodegeneration; large-diameter myelinated neurons accumulate enlarged vacuoles and ubiquitin aggregates while small-diameter neurons activate a non-canonical PIK3C3-independent LC3-positive autophagosome pathway still dependent on ATG7; Pik3c3/Atg7 double-mutant analysis shows the unconventional pathway requires ATG7.","method":"Conditional knockout mice (Cre-lox), electron microscopy, immunohistochemistry, Atg7 conditional KO comparison, double-mutant analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional KO with double-mutant epistasis establishing pathway position, multiple neuron-type comparisons","pmids":["20439739"],"is_preprint":false},{"year":2011,"finding":"Conditional deletion of Vps34 in T lymphocytes severely reduces T cell numbers; Vps34-deficient T cells show increased death and reduced IL-7Rα surface expression despite intact autophagy; intracellular analysis shows mislocalization of EEA1, HRS, and Vps36, preventing IL-7Rα retromer-pathway recycling to the cell surface.","method":"Conditional KO mice, flow cytometry, intracellular trafficking assays, endosomal marker localization","journal":"Journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO with defined trafficking phenotype, single lab","pmids":["22021616"],"is_preprint":false},{"year":2014,"finding":"PIK3C3 generates PI(3)P that recruits ankyrin-B (AnkB) via PtdIns(3)P binding; AnkB bridges the dynactin subunit p62 and PI(3)P-enriched organelle membranes to promote dynein-mediated fast axonal transport of synaptic vesicles, mitochondria, endosomes, and lysosomes; loss of PIK3C3 or AnkB impairs retrograde organelle transport and shortens axon tracts.","method":"AnkB knockout, PIK3C3 loss-of-function, dynactin membrane association assay, live-cell organelle transport imaging in hippocampal neurons, 3D-STORM","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO with quantitative transport assays and domain-interaction mapping, single lab","pmids":["25533844"],"is_preprint":false},{"year":2015,"finding":"FBXL20, an F-box protein whose expression is induced by p53-dependent transcription after DNA damage, ubiquitinates Vps34 (via SCF-Skp1-Cullin1 complex) for proteasomal degradation; CDK-mediated phosphorylation of Vps34 provides the signal for FBXL20-mediated ubiquitination, leading to inhibition of autophagy and receptor endocytosis.","method":"Ubiquitination assay, proteasome inhibitor treatment, CDK phosphorylation assay, FBXL20 overexpression/knockdown, autophagy and receptor endocytosis assays","journal":"Genes & development","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical ubiquitination assay combined with functional autophagy and trafficking readouts, single lab","pmids":["25593308"],"is_preprint":false},{"year":2016,"finding":"Vps34 PI(3)P on late endosomes recruits the Rab7-GAP Armus (TBC1D2) via Armus's PH domain binding to PI(3)P; in Vps34-deficient cells, Armus fails to localize to late endosomes, causing Rab7-GTP accumulation, enlarged late endosomes, impaired intraluminal vesicle formation, and defective EGFR degradation; Rab7 silencing or Armus overexpression rescues vacuolization.","method":"Vps34−/− MEFs, protein-lipid overlay and liposome-binding assays, Rab7-GTP pull-down, EGFR degradation assay, rescue experiments","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Moderate — KO cells with direct PI(3)P-binding assay and multiple rescue experiments establishing pathway: Vps34→PI(3)P→Armus→Rab7-GAP activity","pmids":["27793976"],"is_preprint":false},{"year":2017,"finding":"VPS34 promotes K63-linked ubiquitination of VPS34 by UBC-13/UEV-1/CHN-1 in C. elegans (ortholog), which stabilizes VPS34 protein; loss of this ubiquitination reduces VPS34 levels and impairs phagosome PI(3)P generation and maturation; UBE3C/TRABID reciprocally regulate K29/K48-branched ubiquitination of VPS34 targeting it to proteasomal degradation in mammals.","method":"In vitro ubiquitination assay, C. elegans genetics, VPS34 protein level measurement, phagosome maturation assay","journal":"The Journal of cell biology / Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro ubiquitination reconstitution with genetic validation in C. elegans, single lab per study","pmids":["29092895","33637724"],"is_preprint":false},{"year":2018,"finding":"ULK1 O-GlcNAcylation at Thr754 (by OGT, following PP1-mediated dephosphorylation of adjacent mTOR site Ser757 and AMPK phosphorylation) is required for ULK1 to bind and phosphorylate ATG14L, which in turn activates VPS34 lipid kinase activity for PI(3)P production and phagophore formation.","method":"O-GlcNAc modification mapping, ULK1 phosphomutants, ATG14L binding assay, VPS34 lipid kinase assay, autophagy flux assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — phosphosite and O-GlcNAc site identification with functional kinase assays, single lab","pmids":["30517873"],"is_preprint":false},{"year":2020,"finding":"Membrane physicochemical properties (degree of lipid unsaturation, negative charge, and curvature) strongly modulate VPS34 complex activity; the BATS domain of ATG14L makes autophagy complex I more active than endocytic complex II on membranes; the Beclin1 BARA domain membrane-interacting loops are critical for complex II but have minor roles for complex I.","method":"In vitro lipid kinase assays with defined liposome compositions, HDX-MS of complexes on membranes","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with defined lipid compositions and HDX-MS structural data, multiple orthogonal approaches in one study","pmids":["32602837"],"is_preprint":false},{"year":2021,"finding":"AHCYL1 senses intracellular S-adenosyl-L-homocysteine (SAH); SAH binding to the AHCYL1 C-terminus promotes binding of the AHCYL1 N-terminus to the PIK3C3 catalytic domain, inhibiting PIK3C3 and suppressing autophagy in an mTORC1-independent manner.","method":"Co-immunoprecipitation, domain-mapping pulldown, SAH-binding assay, PIK3C3 kinase activity assay, autophagy flux assay, in vivo validation","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding with domain mapping and kinase activity measurement, validated in vivo, single lab","pmids":["33993848"],"is_preprint":false},{"year":2023,"finding":"ULK1 phosphorylates LDHA at Ser196 under nutrient deprivation, increasing lactate production; lactate then lactylates Vps34 at Lys356 and Lys781 (mediated by acetyltransferase KAT5/TIP60); Vps34 lactylation enhances its association with Beclin1, Atg14L, and UVRAG and increases Vps34 lipid kinase activity to promote autophagy and endolysosomal trafficking.","method":"Lactylation site mapping, KAT5 acetyltransferase assay, co-immunoprecipitation of Vps34 complexes, VPS34 lipid kinase assay, autophagy flux assay","journal":"Science advances","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — novel PTM identified with acetyltransferase assay and kinase activity measurement, single lab","pmids":["37267363"],"is_preprint":false},{"year":2014,"finding":"NRBF2 is a specific subunit of Vps34 Complex I (with Vps34, Vps15, Beclin-1, ATG14L) but not Complex II; NRBF2 directly interacts with the Vps15 WD40 domain; NRBF2 knockdown inhibits starvation-induced autophagosome formation (GFP-LC3 puncta, LC3-II lipidation) and increases p62, establishing NRBF2 as a positive regulator of autophagy within Complex I.","method":"Co-immunoprecipitation, direct binding assay, siRNA knockdown, autophagy flux assays","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP with functional siRNA knockdown, single lab","pmids":["24785657"],"is_preprint":false},{"year":2016,"finding":"Atg38/NRBF2 uses its MIT domain to bridge Atg14 and Vps30 coiled-coil I regions within Complex I; the Atg38 C-terminal domain mediates homodimerization (2.2 Å crystal structure) and phagophore assembly site localization; one Atg38 homodimer engages a single Complex I, whereas human NRBF2 homodimer can bridge two Complex I assemblies.","method":"HDX-MS, X-ray crystallography (2.2 Å), electron microscopy, yeast genetics","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with HDX-MS and EM in single study, functional validation by yeast genetics","pmids":["27630019"],"is_preprint":false},{"year":2016,"finding":"Vps34-generated PI(3)P recruits Armus (Rab7-GAP) and is required for Rab7 inactivation during late endosome maturation; separately, C. elegans VPS-34 recruits TBC-2 (Rab5-GAP) via PI(3)P binding to inactivate RAB-5 and ensure directionality of endosome maturation.","method":"Vps34 KO MEFs, Rab7-GTP assay, C. elegans VPS-34 genetics, TBC-2 endosome localization, PH domain PI(3)P binding","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO with Rab-GTP measurement and lipid-binding domain validation, two organisms, single lab","pmids":["28455411"],"is_preprint":false},{"year":2022,"finding":"VPS34 generates PI(3)P that serves as substrate for PIKfyve to produce PI(3,5)P2; this VPS34→PIKfyve phosphoinositide cascade positively regulates the Retriever/WASH/CCC recycling pathway; PIKfyve inhibition displaces Retriever and CCC from endosomes; VPS34-dependent PI(3)P is required for initial SNX17 recruitment in this recycling pathway.","method":"VPS34 and PIKfyve inhibitors, endogenous colocalization, PI(3)P/PI(3,5)P2 assays, cargo recycling assays (integrin surface levels)","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pharmacological inhibition with multiple cargo and complex localization readouts, single lab","pmids":["35040777"],"is_preprint":false},{"year":2011,"finding":"Pik3c3 null embryos are lethal between E7.5 and E8.5 with failure of mesoderm formation and severely reduced cell proliferation; mTOR signaling is drastically reduced in null embryos, suggesting PIK3C3-dependent mTOR activation is a major contributor to early embryonic cell proliferation.","method":"Pik3c3 null mouse generation, embryo morphology, BrdU proliferation assay, mTOR signaling western blot, blastocyst culture","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with signaling readout in vivo, single lab","pmids":["21283715"],"is_preprint":false},{"year":2024,"finding":"The pro-oxidant menadione sodium bisulfite (MSB) inhibits VPS34 lipid kinase activity through oxidation of key cysteine residues, disrupting endosome identity and sorting; in a myotubular myopathy (MTM1-loss) model, dietary MSB improved muscle histology, function, and extended lifespan, consistent with VPS34 being the pathogenic kinase when its phosphatase antagonist MTM1 is absent.","method":"VPS34 kinase activity assay under oxidative conditions, cysteine oxidation mapping, MTM1-deficient mouse dietary treatment, muscle histology and functional assays","journal":"Science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical mechanism (cysteine oxidation inhibiting kinase) with in vivo therapeutic validation, single lab","pmids":["39446948"],"is_preprint":false},{"year":2015,"finding":"Disruption of the Beclin 1–ATG14L protein–protein interaction (required for VPS34 Complex I formation and localization but not Complex II) selectively inhibits autophagy without disrupting Beclin 1–UVRAG interaction or vesicle trafficking, demonstrating that Complex I and Complex II have separable functions accessible through their unique subunit interfaces.","method":"NanoBRET cellular PPI assay, VPS34 Complex I/II immunoprecipitation, autophagy assays, transferrin recycling assay","journal":"Journal of the American Chemical Society","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cellular PPI assay with complex-specific IP and functional autophagy/trafficking readouts, single lab","pmids":["32320221"],"is_preprint":false}],"current_model":"PIK3C3/VPS34 is the sole class III phosphatidylinositol 3-kinase that phosphorylates PI to PI(3)P; it obligatorily functions within at least two heterotetrameric complexes—autophagy-specific Complex I (VPS34/VPS15/Beclin1/ATG14L) and endosomal Complex II (VPS34/VPS15/Beclin1/UVRAG)—whose structures are now resolved crystallographically and by cryo-ET, and whose activities are controlled by allosteric dislodging of the VPS34 catalytic domain, Rab GTPase recruitment (Rab1a for Complex I, Rab5a for Complex II), membrane physicochemical properties, and extensive post-translational regulation including phosphorylation (by ULK1 of Beclin1-Ser14, VPS15, and ATG14L; by mTORC1 of ATG14L and UVRAG), acetylation (by p300 at K771/K29, repressing activity), lactylation (by KAT5 at K356/K781, activating), SUMOylation (KAP1-mediated at K840, activating), and ubiquitination (K63-linked stabilizing; K29/K48-branched targeting to proteasome); the PI(3)P product recruits effectors including FYVE/PX-domain proteins (EEA1, SGK3, Armus/TBC1D2) to control endosomal maturation, receptor recycling, and lysosome reformation, while its depletion arrests these trafficking events and blocks autophagosome nucleation."},"narrative":{"mechanistic_narrative":"PIK3C3/VPS34 is the catalytic class III phosphatidylinositol 3-kinase that phosphorylates phosphatidylinositol to PI(3)P, an activity first defined in yeast where Vps34 is required for vacuolar protein sorting and the protein associates with membranes through protein–protein rather than transmembrane contacts [PMID:8385367, PMID:2247081]. It functions obligatorily within heterotetrameric complexes built on the pseudokinase adaptor VPS15/p150 and the shared subunit Beclin1, partitioning into an autophagy-specific Complex I (with ATG14L) and an endosomal Complex II (with UVRAG); the identity of the fourth subunit dictates pathway specificity, with Beclin1 directing VPS34 into autophagy and the Beclin1–ATG14L interface being separable from Complex II trafficking functions [PMID:11157979, PMID:16390869, PMID:32320221]. Structural and biophysical work resolved these assemblies as Y-shaped complexes in which the VPS15 kinase domain engages the VPS34 activation loop, and catalytic-domain dislodging tethered by a disordered linker acts as an allosteric on/off switch; membrane physicochemical properties and complex-specific membrane-binding modules (ATG14L BATS, Beclin1 BARA) further tune activity [PMID:26450213, PMID:28757208, PMID:32602837]. VPS15 is also required for VPS34 lipid kinase activity in mammalian cells [PMID:18957027]. Complex activity is gated by Rab GTPases—Rab5a recruits and activates Complex II while Rab1a activates Complex I through the same VPS34 interface—and by an extensive post-translational network: ULK1 phosphorylation of Beclin1-Ser14 and VPS15-Ser861 and mTORC1/AMPK phosphorylation of ATG14L and UVRAG impose nutrient and energy control, while acetylation by p300 (repressing), SUMOylation at Lys840 (activating), KAT5-mediated lactylation (activating), and differential ubiquitination set activity and protein stability [PMID:23685627, PMID:34121209, PMID:24013218, PMID:23669030, PMID:26139536, PMID:28844862, PMID:23569248, PMID:37267363, PMID:25593308, PMID:29092895, PMID:33637724]. The PI(3)P product is read by FYVE/PX/PH-domain effectors to drive endosomal maturation and recycling—recruiting the Rab7-GAP Armus/TBC1D2, enabling SGK3 activation, ankyrin-B-mediated axonal organelle transport, and a VPS34→PIKfyve cascade feeding the Retriever/WASH/CCC recycling pathway—so that VPS34 loss enlarges late endosomes, blocks MVB vesiculation and receptor degradation, and arrests autophagosome nucleation [PMID:16522686, PMID:25177796, PMID:25533844, PMID:27793976, PMID:35040777]. VPS34 is essential for mouse development and tissue homeostasis, with deletion causing early embryonic lethality and rapid neurodegeneration, and its dysregulation underlies muscle pathology when its phosphatase antagonist MTM1 is lost [PMID:21283715, PMID:20439739, PMID:39446948].","teleology":[{"year":1993,"claim":"Established that VPS34 is itself a PI 3-kinase and links that catalytic activity to a specific cellular process—vacuolar protein sorting—answering what the gene product enzymatically does.","evidence":"Yeast vps34 deletion, overexpression, in vitro PI3K assay, and immunoprecipitation","pmids":["8385367","2247081"],"confidence":"High","gaps":["Did not define mammalian substrate specificity or product (PI(3)P) in cells","No partner subunits identified at this stage"]},{"year":2001,"claim":"Resolved how one kinase serves two pathways by showing Vps34 partitions into two distinct complexes that share Vps15/Vps30 but differ in a fourth subunit dictating autophagy vs. CPY sorting.","evidence":"Reciprocal Co-IP, pull-down, MS subunit identification, and deletion phenotyping in yeast","pmids":["11157979"],"confidence":"High","gaps":["Mammalian orthologs of the complexes not yet defined","Mechanism of fourth-subunit pathway routing unknown"]},{"year":2003,"claim":"Connected mammalian hVPS34 to endosomal localization and showed Rab GTPase nucleotide cycling controls its lipid kinase output, framing Rabs as upstream regulators.","evidence":"Co-IP, colocalization, PI3K activity assays with Rab5/Rab7 nucleotide-state mutants","pmids":["12010460","14617358"],"confidence":"Medium","gaps":["Whether Rabs recruit vs. activate the complex was ambiguous (Rab5 did not recruit from cytosol)","Structural basis of Rab–VPS34 interaction unknown"]},{"year":2005,"claim":"Positioned hVPS34 as a nutrient sensor acting upstream of mTOR/S6K1, expanding its role beyond trafficking into growth signaling.","evidence":"siRNA knockdown, inhibitory antibody microinjection, FYVE-domain PI(3)P sequestration, kinase assays","pmids":["16049009"],"confidence":"High","gaps":["Molecular link from VPS34 PI(3)P to mTOR activation not defined","Did not establish which complex mediates the mTOR effect"]},{"year":2006,"claim":"Defined Beclin1 as the molecular switch routing hVps34 into autophagy versus general endosomal trafficking, and pinpointed late endosomes/MVBs as the site of VPS34-dependent PI(3)P.","evidence":"Reciprocal Co-IP, siRNA, autophagy/EGFR degradation/cathepsin D assays, EM, GFP-2×FYVE probe","pmids":["16390869","16522686","16839886"],"confidence":"High","gaps":["Did not resolve how Beclin1 selects ATG14L vs UVRAG partners","Effector proteins reading the PI(3)P pool not yet identified"]},{"year":2008,"claim":"Tested how amino acids activate the kinase, identifying Ca2+/calmodulin binding to a conserved motif as a direct activating input feeding mTORC1.","evidence":"Ca2+ imaging, direct CaM-binding assay, CaM-motif mutagenesis, lipid kinase assays","pmids":["18460336","12925680"],"confidence":"High","gaps":["A subsequent study found cellular VPS34 activity Ca2+/CaM-independent (#8), leaving the physiological role of CaM binding contested","Context dependence (phagosome vs. cytosolic VPS34) not reconciled"]},{"year":2009,"claim":"Established VPS15 as an obligatory activator of mammalian VPS34 lipid kinase activity required for Beclin1/UVRAG-dependent stimulation.","evidence":"In vitro reconstitution with/without hVPS15, BAPTA/EGTA/W7 CaM perturbations","pmids":["18957027"],"confidence":"High","gaps":["Structural mechanism of VPS15 activation not resolved","Apparent conflict with Ca2+/CaM model left open"]},{"year":2010,"claim":"Identified negative regulation of the complex by Rubicon, which binds the VPS34 catalytic subunit to suppress lipid kinase activity.","evidence":"Co-IP, in vitro PI3K assay, RUN-domain deletion, siRNA complementation","pmids":["21062745"],"confidence":"Medium","gaps":["Single lab; structural basis of inhibition undefined","Complex-selectivity of Rubicon inhibition not fully mapped"]},{"year":2011,"claim":"Demonstrated that VPS34 is essential at the organismal level—for early embryonic proliferation/mesoderm formation and for T-cell endosomal receptor recycling—linking its biochemistry to physiology.","evidence":"Pik3c3 null embryos with mTOR readout; conditional T-cell KO with IL-7Rα trafficking and EEA1/HRS localization","pmids":["21283715","22021616"],"confidence":"Medium","gaps":["Whether embryonic lethality reflects autophagy vs. trafficking vs. mTOR loss not dissected","Cell-type-specific complex usage unresolved"]},{"year":2013,"claim":"Resolved how nutrient/energy signals are transduced onto specific complexes: ULK1 phosphorylates Beclin1-Ser14 to activate the ATG14L complex, while mTORC1 and AMPK phosphorylate ATG14/Beclin1 to selectively gate the autophagic versus non-autophagic complexes.","evidence":"In vitro kinase assays, phosphomutants, complex-specific lipid kinase assays, C. elegans rescue","pmids":["23685627","24013218","23669030","23569248"],"confidence":"High","gaps":["Quantitative integration of opposing kinase inputs on the same complex not modeled","AMPK→VPS34 details compressed in commentary (#14)"]},{"year":2014,"claim":"Delivered selective chemical tools (VPS34-IN1) and downstream effector logic, showing endosomal PI(3)P controls SGK3 activation and ankyrin-B-mediated axonal organelle transport, and defining NRBF2 as a Complex I-specific positive subunit.","evidence":"Selective inhibitor + PI(3)P probe imaging and SGK3/PX-domain assays; AnkB/dynactin transport imaging; NRBF2 Co-IP/binding and autophagy flux","pmids":["25177796","25533844","24785657"],"confidence":"High","gaps":["Dual PI(3)P pools (class I- vs class III-derived) complicate effector attribution","NRBF2 stoichiometry within Complex I not yet defined at this stage"]},{"year":2015,"claim":"Provided the first structure of the endosomal complex and extended PTM control, showing mTOR-UVRAG phosphorylation drives lysosomal PI(3)P for autolysosome reformation, FBXL20 ubiquitination couples DNA-damage/p53 to VPS34 degradation, and Complex I/II functions are separable through their unique interfaces.","evidence":"X-ray crystallography (4.4 Å) + HDX-MS; mTOR/UVRAG phosphomutants with tubulation/cell-death assays; ubiquitination assays; NanoBRET PPI dissection","pmids":["26450213","26139536","25593308","32320221"],"confidence":"High","gaps":["Low-resolution structure limited atomic detail of the active site","How distinct phospho-inputs converge structurally not resolved"]},{"year":2016,"claim":"Defined the effector axis controlling endosome maturation directionality, with VPS34-generated PI(3)P recruiting Rab-GAPs (Armus/TBC1D2 for Rab7; TBC-2 for Rab5) to enforce ordered conversion of endosomal Rab identity.","evidence":"Vps34-/- MEFs, protein-lipid overlay/liposome binding, Rab-GTP pull-downs, EGFR degradation, rescue, C. elegans genetics","pmids":["27793976","28455411"],"confidence":"High","gaps":["Temporal coordination of opposing Rab-GAP recruitment not resolved","Generality across cell types untested"]},{"year":2017,"claim":"Established acetylation as a direct, kinase-independent control node and identified the allosteric mechanism of activation—VPS15-regulated dislodging of the VPS34 catalytic domain—plus ubiquitin-dependent stability control.","evidence":"p300 acetyltransferase assays in triple-KO MEFs and liver fasting; EM/XL-MS with leashed-construct functional tests; in vitro ubiquitination + C. elegans genetics","pmids":["28844862","28757208","29092895"],"confidence":"High","gaps":["How acetylation and dislodging interface mechanistically not connected","In vivo dynamics of the dislodging switch unmeasured"]},{"year":2018,"claim":"Extended upstream control to glycosylation, showing ULK1 O-GlcNAcylation is required for ULK1 to bind/phosphorylate ATG14L and thereby activate VPS34.","evidence":"O-GlcNAc/phosphosite mapping, ULK1 mutants, ATG14L binding and VPS34 lipid kinase assays","pmids":["30517873"],"confidence":"Medium","gaps":["Single lab; indirect (acts via ULK1) rather than on VPS34 itself","Physiological signal driving OGT activity here undefined"]},{"year":2020,"claim":"Demonstrated that membrane physicochemistry, not just protein inputs, tunes activity, with complex-specific membrane modules giving Complex I and II distinct membrane preferences.","evidence":"In vitro lipid kinase assays on defined liposomes plus HDX-MS of complexes on membranes","pmids":["32602837"],"confidence":"High","gaps":["In-cell membrane environments controlling each complex not mapped","Coupling of membrane sensing to Rab/PTM inputs unresolved"]},{"year":2021,"claim":"Resolved how Rabs activate the complex on membranes—Rab5a-GTP binds between the VPS34 C2 and VPS15 WD40 domains to release the kinase domain, while Rab1a activates Complex I via the same interface—and added VPS15-Ser861 as a ULK substrate.","evidence":"Cryo-ET on Rab-decorated vesicles + HDX-MS + Rab mutants/activity assays; phosphoproteomics with VPS15 phosphomutant reconstitution","pmids":["33692360","34121209"],"confidence":"High","gaps":["How Rab1a vs Rab5a achieve complex-selectivity through one interface not fully explained","Integration with catalytic-domain dislodging model incomplete"]},{"year":2021,"claim":"Identified metabolite-sensing inhibition via AHCYL1, which on binding S-adenosylhomocysteine engages the VPS34 catalytic domain to suppress autophagy independently of mTORC1.","evidence":"Co-IP, domain mapping, SAH-binding and PIK3C3 kinase assays, autophagy flux, in vivo validation","pmids":["33993848"],"confidence":"Medium","gaps":["Single lab; structural basis of inhibition undefined","Physiological contexts where SAH gates VPS34 not delineated"]},{"year":2023,"claim":"Added lactate-driven activation, with ULK1→LDHA-derived lactate enabling KAT5-mediated VPS34 lactylation that boosts complex assembly and lipid kinase activity.","evidence":"Lactylation site mapping, KAT5 acetyltransferase assay, complex Co-IP, lipid kinase and autophagy flux assays","pmids":["37267363"],"confidence":"Medium","gaps":["Single lab; abundance/stoichiometry of lactylation in vivo unknown","Interplay with competing acetylation at nearby lysines unresolved"]},{"year":2024,"claim":"Linked VPS34 redox sensitivity to disease, showing cysteine oxidation inhibits its kinase activity and that pharmacological VPS34 inhibition rescues MTM1-loss myopathy, defining VPS34 as the pathogenic kinase opposed by phosphatase MTM1.","evidence":"VPS34 kinase assay under oxidation, cysteine mapping, MTM1-deficient mouse dietary treatment with muscle phenotyping","pmids":["39446948"],"confidence":"Medium","gaps":["Single lab; selectivity of MSB beyond VPS34 not fully excluded","Whether physiological oxidative signals regulate VPS34 in vivo untested"]},{"year":null,"claim":"How the many convergent inputs—Rab recruitment, catalytic-domain dislodging, membrane physicochemistry, and the dense, sometimes opposing PTM code—are quantitatively integrated to set VPS34 output at a given membrane in real time remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model reconciling Ca2+/CaM vs CaM-independent activation","Atomic-resolution active complex on native membranes not yet resolved","Spatiotemporal regulation distinguishing Complex I vs II in cells incompletely defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140097","term_label":"catalytic activity, acting on DNA","supporting_discovery_ids":[0,16]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,8]},{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[16,17]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[5,9,10,30]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[17,19]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,10]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[2,4,12,26]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[5,27,30,39]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3,16]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[0,1,27]}],"complexes":["PI3KC3 Complex I (VPS34/VPS15/Beclin1/ATG14L)","PI3KC3 Complex II (VPS34/VPS15/Beclin1/UVRAG)"],"partners":["PIK3R4/VPS15","BECN1","ATG14","UVRAG","NRBF2","RUBCN","MTM1","AHCYL1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8NEB9","full_name":"Phosphatidylinositol 3-kinase catalytic subunit type 3","aliases":["Phosphatidylinositol 3-kinase p100 subunit","Phosphoinositide-3-kinase class 3","hVps34"],"length_aa":887,"mass_kda":101.5,"function":"Catalytic subunit of the PI3K complex that mediates formation of phosphatidylinositol 3-phosphate; different complex forms are believed to play a role in multiple membrane trafficking pathways: PI3KC3-C1 is involved in initiation of autophagosomes and PI3KC3-C2 in maturation of autophagosomes and endocytosis (PubMed:14617358, PubMed:33637724, PubMed:7628435). As part of PI3KC3-C1, promotes endoplasmic reticulum membrane curvature formation prior to vesicle budding (PubMed:32690950). Involved in regulation of degradative endocytic trafficking and required for the abscission step in cytokinesis, probably in the context of PI3KC3-C2 (PubMed:20208530, PubMed:20643123). Involved in the transport of lysosomal enzyme precursors to lysosomes (By similarity). Required for transport from early to late endosomes (By similarity) (Microbial infection) Kinase activity is required for SARS coronavirus-2/SARS-CoV-2 replication","subcellular_location":"Midbody; Late endosome; Cytoplasmic vesicle, autophagosome","url":"https://www.uniprot.org/uniprotkb/Q8NEB9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/PIK3C3","classification":"Common Essential","n_dependent_lines":922,"n_total_lines":1208,"dependency_fraction":0.7632450331125827},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000078142","cell_line_id":"CID000168","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"vesicles","grade":2}],"interactors":[{"gene":"ATG14","stoichiometry":10.0},{"gene":"BECN1","stoichiometry":10.0},{"gene":"PIK3R4","stoichiometry":10.0},{"gene":"UVRAG","stoichiometry":10.0},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"CSNK2A1","stoichiometry":0.2},{"gene":"CSNK2A2","stoichiometry":0.2},{"gene":"KIAA0226","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000168","total_profiled":1310},"omim":[{"mim_id":"618990","title":"EVA1 HOMOLOG A, REGULATOR OF PROGRAMMED CELL DEATH; EVA1A","url":"https://www.omim.org/entry/618990"},{"mim_id":"617679","title":"KELCH-LIKE 20; KLHL20","url":"https://www.omim.org/entry/617679"},{"mim_id":"616477","title":"NUCLEAR RECEPTOR-BINDING FACTOR 2; NRBF2","url":"https://www.omim.org/entry/616477"},{"mim_id":"615687","title":"BECLIN 2; BECN2","url":"https://www.omim.org/entry/615687"},{"mim_id":"613516","title":"RUN DOMAIN- AND CYSTEINE-RICH DOMAIN-CONTAINING BECLIN-1-INTERACTING PROTEIN; RUBCN","url":"https://www.omim.org/entry/613516"}],"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/PIK3C3"},"hgnc":{"alias_symbol":["Vps34","hVps34"],"prev_symbol":[]},"alphafold":{"accession":"Q8NEB9","domains":[{"cath_id":"2.60.40.150","chopping":"8-163_172-233","consensus_level":"high","plddt":85.4363,"start":8,"end":233},{"cath_id":"1.10.1070.11","chopping":"682-882","consensus_level":"high","plddt":89.3063,"start":682,"end":882}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NEB9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NEB9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NEB9-F1-predicted_aligned_error_v6.png","plddt_mean":83.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PIK3C3","jax_strain_url":"https://www.jax.org/strain/search?query=PIK3C3"},"sequence":{"accession":"Q8NEB9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8NEB9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8NEB9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NEB9"}},"corpus_meta":[{"pmid":"23685627","id":"PMC_23685627","title":"ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase.","date":"2013","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/23685627","citation_count":1303,"is_preprint":false},{"pmid":"8385367","id":"PMC_8385367","title":"Phosphatidylinositol 3-kinase encoded by yeast VPS34 gene essential for protein sorting.","date":"1993","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/8385367","citation_count":871,"is_preprint":false},{"pmid":"11157979","id":"PMC_11157979","title":"Two distinct Vps34 phosphatidylinositol 3-kinase complexes function in autophagy and carboxypeptidase Y sorting in Saccharomyces cerevisiae.","date":"2001","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/11157979","citation_count":846,"is_preprint":false},{"pmid":"20356743","id":"PMC_20356743","title":"The Beclin 1-VPS34 complex--at the crossroads of autophagy and beyond.","date":"2010","source":"Trends in cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/20356743","citation_count":649,"is_preprint":false},{"pmid":"18215151","id":"PMC_18215151","title":"The regulation and function of Class III PI3Ks: novel roles for Vps34.","date":"2008","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/18215151","citation_count":524,"is_preprint":false},{"pmid":"16049009","id":"PMC_16049009","title":"hVps34 is a nutrient-regulated lipid kinase required for activation of p70 S6 kinase.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16049009","citation_count":432,"is_preprint":false},{"pmid":"25326666","id":"PMC_25326666","title":"A highly potent and selective Vps34 inhibitor alters vesicle trafficking and autophagy.","date":"2014","source":"Nature chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/25326666","citation_count":403,"is_preprint":false},{"pmid":"2247081","id":"PMC_2247081","title":"Characterization of VPS34, a gene required for vacuolar protein sorting and vacuole segregation in Saccharomyces cerevisiae.","date":"1990","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/2247081","citation_count":384,"is_preprint":false},{"pmid":"16390869","id":"PMC_16390869","title":"Functional specificity of the mammalian Beclin-Vps34 PI 3-kinase complex in macroautophagy versus endocytosis and lysosomal enzyme trafficking.","date":"2006","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/16390869","citation_count":296,"is_preprint":false},{"pmid":"18460336","id":"PMC_18460336","title":"Amino acids activate mTOR complex 1 via Ca2+/CaM signaling to hVps34.","date":"2008","source":"Cell metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/18460336","citation_count":295,"is_preprint":false},{"pmid":"12925680","id":"PMC_12925680","title":"Tuberculosis toxin blocking phagosome maturation inhibits a novel Ca2+/calmodulin-PI3K hVPS34 cascade.","date":"2003","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/12925680","citation_count":258,"is_preprint":false},{"pmid":"25177796","id":"PMC_25177796","title":"Characterization of VPS34-IN1, a selective inhibitor of Vps34, reveals that the phosphatidylinositol 3-phosphate-binding SGK3 protein kinase is a downstream target of class III phosphoinositide 3-kinase.","date":"2014","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/25177796","citation_count":258,"is_preprint":false},{"pmid":"24013218","id":"PMC_24013218","title":"Regulation of PIK3C3/VPS34 complexes by MTOR in nutrient stress-induced autophagy.","date":"2013","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/24013218","citation_count":229,"is_preprint":false},{"pmid":"32494661","id":"PMC_32494661","title":"Inhibition of Vps34 reprograms cold into hot inflamed tumors and improves anti-PD-1/PD-L1 immunotherapy.","date":"2020","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/32494661","citation_count":217,"is_preprint":false},{"pmid":"20439739","id":"PMC_20439739","title":"Deletion of PIK3C3/Vps34 in sensory neurons causes rapid neurodegeneration by disrupting the endosomal but not the autophagic pathway.","date":"2010","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/20439739","citation_count":205,"is_preprint":false},{"pmid":"37267363","id":"PMC_37267363","title":"ULK1-mediated metabolic reprogramming regulates Vps34 lipid kinase activity by its lactylation.","date":"2023","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/37267363","citation_count":202,"is_preprint":false},{"pmid":"26450213","id":"PMC_26450213","title":"Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes.","date":"2015","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/26450213","citation_count":196,"is_preprint":false},{"pmid":"27470591","id":"PMC_27470591","title":"The intricate regulation and complex functions of the Class III phosphoinositide 3-kinase Vps34.","date":"2016","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/27470591","citation_count":194,"is_preprint":false},{"pmid":"16839886","id":"PMC_16839886","title":"Activation of the phosphatidylinositol 3-kinase Vps34 by a G protein alpha subunit at the endosome.","date":"2006","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/16839886","citation_count":189,"is_preprint":false},{"pmid":"23569248","id":"PMC_23569248","title":"Acetylated hsp70 and KAP1-mediated Vps34 SUMOylation is required for autophagosome creation in autophagy.","date":"2013","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/23569248","citation_count":172,"is_preprint":false},{"pmid":"12010460","id":"PMC_12010460","title":"Role of Rab5 in the recruitment of hVps34/p150 to the early endosome.","date":"2002","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/12010460","citation_count":160,"is_preprint":false},{"pmid":"20634405","id":"PMC_20634405","title":"The epidermal growth factor receptor antibody cetuximab induces autophagy in cancer cells by downregulating HIF-1alpha and Bcl-2 and activating the beclin 1/hVps34 complex.","date":"2010","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/20634405","citation_count":156,"is_preprint":false},{"pmid":"25905679","id":"PMC_25905679","title":"SAR405, a PIK3C3/Vps34 inhibitor that prevents autophagy and synergizes with MTOR inhibition in tumor cells.","date":"2015","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/25905679","citation_count":152,"is_preprint":false},{"pmid":"9852157","id":"PMC_9852157","title":"Distinct roles for the p110alpha and hVPS34 phosphatidylinositol 3'-kinases in vesicular trafficking, regulation of the actin cytoskeleton, and mitogenesis.","date":"1998","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/9852157","citation_count":142,"is_preprint":false},{"pmid":"14617358","id":"PMC_14617358","title":"Human VPS34 and p150 are Rab7 interacting partners.","date":"2003","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/14617358","citation_count":140,"is_preprint":false},{"pmid":"21835792","id":"PMC_21835792","title":"Rab5 and class III phosphoinositide 3-kinase Vps34 are involved in hepatitis C virus NS4B-induced autophagy.","date":"2011","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/21835792","citation_count":139,"is_preprint":false},{"pmid":"26565689","id":"PMC_26565689","title":"MTOR, PIK3C3, and autophagy: Signaling the beginning from the end.","date":"2015","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/26565689","citation_count":135,"is_preprint":false},{"pmid":"28844862","id":"PMC_28844862","title":"VPS34 Acetylation Controls Its Lipid Kinase Activity and the Initiation of Canonical and Non-canonical Autophagy.","date":"2017","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/28844862","citation_count":128,"is_preprint":false},{"pmid":"26139536","id":"PMC_26139536","title":"mTOR activates the VPS34-UVRAG complex to regulate autolysosomal tubulation and cell survival.","date":"2015","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/26139536","citation_count":127,"is_preprint":false},{"pmid":"21062745","id":"PMC_21062745","title":"The RUN domain of rubicon is important for hVps34 binding, lipid kinase inhibition, and autophagy suppression.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21062745","citation_count":116,"is_preprint":false},{"pmid":"30397185","id":"PMC_30397185","title":"VPS34 complexes from a structural perspective.","date":"2018","source":"Journal of lipid research","url":"https://pubmed.ncbi.nlm.nih.gov/30397185","citation_count":115,"is_preprint":false},{"pmid":"33664238","id":"PMC_33664238","title":"SRSF1 inhibits autophagy through regulating Bcl-x splicing and interacting with PIK3C3 in lung cancer.","date":"2021","source":"Signal transduction and targeted therapy","url":"https://pubmed.ncbi.nlm.nih.gov/33664238","citation_count":98,"is_preprint":false},{"pmid":"33692360","id":"PMC_33692360","title":"Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33692360","citation_count":97,"is_preprint":false},{"pmid":"34320401","id":"PMC_34320401","title":"Inhibitors of VPS34 and fatty-acid metabolism suppress SARS-CoV-2 replication.","date":"2021","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/34320401","citation_count":96,"is_preprint":false},{"pmid":"28757208","id":"PMC_28757208","title":"Vps34 Kinase Domain Dynamics Regulate the Autophagic PI 3-Kinase Complex.","date":"2017","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/28757208","citation_count":93,"is_preprint":false},{"pmid":"16522686","id":"PMC_16522686","title":"Gene silencing reveals a specific function of hVps34 phosphatidylinositol 3-kinase in late versus early endosomes.","date":"2006","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/16522686","citation_count":92,"is_preprint":false},{"pmid":"17321123","id":"PMC_17321123","title":"hvps34, an ancient player, enters a growing game: mTOR Complex1/S6K1 signaling.","date":"2007","source":"Current opinion in cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/17321123","citation_count":91,"is_preprint":false},{"pmid":"18957027","id":"PMC_18957027","title":"hVps15, but not Ca2+/CaM, is required for the activity and regulation of hVps34 in mammalian cells.","date":"2009","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/18957027","citation_count":83,"is_preprint":false},{"pmid":"12186856","id":"PMC_12186856","title":"Novel PtdIns(3)P-binding protein Etf1 functions as an effector of the Vps34 PtdIns 3-kinase in autophagy.","date":"2002","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/12186856","citation_count":83,"is_preprint":false},{"pmid":"21283715","id":"PMC_21283715","title":"The mammalian class 3 PI3K (PIK3C3) is required for early embryogenesis and cell proliferation.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21283715","citation_count":80,"is_preprint":false},{"pmid":"22021616","id":"PMC_22021616","title":"The class III kinase Vps34 promotes T lymphocyte survival through regulating IL-7Rα surface expression.","date":"2011","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/22021616","citation_count":77,"is_preprint":false},{"pmid":"30517873","id":"PMC_30517873","title":"ULK1 O-GlcNAcylation Is Crucial for Activating VPS34 via ATG14L during Autophagy Initiation.","date":"2018","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/30517873","citation_count":75,"is_preprint":false},{"pmid":"25533844","id":"PMC_25533844","title":"A PIK3C3-ankyrin-B-dynactin pathway promotes axonal growth and multiorganelle transport.","date":"2014","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/25533844","citation_count":74,"is_preprint":false},{"pmid":"33637724","id":"PMC_33637724","title":"VPS34 K29/K48 branched ubiquitination governed by UBE3C and TRABID regulates autophagy, proteostasis and liver metabolism.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33637724","citation_count":73,"is_preprint":false},{"pmid":"17651088","id":"PMC_17651088","title":"Myotubularin lipid phosphatase binds the hVPS15/hVPS34 lipid kinase complex on endosomes.","date":"2007","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/17651088","citation_count":71,"is_preprint":false},{"pmid":"27481935","id":"PMC_27481935","title":"The hVps34-SGK3 pathway alleviates sustained PI3K/Akt inhibition by stimulating mTORC1 and tumour growth.","date":"2016","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/27481935","citation_count":68,"is_preprint":false},{"pmid":"27793976","id":"PMC_27793976","title":"Vps34 regulates Rab7 and late endocytic trafficking through recruitment of the GTPase-activating protein Armus.","date":"2016","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/27793976","citation_count":68,"is_preprint":false},{"pmid":"25593308","id":"PMC_25593308","title":"FBXL20-mediated Vps34 ubiquitination as a p53 controlled checkpoint in regulating autophagy and receptor degradation.","date":"2015","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/25593308","citation_count":68,"is_preprint":false},{"pmid":"29180704","id":"PMC_29180704","title":"Vps34 PI 3-kinase inactivation enhances insulin sensitivity through reprogramming of mitochondrial metabolism.","date":"2017","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/29180704","citation_count":67,"is_preprint":false},{"pmid":"24785657","id":"PMC_24785657","title":"NRBF2 regulates macroautophagy as a component of Vps34 Complex I.","date":"2014","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/24785657","citation_count":67,"is_preprint":false},{"pmid":"32268825","id":"PMC_32268825","title":"Autophagy-related protein PIK3C3/VPS34 controls T cell metabolism and function.","date":"2020","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/32268825","citation_count":66,"is_preprint":false},{"pmid":"28716903","id":"PMC_28716903","title":"Autophagy-related protein Vps34 controls the homeostasis and function of antigen cross-presenting CD8α+ dendritic cells.","date":"2017","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/28716903","citation_count":66,"is_preprint":false},{"pmid":"33661763","id":"PMC_33661763","title":"Macrophage SR-BI modulates autophagy via VPS34 complex and PPARα transcription of Tfeb in atherosclerosis.","date":"2021","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/33661763","citation_count":65,"is_preprint":false},{"pmid":"28846113","id":"PMC_28846113","title":"VPS34 stimulation of p62 phosphorylation for cancer progression.","date":"2017","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/28846113","citation_count":63,"is_preprint":false},{"pmid":"24980960","id":"PMC_24980960","title":"Dapper1 promotes autophagy by enhancing the Beclin1-Vps34-Atg14L complex formation.","date":"2014","source":"Cell research","url":"https://pubmed.ncbi.nlm.nih.gov/24980960","citation_count":63,"is_preprint":false},{"pmid":"31941925","id":"PMC_31941925","title":"PI3KC2α-dependent and VPS34-independent generation of PI3P controls primary cilium-mediated autophagy in response to shear stress.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/31941925","citation_count":62,"is_preprint":false},{"pmid":"27630019","id":"PMC_27630019","title":"Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex.","date":"2016","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/27630019","citation_count":54,"is_preprint":false},{"pmid":"32320221","id":"PMC_32320221","title":"Beclin 1-ATG14L Protein-Protein Interaction Inhibitor Selectively Inhibits Autophagy through Disruption of VPS34 Complex I.","date":"2020","source":"Journal of the American Chemical Society","url":"https://pubmed.ncbi.nlm.nih.gov/32320221","citation_count":53,"is_preprint":false},{"pmid":"30625229","id":"PMC_30625229","title":"Recruitment of Vps34 PI3K and enrichment of PI3P phosphoinositide in the viral replication compartment is crucial for replication of a positive-strand RNA virus.","date":"2019","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/30625229","citation_count":53,"is_preprint":false},{"pmid":"32044640","id":"PMC_32044640","title":"Arsenic induces dysfunctional autophagy via dual regulation of mTOR pathway and Beclin1-Vps34/PI3K complex in MLTC-1 cells.","date":"2020","source":"Journal of hazardous materials","url":"https://pubmed.ncbi.nlm.nih.gov/32044640","citation_count":52,"is_preprint":false},{"pmid":"34121209","id":"PMC_34121209","title":"Phosphoproteomic identification of ULK substrates reveals VPS15-dependent ULK/VPS34 interplay in the regulation of autophagy.","date":"2021","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/34121209","citation_count":52,"is_preprint":false},{"pmid":"34831348","id":"PMC_34831348","title":"Activation Mechanisms of the VPS34 Complexes.","date":"2021","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/34831348","citation_count":47,"is_preprint":false},{"pmid":"17319803","id":"PMC_17319803","title":"Phosphoinositide-regulated retrograde transport of ricin: crosstalk between hVps34 and sorting nexins.","date":"2007","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/17319803","citation_count":47,"is_preprint":false},{"pmid":"29222162","id":"PMC_29222162","title":"Dual Inhibition of PIK3C3 and FGFR as a New Therapeutic Approach to Treat Bladder Cancer.","date":"2017","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/29222162","citation_count":47,"is_preprint":false},{"pmid":"35040777","id":"PMC_35040777","title":"Lipid kinases VPS34 and PIKfyve coordinate a phosphoinositide cascade to regulate retriever-mediated recycling on endosomes.","date":"2022","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/35040777","citation_count":44,"is_preprint":false},{"pmid":"28455411","id":"PMC_28455411","title":"The VPS34 PI3K negatively regulates RAB-5 during endosome maturation.","date":"2017","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/28455411","citation_count":43,"is_preprint":false},{"pmid":"20955765","id":"PMC_20955765","title":"Pik3c3 deletion in pyramidal neurons results in loss of synapses, extensive gliosis and progressive neurodegeneration.","date":"2010","source":"Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/20955765","citation_count":43,"is_preprint":false},{"pmid":"25006588","id":"PMC_25006588","title":"Atg6/UVRAG/Vps34-containing lipid kinase complex is required for receptor downregulation through endolysosomal degradation and epithelial polarity during Drosophila wing development.","date":"2014","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/25006588","citation_count":41,"is_preprint":false},{"pmid":"31113939","id":"PMC_31113939","title":"MeHg-induced autophagy via JNK/Vps34 complex pathway promotes autophagosome accumulation and neuronal cell death.","date":"2019","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/31113939","citation_count":39,"is_preprint":false},{"pmid":"33093450","id":"PMC_33093450","title":"Antileukemic activity of the VPS34-IN1 inhibitor in acute myeloid leukemia.","date":"2020","source":"Oncogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/33093450","citation_count":38,"is_preprint":false},{"pmid":"39446948","id":"PMC_39446948","title":"Dietary pro-oxidant therapy by a vitamin K precursor targets PI 3-kinase VPS34 function.","date":"2024","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/39446948","citation_count":36,"is_preprint":false},{"pmid":"32602837","id":"PMC_32602837","title":"Membrane characteristics tune activities of endosomal and autophagic human VPS34 complexes.","date":"2020","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/32602837","citation_count":36,"is_preprint":false},{"pmid":"32513919","id":"PMC_32513919","title":"PIK3C3 regulates the expansion of liver CSCs and PIK3C3 inhibition counteracts liver cancer stem cell activity induced by PI3K inhibitor.","date":"2020","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/32513919","citation_count":35,"is_preprint":false},{"pmid":"32892693","id":"PMC_32892693","title":"Lighting up the fire in cold tumors to improve cancer immunotherapy by blocking the activity of the autophagy-related protein PIK3C3/VPS34.","date":"2020","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/32892693","citation_count":33,"is_preprint":false},{"pmid":"29092895","id":"PMC_29092895","title":"Ubiquitination of the PI3-kinase VPS-34 promotes VPS-34 stability and phagosome maturation.","date":"2017","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/29092895","citation_count":33,"is_preprint":false},{"pmid":"23669030","id":"PMC_23669030","title":"AMPK connects energy stress to PIK3C3/VPS34 regulation.","date":"2013","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/23669030","citation_count":31,"is_preprint":false},{"pmid":"31885313","id":"PMC_31885313","title":"Binding of Avibirnavirus VP3 to the PIK3C3-PDPK1 complex inhibits autophagy by activating the AKT-MTOR pathway.","date":"2019","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/31885313","citation_count":31,"is_preprint":false},{"pmid":"34870550","id":"PMC_34870550","title":"Adaptor SH3BGRL drives autophagy-mediated chemoresistance through promoting PIK3C3 translation and ATG12 stability in breast cancers.","date":"2021","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/34870550","citation_count":30,"is_preprint":false},{"pmid":"24726497","id":"PMC_24726497","title":"Conditional knockout of pik3c3 causes a murine muscular dystrophy.","date":"2014","source":"The American journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/24726497","citation_count":30,"is_preprint":false},{"pmid":"23621784","id":"PMC_23621784","title":"Class III phosphoinositide 3-kinase/VPS34 and dynamin are critical for apical endocytic recycling.","date":"2013","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/23621784","citation_count":30,"is_preprint":false},{"pmid":"32939326","id":"PMC_32939326","title":"Firing up the cold tumors by targeting Vps34.","date":"2020","source":"Oncoimmunology","url":"https://pubmed.ncbi.nlm.nih.gov/32939326","citation_count":29,"is_preprint":false},{"pmid":"32743584","id":"PMC_32743584","title":"Inhibitors of VPS34 and lipid metabolism suppress SARS-CoV-2 replication.","date":"2020","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/32743584","citation_count":29,"is_preprint":false},{"pmid":"26686095","id":"PMC_26686095","title":"Nuclear trafficking of EGFR by Vps34 represses Arf expression to promote lung tumor cell survival.","date":"2015","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/26686095","citation_count":29,"is_preprint":false},{"pmid":"33993848","id":"PMC_33993848","title":"AHCYL1 senses SAH to inhibit autophagy through interaction with PIK3C3 in an MTORC1-independent manner.","date":"2021","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/33993848","citation_count":28,"is_preprint":false},{"pmid":"37178482","id":"PMC_37178482","title":"Targeting VPS34 in autophagy: An update on pharmacological small-molecule compounds.","date":"2023","source":"European journal of medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37178482","citation_count":28,"is_preprint":false},{"pmid":"31177902","id":"PMC_31177902","title":"Group A Streptococcus modulates RAB1- and PIK3C3 complex-dependent autophagy.","date":"2019","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/31177902","citation_count":27,"is_preprint":false},{"pmid":"32876514","id":"PMC_32876514","title":"PDPK1 regulates autophagosome biogenesis by binding to PIK3C3.","date":"2020","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/32876514","citation_count":26,"is_preprint":false},{"pmid":"35217810","id":"PMC_35217810","title":"Corynoxine B derivative CB6 prevents Parkinsonian toxicity in mice by inducing PIK3C3 complex-dependent autophagy.","date":"2022","source":"Acta pharmacologica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/35217810","citation_count":26,"is_preprint":false},{"pmid":"27409169","id":"PMC_27409169","title":"VPS34 regulates TSC1/TSC2 heterodimer to mediate RheB and mTORC1/S6K1 activation and cellular transformation.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/27409169","citation_count":25,"is_preprint":false},{"pmid":"26636486","id":"PMC_26636486","title":"GADD45A inhibits autophagy by regulating the interaction between BECN1 and PIK3C3.","date":"2015","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/26636486","citation_count":25,"is_preprint":false},{"pmid":"25679028","id":"PMC_25679028","title":"Ironing out VPS34 inhibition.","date":"2015","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/25679028","citation_count":24,"is_preprint":false},{"pmid":"31193773","id":"PMC_31193773","title":"Aurone derivatives as Vps34 inhibitors that modulate autophagy.","date":"2019","source":"Acta pharmaceutica Sinica. B","url":"https://pubmed.ncbi.nlm.nih.gov/31193773","citation_count":23,"is_preprint":false},{"pmid":"23614954","id":"PMC_23614954","title":"The class III phosphatidylinositol 3-kinase PIK3C3/VPS34 regulates endocytosis and autophagosome-autolysosome formation in podocytes.","date":"2013","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/23614954","citation_count":22,"is_preprint":false},{"pmid":"33235386","id":"PMC_33235386","title":"Pik3c3 deficiency in myeloid cells imparts partial resistance to experimental autoimmune encephalomyelitis associated with reduced IL-1β production.","date":"2020","source":"Cellular & molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/33235386","citation_count":22,"is_preprint":false},{"pmid":"28097232","id":"PMC_28097232","title":"Vps34 regulates myofibril proteostasis to prevent hypertrophic cardiomyopathy.","date":"2017","source":"JCI insight","url":"https://pubmed.ncbi.nlm.nih.gov/28097232","citation_count":22,"is_preprint":false},{"pmid":"27447747","id":"PMC_27447747","title":"Simultaneous inhibition of Vps34 kinase would enhance PI3Kδ inhibitor cytotoxicity in the B-cell malignancies.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/27447747","citation_count":22,"is_preprint":false},{"pmid":"36445937","id":"PMC_36445937","title":"VPS34-dependent control of apical membrane function of proximal tubule cells and nutrient recovery by the kidney.","date":"2022","source":"Science signaling","url":"https://pubmed.ncbi.nlm.nih.gov/36445937","citation_count":22,"is_preprint":false},{"pmid":"28299793","id":"PMC_28299793","title":"FoxO1-AMPK-ULK1 Regulates Ethanol-Induced Autophagy in Muscle by Enhanced ATG14 Association with the BECN1-PIK3C3 Complex.","date":"2017","source":"Alcoholism, clinical and experimental research","url":"https://pubmed.ncbi.nlm.nih.gov/28299793","citation_count":22,"is_preprint":false},{"pmid":"32174250","id":"PMC_32174250","title":"The NEDD4-USP13 axis facilitates autophagy via deubiquitinating PIK3C3.","date":"2020","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/32174250","citation_count":22,"is_preprint":false},{"pmid":"36574710","id":"PMC_36574710","title":"Lipid kinase PIK3C3 maintains healthy brown and white adipose tissues to prevent metabolic diseases.","date":"2022","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/36574710","citation_count":21,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":49509,"output_tokens":11182,"usd":0.158129,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":21678,"output_tokens":6919,"usd":0.140682,"stage2_stop_reason":"end_turn"},"total_usd":0.298811,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1993,\n      \"finding\": \"Yeast VPS34 encodes a phosphatidylinositol 3-kinase (PI3K) required for vacuolar protein sorting; vps34 deletion strains lack detectable PI3K activity and exhibit severe vacuolar protein sorting defects, and overexpression of Vps34p increases PI3K activity specifically precipitated with anti-Vps34p antisera.\",\n      \"method\": \"Gene deletion, overexpression, in vitro PI3K assay, immunoprecipitation\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro kinase assay with direct immunoprecipitation, replicated by multiple subsequent labs\",\n      \"pmids\": [\"8385367\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1990,\n      \"finding\": \"VPS34 protein (875 aa, ~95 kDa) lacks signal sequence or transmembrane domains; it is found partly in a particulate fraction solubilized by urea but not Triton X-100, indicating membrane association via protein–protein interactions; Vps34p-null cells show defects in vacuolar protein sorting and vacuole segregation to daughter cells.\",\n      \"method\": \"Gene cloning/sequencing, immunoprecipitation, cell fractionation, fluorescence microscopy of vacuoles\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (fractionation, IP, imaging) in founding paper, replicated by subsequent work\",\n      \"pmids\": [\"2247081\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Two distinct yeast Vps34 PI3K complexes exist: Complex I (Vps15p/Vps30p/Apg14p/Vps34p) required for autophagy, and Complex II (Vps15p/Vps30p/Vps38p/Vps34p) required for CPY vacuolar protein sorting; Vps30p functions as a shared subunit of both.\",\n      \"method\": \"Co-immunoprecipitation, pull-down, mass spectrometry identification of subunits, phenotypic analysis of deletion mutants\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — reciprocal Co-IP, pulldown, and genetic phenotyping in single rigorous study; foundational finding replicated extensively\",\n      \"pmids\": [\"11157979\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"hVps34 is a nutrient-regulated lipid kinase required for activation of S6K1 and mTOR signaling; hVps34 is inhibited by amino acid or glucose starvation and by AMPK activation; it acts upstream of mTOR, as hVps34 knockdown inhibits phosphorylation of both S6K1 and 4EBP1.\",\n      \"method\": \"siRNA knockdown, anti-hVps34 antibody microinjection, FYVE-domain PI3P sequestration, overexpression, kinase activity assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal loss-of-function approaches (siRNA, inhibitory antibody, dominant-negative lipid sequestration) converging on same phenotype\",\n      \"pmids\": [\"16049009\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Beclin 1 co-immunoprecipitates with hVps34 in glioblastoma cells; siRNA depletion of Beclin 1 specifically blunts the autophagic response to nutrient deprivation or ceramide without affecting EGF receptor post-endocytic sorting, cathepsin D TGN-to-lysosome trafficking, or early endosomal EEA1 association, demonstrating that Beclin 1 selectively directs hVps34 into the autophagic rather than general trafficking pathway.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, autophagy assays, EGFR degradation assay, fluid-phase endocytosis\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP plus multiple functional assays in a single study\",\n      \"pmids\": [\"16390869\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"hVps34 siRNA knockdown causes accumulation of enlarged LAMP1-positive late endosomes depleted of PI(3)P, impairs inward vesiculation of multivesicular bodies, slows cathepsin D maturation, and delays EGFR degradation, but does not block early endocytic uptake or TGN-to-late-endosome cathepsin D traffic, identifying hVps34 as specifically required for PI(3)P generation in late endosomes/MVBs.\",\n      \"method\": \"siRNA knockdown, electron microscopy, GFP-2×FYVE PI(3)P probe, EGFR degradation assay, cathepsin D processing assay\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA knockdown with multiple orthogonal readouts (EM, lipid probe, receptor trafficking) in single study\",\n      \"pmids\": [\"16522686\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Gpa1 (Gα subunit) is present at endosomes and directly interacts with both Vps34 and Vps15 to stimulate PI3P production; Vps15 resembles a Gβ subunit (seven-WD repeat) and binds GDP-Gpa1, revealing a preformed effector–Gβ-like assembly at the endosome.\",\n      \"method\": \"Genetic epistasis screen (~5000 deletion strains), direct protein interaction assay, PI3P production measurement at endosomes\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genome-wide epistasis plus direct interaction and lipid kinase assays in single study\",\n      \"pmids\": [\"16839886\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Amino acids trigger a rise in intracellular Ca2+ that activates hVps34 via direct binding of Ca2+/calmodulin (CaM) to an evolutionarily conserved motif in hVps34; this CaM binding is required for hVps34 lipid kinase activity and for subsequent mTOR Complex 1 activation.\",\n      \"method\": \"Ca2+ imaging, direct CaM-binding assay, lipid kinase activity assay, CaM-binding motif mutagenesis\",\n      \"journal\": \"Cell metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct binding assay with mutagenesis of CaM-binding motif plus in vitro kinase activity measurement\",\n      \"pmids\": [\"18460336\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"hVps15 is required for hVps34 lipid kinase activity in mammalian cells; co-expression with hVps15 markedly increases hVps34 activity, and Beclin 1/UVRAG activation of hVps34 requires hVps15 co-expression; hVps34 activity in cells is independent of Ca2+/CaM (chelation of Ca2+ or CaM has no effect on hVps34 activity in vitro or in cells).\",\n      \"method\": \"In vitro lipid kinase assay, co-expression, BAPTA/AM treatment, EDTA/EGTA wash, W7 CaM inhibitor\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution of kinase activity with and without hVps15, with multiple CaM perturbation approaches\",\n      \"pmids\": [\"18957027\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"hVPS34 and its adaptor p150 colocalize with Rab7 on late endosomes; hVPS34 PI3K activity is dependent on nucleotide cycling of Rab7; total cellular PI3P levels are modulated by Rab7 expression, identifying Rab7 as a regulator of late endosomal hVPS34 function.\",\n      \"method\": \"Co-immunoprecipitation, colocalization imaging, PI3K activity assay, Rab7 nucleotide-state mutants\",\n      \"journal\": \"Traffic\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and activity assay with Rab7 mutants, single lab\",\n      \"pmids\": [\"14617358\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Rab5-GTP promotes endosomal localization of hVps34/p150; the p150 HEAT and WD40 domains are required for Rab5 binding; p150 is required for EEA1 endosomal targeting (recombinant p150 fragments displace EEA1); however, Rab5 does not significantly recruit hVps34/p150 from cytosol to membrane, indicating Rab5 regulates localization rather than membrane recruitment.\",\n      \"method\": \"Dominant-active Rab5 expression, recombinant fragment competition, subcellular fractionation, immunofluorescence colocalization\",\n      \"journal\": \"Traffic\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple methods (fractionation, competition, imaging), single lab\",\n      \"pmids\": [\"12010460\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"M. tuberculosis virulence toxin lipoarabinomannan (LAM) blocks phagosome maturation by inhibiting a Ca2+/calmodulin–hVPS34 cascade; Ca2+ and calmodulin are required for hVPS34-mediated PI3P production on phagosomes in vivo, and LAM from virulent (but not avirulent) mycobacteria blocks cytosolic Ca2+ rise to prevent PI3P generation.\",\n      \"method\": \"In vitro PI3P production assay on liposomes, in vivo phagosomal PI3P imaging, Ca2+ chelation, calmodulin inhibition\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro and in vivo PI3P assays with Ca2+/CaM perturbation, single lab\",\n      \"pmids\": [\"12925680\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"ULK1 phosphorylates Beclin 1 at Ser14 following amino acid starvation or mTOR inhibition, enhancing the lipid kinase activity of the ATG14L-containing VPS34 complex; this phosphorylation is required for full autophagic induction in mammals and C. elegans.\",\n      \"method\": \"In vitro kinase assay, site-directed mutagenesis (S14A), VPS34 complex immunoprecipitation and lipid kinase assay, C. elegans genetic rescue\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro kinase assay with mutagenesis, complex-specific activity measurement, cross-species validation\",\n      \"pmids\": [\"23685627\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"MTORC1 directly phosphorylates ATG14 to inhibit the ATG14-containing PIK3C3 complex specifically; MTORC1 inactivation by nutrient starvation selectively activates the ATG14-containing (autophagy-specific) PIK3C3 complex without affecting UVRAG-containing PIK3C3 complexes.\",\n      \"method\": \"In vitro kinase assay (MTORC1 phosphorylation of ATG14), lipid kinase assay of immunopurified complexes, starvation/rapamycin treatment\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution of MTORC1→ATG14→PIK3C3 inhibition with complex-selective activity assays\",\n      \"pmids\": [\"24013218\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"AMPK directly phosphorylates PIK3C3/VPS34 and BECN1 to differentially regulate PIK3C3 complexes in response to energy starvation: AMPK inhibits non-autophagic PIK3C3 complexes while activating pro-autophagic (ATG14-containing) complexes via Beclin 1 phosphorylation.\",\n      \"method\": \"In vitro kinase assay, complex-specific lipid kinase assay, phosphorylation site mapping\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro kinase assay described in review/commentary, single lab, details compressed in abstract\",\n      \"pmids\": [\"23669030\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Acetylated Hsp70 binds the Beclin 1–Vps34 complex upon autophagy-inducing stress and recruits the E3 SUMO ligase KAP1, which SUMOylates Vps34 at Lys840, increasing Vps34 lipid kinase activity; Hsp70 knockdown abolishes Beclin 1–Vps34 complex formation and prevents autophagosome formation.\",\n      \"method\": \"Co-immunoprecipitation, Vps34 SUMO modification assay, lipid kinase assay, siRNA knockdown, autophagosome formation assay in Hsp70 KO MEFs\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus SUMO modification plus functional KO MEF experiments, single lab\",\n      \"pmids\": [\"23569248\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"VPS34-IN1 (25 nM IC50 in vitro) is a highly selective Vps34 inhibitor; its administration rapidly disperses PI(3)P from endosomal membranes within 1 minute; Vps34-produced PI(3)P at endosomes controls SGK3 activation by enabling PDK1-site and hydrophobic-motif phosphorylation via SGK3's PX domain; a second pool of PI(3)P from class I PI3K→PI(3,4,5)P3→PI(3)P conversion also contributes to SGK3 activity.\",\n      \"method\": \"In vitro kinase selectivity panel (340 protein kinases, 25 lipid kinases), PI(3)P probe imaging, SGK3 phosphorylation assays, PX-domain mutation\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — highly selective inhibitor characterized against broad kinase panel, multiple orthogonal methods (lipid imaging, kinase assays, domain mutants)\",\n      \"pmids\": [\"25177796\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"SAR405 (KD 1.5 nM) selectively inhibits Vps34 kinase activity; its unique binding mode within the ATP-binding cleft explains selectivity; Vps34 inhibition by SAR405 disrupts late endosome–lysosome compartments and prevents autophagy.\",\n      \"method\": \"Biophysical binding assay (KD measurement), crystal structure of inhibitor-Vps34 complex, cell-based autophagy and vesicle trafficking assays\",\n      \"journal\": \"Nature chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus in vitro binding plus functional cellular assays in a single study\",\n      \"pmids\": [\"25326666\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Crystal structure of the 385-kDa endosomal Vps34 complex II (PIK3C3-CII: Vps34/Vps15/Beclin1/UVRAG) at 4.4 Å reveals a Y-shaped assembly centered on the Vps34 C2 domain; Vps15 kinase domain engages the Vps34 activation loop to regulate its activity; HDX-MS identifies a Vps30/Beclin1 loop critical for complex II activity on giant liposomes but not for complex I.\",\n      \"method\": \"X-ray crystallography (4.4 Å), hydrogen-deuterium exchange mass spectrometry, liposome-based lipid kinase assay\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional HDX-MS and membrane activity assays in single rigorous study\",\n      \"pmids\": [\"26450213\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"mTOR directly phosphorylates UVRAG at Ser550 and Ser571 to activate the VPS34-UVRAG complex; this activation generates a lysosomal PI(3)P pool required for autolysosomal tubulation and lysosome reformation (ALR); loss of these phosphorylation sites reduces VPS34 lipid kinase activity and causes massive cell death due to impaired ALR.\",\n      \"method\": \"In vitro mTOR kinase assay, phosphomutant UVRAG constructs, VPS34 lipid kinase assay, lysosomal tubulation imaging, cell survival assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro kinase assay with defined phosphosites, complex-specific activity measurement, and functional tubulation/cell death readouts\",\n      \"pmids\": [\"26139536\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"VPS34 is specifically acetylated by p300 at K771 (reducing affinity for PI substrate) and K29 (hindering VPS34–Beclin 1 complex formation); p300 inhibition induces VPS34 deacetylation and autophagy even in AMPK−/−, TSC2−/−, or ULK1−/− cells, establishing p300-dependent acetylation as a direct control of VPS34 activity independent of upstream kinases.\",\n      \"method\": \"Acetyltransferase assay, acetylation site mutagenesis, in vitro lipid kinase assay, autophagy induction in triple-knockout MEFs, liver fasting model\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with mutagenesis, genetic epistasis via KO cells, and physiological validation in vivo\",\n      \"pmids\": [\"28844862\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"EM and crosslinking mass spectrometry reveal five conformational substates of PI3KC3-C1; in one substate the VPS34 catalytic domain is dislodged from the complex while remaining tethered by an intrinsically disordered linker; a 'leashed' construct that prevents dislodging blocks enzyme activity in vitro and autophagy induction in yeast, identifying catalytic-domain dislodging as an allosteric switch regulated by VPS15.\",\n      \"method\": \"Electron microscopy, crosslinking mass spectrometry, in vitro lipid kinase assay, yeast genetic autophagy assay\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — structural analysis combined with mutagenesis and in vitro/in vivo functional assays in single study\",\n      \"pmids\": [\"28757208\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Cryo-electron tomography of complex II on Rab5a-GTP-decorated vesicles shows Rab5a-GTP recruits and activates complex II by binding between the VPS34 C2 domain and VPS15 WD40 domain, releasing the VPS34 kinase domain from VPS15-mediated inhibition into a catalysis-competent position; Rab1a specifically recruits and activates autophagy complex I (not complex II) via the same VPS34 interface but in a distinct manner.\",\n      \"method\": \"Electron cryotomography, hydrogen-deuterium exchange mass spectrometry, Rab GTPase mutant binding assays, in vitro lipid kinase assay on vesicles\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-ET structural data combined with HDX-MS, GTPase mutants, and activity assays on membranes in a single rigorous study\",\n      \"pmids\": [\"33692360\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ULK1/2 phosphorylates VPS15 at six sites including the major site Ser861; mutation of these sites reduces autophagosome formation in cells and VPS34 lipid kinase activity in vitro, establishing VPS15 as a ULK substrate that links ULK activity to VPS34 complex regulation.\",\n      \"method\": \"Phosphoproteomics in Ulk1/2 DKO MEFs, in vitro VPS34 lipid kinase assay with phosphomutant VPS15, autophagosome formation assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — phosphoproteomics discovery plus in vitro kinase reconstitution with mutagenesis in single study\",\n      \"pmids\": [\"34121209\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The Rubicon RUN domain directly interacts with the hVps34 catalytic subunit and contributes to efficient inhibition of PI3KC3 lipid kinase activity; a RUN domain deletion mutant fails to rescue autophagy deficiency in Rubicon-depleted cells.\",\n      \"method\": \"Co-immunoprecipitation, in vitro PI3K lipid kinase assay, deletion mutagenesis, siRNA complementation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding demonstrated with domain-deletion mutants and functional lipid kinase inhibition assay, single lab\",\n      \"pmids\": [\"21062745\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"The myotubularin PI3-phosphatase MTM1 directly binds the hVPS15/hVPS34 complex via the WD40 domain of hVPS15; overexpression of catalytically active (but not dead) MTM1 depletes endosomal PI(3)P; the hVPS15/hVPS34 complex forms mutually exclusive complexes with Rab5, Rab7, or MTM1, suggesting Rab GTPases and MTM1 act as molecular switches controlling PI(3)P synthesis and degradation.\",\n      \"method\": \"Co-immunoprecipitation, PI(3)P level measurement, catalytic-dead mutant controls, domain-mapping pulldown\",\n      \"journal\": \"Traffic\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP with domain mapping and catalytic-dead controls, single lab\",\n      \"pmids\": [\"17651088\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Conditional deletion of Pik3c3 in differentiated sensory neurons causes rapid neurodegeneration; large-diameter myelinated neurons accumulate enlarged vacuoles and ubiquitin aggregates while small-diameter neurons activate a non-canonical PIK3C3-independent LC3-positive autophagosome pathway still dependent on ATG7; Pik3c3/Atg7 double-mutant analysis shows the unconventional pathway requires ATG7.\",\n      \"method\": \"Conditional knockout mice (Cre-lox), electron microscopy, immunohistochemistry, Atg7 conditional KO comparison, double-mutant analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional KO with double-mutant epistasis establishing pathway position, multiple neuron-type comparisons\",\n      \"pmids\": [\"20439739\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Conditional deletion of Vps34 in T lymphocytes severely reduces T cell numbers; Vps34-deficient T cells show increased death and reduced IL-7Rα surface expression despite intact autophagy; intracellular analysis shows mislocalization of EEA1, HRS, and Vps36, preventing IL-7Rα retromer-pathway recycling to the cell surface.\",\n      \"method\": \"Conditional KO mice, flow cytometry, intracellular trafficking assays, endosomal marker localization\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO with defined trafficking phenotype, single lab\",\n      \"pmids\": [\"22021616\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"PIK3C3 generates PI(3)P that recruits ankyrin-B (AnkB) via PtdIns(3)P binding; AnkB bridges the dynactin subunit p62 and PI(3)P-enriched organelle membranes to promote dynein-mediated fast axonal transport of synaptic vesicles, mitochondria, endosomes, and lysosomes; loss of PIK3C3 or AnkB impairs retrograde organelle transport and shortens axon tracts.\",\n      \"method\": \"AnkB knockout, PIK3C3 loss-of-function, dynactin membrane association assay, live-cell organelle transport imaging in hippocampal neurons, 3D-STORM\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO with quantitative transport assays and domain-interaction mapping, single lab\",\n      \"pmids\": [\"25533844\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"FBXL20, an F-box protein whose expression is induced by p53-dependent transcription after DNA damage, ubiquitinates Vps34 (via SCF-Skp1-Cullin1 complex) for proteasomal degradation; CDK-mediated phosphorylation of Vps34 provides the signal for FBXL20-mediated ubiquitination, leading to inhibition of autophagy and receptor endocytosis.\",\n      \"method\": \"Ubiquitination assay, proteasome inhibitor treatment, CDK phosphorylation assay, FBXL20 overexpression/knockdown, autophagy and receptor endocytosis assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical ubiquitination assay combined with functional autophagy and trafficking readouts, single lab\",\n      \"pmids\": [\"25593308\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Vps34 PI(3)P on late endosomes recruits the Rab7-GAP Armus (TBC1D2) via Armus's PH domain binding to PI(3)P; in Vps34-deficient cells, Armus fails to localize to late endosomes, causing Rab7-GTP accumulation, enlarged late endosomes, impaired intraluminal vesicle formation, and defective EGFR degradation; Rab7 silencing or Armus overexpression rescues vacuolization.\",\n      \"method\": \"Vps34−/− MEFs, protein-lipid overlay and liposome-binding assays, Rab7-GTP pull-down, EGFR degradation assay, rescue experiments\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO cells with direct PI(3)P-binding assay and multiple rescue experiments establishing pathway: Vps34→PI(3)P→Armus→Rab7-GAP activity\",\n      \"pmids\": [\"27793976\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"VPS34 promotes K63-linked ubiquitination of VPS34 by UBC-13/UEV-1/CHN-1 in C. elegans (ortholog), which stabilizes VPS34 protein; loss of this ubiquitination reduces VPS34 levels and impairs phagosome PI(3)P generation and maturation; UBE3C/TRABID reciprocally regulate K29/K48-branched ubiquitination of VPS34 targeting it to proteasomal degradation in mammals.\",\n      \"method\": \"In vitro ubiquitination assay, C. elegans genetics, VPS34 protein level measurement, phagosome maturation assay\",\n      \"journal\": \"The Journal of cell biology / Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro ubiquitination reconstitution with genetic validation in C. elegans, single lab per study\",\n      \"pmids\": [\"29092895\", \"33637724\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"ULK1 O-GlcNAcylation at Thr754 (by OGT, following PP1-mediated dephosphorylation of adjacent mTOR site Ser757 and AMPK phosphorylation) is required for ULK1 to bind and phosphorylate ATG14L, which in turn activates VPS34 lipid kinase activity for PI(3)P production and phagophore formation.\",\n      \"method\": \"O-GlcNAc modification mapping, ULK1 phosphomutants, ATG14L binding assay, VPS34 lipid kinase assay, autophagy flux assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — phosphosite and O-GlcNAc site identification with functional kinase assays, single lab\",\n      \"pmids\": [\"30517873\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Membrane physicochemical properties (degree of lipid unsaturation, negative charge, and curvature) strongly modulate VPS34 complex activity; the BATS domain of ATG14L makes autophagy complex I more active than endocytic complex II on membranes; the Beclin1 BARA domain membrane-interacting loops are critical for complex II but have minor roles for complex I.\",\n      \"method\": \"In vitro lipid kinase assays with defined liposome compositions, HDX-MS of complexes on membranes\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with defined lipid compositions and HDX-MS structural data, multiple orthogonal approaches in one study\",\n      \"pmids\": [\"32602837\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"AHCYL1 senses intracellular S-adenosyl-L-homocysteine (SAH); SAH binding to the AHCYL1 C-terminus promotes binding of the AHCYL1 N-terminus to the PIK3C3 catalytic domain, inhibiting PIK3C3 and suppressing autophagy in an mTORC1-independent manner.\",\n      \"method\": \"Co-immunoprecipitation, domain-mapping pulldown, SAH-binding assay, PIK3C3 kinase activity assay, autophagy flux assay, in vivo validation\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding with domain mapping and kinase activity measurement, validated in vivo, single lab\",\n      \"pmids\": [\"33993848\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ULK1 phosphorylates LDHA at Ser196 under nutrient deprivation, increasing lactate production; lactate then lactylates Vps34 at Lys356 and Lys781 (mediated by acetyltransferase KAT5/TIP60); Vps34 lactylation enhances its association with Beclin1, Atg14L, and UVRAG and increases Vps34 lipid kinase activity to promote autophagy and endolysosomal trafficking.\",\n      \"method\": \"Lactylation site mapping, KAT5 acetyltransferase assay, co-immunoprecipitation of Vps34 complexes, VPS34 lipid kinase assay, autophagy flux assay\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — novel PTM identified with acetyltransferase assay and kinase activity measurement, single lab\",\n      \"pmids\": [\"37267363\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NRBF2 is a specific subunit of Vps34 Complex I (with Vps34, Vps15, Beclin-1, ATG14L) but not Complex II; NRBF2 directly interacts with the Vps15 WD40 domain; NRBF2 knockdown inhibits starvation-induced autophagosome formation (GFP-LC3 puncta, LC3-II lipidation) and increases p62, establishing NRBF2 as a positive regulator of autophagy within Complex I.\",\n      \"method\": \"Co-immunoprecipitation, direct binding assay, siRNA knockdown, autophagy flux assays\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP with functional siRNA knockdown, single lab\",\n      \"pmids\": [\"24785657\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Atg38/NRBF2 uses its MIT domain to bridge Atg14 and Vps30 coiled-coil I regions within Complex I; the Atg38 C-terminal domain mediates homodimerization (2.2 Å crystal structure) and phagophore assembly site localization; one Atg38 homodimer engages a single Complex I, whereas human NRBF2 homodimer can bridge two Complex I assemblies.\",\n      \"method\": \"HDX-MS, X-ray crystallography (2.2 Å), electron microscopy, yeast genetics\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with HDX-MS and EM in single study, functional validation by yeast genetics\",\n      \"pmids\": [\"27630019\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Vps34-generated PI(3)P recruits Armus (Rab7-GAP) and is required for Rab7 inactivation during late endosome maturation; separately, C. elegans VPS-34 recruits TBC-2 (Rab5-GAP) via PI(3)P binding to inactivate RAB-5 and ensure directionality of endosome maturation.\",\n      \"method\": \"Vps34 KO MEFs, Rab7-GTP assay, C. elegans VPS-34 genetics, TBC-2 endosome localization, PH domain PI(3)P binding\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO with Rab-GTP measurement and lipid-binding domain validation, two organisms, single lab\",\n      \"pmids\": [\"28455411\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"VPS34 generates PI(3)P that serves as substrate for PIKfyve to produce PI(3,5)P2; this VPS34→PIKfyve phosphoinositide cascade positively regulates the Retriever/WASH/CCC recycling pathway; PIKfyve inhibition displaces Retriever and CCC from endosomes; VPS34-dependent PI(3)P is required for initial SNX17 recruitment in this recycling pathway.\",\n      \"method\": \"VPS34 and PIKfyve inhibitors, endogenous colocalization, PI(3)P/PI(3,5)P2 assays, cargo recycling assays (integrin surface levels)\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pharmacological inhibition with multiple cargo and complex localization readouts, single lab\",\n      \"pmids\": [\"35040777\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Pik3c3 null embryos are lethal between E7.5 and E8.5 with failure of mesoderm formation and severely reduced cell proliferation; mTOR signaling is drastically reduced in null embryos, suggesting PIK3C3-dependent mTOR activation is a major contributor to early embryonic cell proliferation.\",\n      \"method\": \"Pik3c3 null mouse generation, embryo morphology, BrdU proliferation assay, mTOR signaling western blot, blastocyst culture\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with signaling readout in vivo, single lab\",\n      \"pmids\": [\"21283715\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"The pro-oxidant menadione sodium bisulfite (MSB) inhibits VPS34 lipid kinase activity through oxidation of key cysteine residues, disrupting endosome identity and sorting; in a myotubular myopathy (MTM1-loss) model, dietary MSB improved muscle histology, function, and extended lifespan, consistent with VPS34 being the pathogenic kinase when its phosphatase antagonist MTM1 is absent.\",\n      \"method\": \"VPS34 kinase activity assay under oxidative conditions, cysteine oxidation mapping, MTM1-deficient mouse dietary treatment, muscle histology and functional assays\",\n      \"journal\": \"Science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical mechanism (cysteine oxidation inhibiting kinase) with in vivo therapeutic validation, single lab\",\n      \"pmids\": [\"39446948\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Disruption of the Beclin 1–ATG14L protein–protein interaction (required for VPS34 Complex I formation and localization but not Complex II) selectively inhibits autophagy without disrupting Beclin 1–UVRAG interaction or vesicle trafficking, demonstrating that Complex I and Complex II have separable functions accessible through their unique subunit interfaces.\",\n      \"method\": \"NanoBRET cellular PPI assay, VPS34 Complex I/II immunoprecipitation, autophagy assays, transferrin recycling assay\",\n      \"journal\": \"Journal of the American Chemical Society\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cellular PPI assay with complex-specific IP and functional autophagy/trafficking readouts, single lab\",\n      \"pmids\": [\"32320221\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PIK3C3/VPS34 is the sole class III phosphatidylinositol 3-kinase that phosphorylates PI to PI(3)P; it obligatorily functions within at least two heterotetrameric complexes—autophagy-specific Complex I (VPS34/VPS15/Beclin1/ATG14L) and endosomal Complex II (VPS34/VPS15/Beclin1/UVRAG)—whose structures are now resolved crystallographically and by cryo-ET, and whose activities are controlled by allosteric dislodging of the VPS34 catalytic domain, Rab GTPase recruitment (Rab1a for Complex I, Rab5a for Complex II), membrane physicochemical properties, and extensive post-translational regulation including phosphorylation (by ULK1 of Beclin1-Ser14, VPS15, and ATG14L; by mTORC1 of ATG14L and UVRAG), acetylation (by p300 at K771/K29, repressing activity), lactylation (by KAT5 at K356/K781, activating), SUMOylation (KAP1-mediated at K840, activating), and ubiquitination (K63-linked stabilizing; K29/K48-branched targeting to proteasome); the PI(3)P product recruits effectors including FYVE/PX-domain proteins (EEA1, SGK3, Armus/TBC1D2) to control endosomal maturation, receptor recycling, and lysosome reformation, while its depletion arrests these trafficking events and blocks autophagosome nucleation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PIK3C3/VPS34 is the catalytic class III phosphatidylinositol 3-kinase that phosphorylates phosphatidylinositol to PI(3)P, an activity first defined in yeast where Vps34 is required for vacuolar protein sorting and the protein associates with membranes through protein\\u2013protein rather than transmembrane contacts [#0, #1]. It functions obligatorily within heterotetrameric complexes built on the pseudokinase adaptor VPS15/p150 and the shared subunit Beclin1, partitioning into an autophagy-specific Complex I (with ATG14L) and an endosomal Complex II (with UVRAG); the identity of the fourth subunit dictates pathway specificity, with Beclin1 directing VPS34 into autophagy and the Beclin1\\u2013ATG14L interface being separable from Complex II trafficking functions [#2, #4, #42]. Structural and biophysical work resolved these assemblies as Y-shaped complexes in which the VPS15 kinase domain engages the VPS34 activation loop, and catalytic-domain dislodging tethered by a disordered linker acts as an allosteric on/off switch; membrane physicochemical properties and complex-specific membrane-binding modules (ATG14L BATS, Beclin1 BARA) further tune activity [#18, #21, #33]. VPS15 is also required for VPS34 lipid kinase activity in mammalian cells [#8]. Complex activity is gated by Rab GTPases\\u2014Rab5a recruits and activates Complex II while Rab1a activates Complex I through the same VPS34 interface\\u2014and by an extensive post-translational network: ULK1 phosphorylation of Beclin1-Ser14 and VPS15-Ser861 and mTORC1/AMPK phosphorylation of ATG14L and UVRAG impose nutrient and energy control, while acetylation by p300 (repressing), SUMOylation at Lys840 (activating), KAT5-mediated lactylation (activating), and differential ubiquitination set activity and protein stability [#12, #23, #13, #14, #19, #20, #15, #35, #29, #31]. The PI(3)P product is read by FYVE/PX/PH-domain effectors to drive endosomal maturation and recycling\\u2014recruiting the Rab7-GAP Armus/TBC1D2, enabling SGK3 activation, ankyrin-B-mediated axonal organelle transport, and a VPS34\\u2192PIKfyve cascade feeding the Retriever/WASH/CCC recycling pathway\\u2014so that VPS34 loss enlarges late endosomes, blocks MVB vesiculation and receptor degradation, and arrests autophagosome nucleation [#5, #16, #28, #30, #39]. VPS34 is essential for mouse development and tissue homeostasis, with deletion causing early embryonic lethality and rapid neurodegeneration, and its dysregulation underlies muscle pathology when its phosphatase antagonist MTM1 is lost [#40, #26, #41].\"\n  ,\n  \"teleology\": [\n    {\n      \"year\": 1993,\n      \"claim\": \"Established that VPS34 is itself a PI 3-kinase and links that catalytic activity to a specific cellular process\\u2014vacuolar protein sorting\\u2014answering what the gene product enzymatically does.\",\n      \"evidence\": \"Yeast vps34 deletion, overexpression, in vitro PI3K assay, and immunoprecipitation\",\n      \"pmids\": [\"8385367\", \"2247081\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define mammalian substrate specificity or product (PI(3)P) in cells\", \"No partner subunits identified at this stage\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Resolved how one kinase serves two pathways by showing Vps34 partitions into two distinct complexes that share Vps15/Vps30 but differ in a fourth subunit dictating autophagy vs. CPY sorting.\",\n      \"evidence\": \"Reciprocal Co-IP, pull-down, MS subunit identification, and deletion phenotyping in yeast\",\n      \"pmids\": [\"11157979\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mammalian orthologs of the complexes not yet defined\", \"Mechanism of fourth-subunit pathway routing unknown\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Connected mammalian hVPS34 to endosomal localization and showed Rab GTPase nucleotide cycling controls its lipid kinase output, framing Rabs as upstream regulators.\",\n      \"evidence\": \"Co-IP, colocalization, PI3K activity assays with Rab5/Rab7 nucleotide-state mutants\",\n      \"pmids\": [\"12010460\", \"14617358\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether Rabs recruit vs. activate the complex was ambiguous (Rab5 did not recruit from cytosol)\", \"Structural basis of Rab\\u2013VPS34 interaction unknown\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Positioned hVPS34 as a nutrient sensor acting upstream of mTOR/S6K1, expanding its role beyond trafficking into growth signaling.\",\n      \"evidence\": \"siRNA knockdown, inhibitory antibody microinjection, FYVE-domain PI(3)P sequestration, kinase assays\",\n      \"pmids\": [\"16049009\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular link from VPS34 PI(3)P to mTOR activation not defined\", \"Did not establish which complex mediates the mTOR effect\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Defined Beclin1 as the molecular switch routing hVps34 into autophagy versus general endosomal trafficking, and pinpointed late endosomes/MVBs as the site of VPS34-dependent PI(3)P.\",\n      \"evidence\": \"Reciprocal Co-IP, siRNA, autophagy/EGFR degradation/cathepsin D assays, EM, GFP-2\\u00d7FYVE probe\",\n      \"pmids\": [\"16390869\", \"16522686\", \"16839886\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve how Beclin1 selects ATG14L vs UVRAG partners\", \"Effector proteins reading the PI(3)P pool not yet identified\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Tested how amino acids activate the kinase, identifying Ca2+/calmodulin binding to a conserved motif as a direct activating input feeding mTORC1.\",\n      \"evidence\": \"Ca2+ imaging, direct CaM-binding assay, CaM-motif mutagenesis, lipid kinase assays\",\n      \"pmids\": [\"18460336\", \"12925680\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"A subsequent study found cellular VPS34 activity Ca2+/CaM-independent (#8), leaving the physiological role of CaM binding contested\", \"Context dependence (phagosome vs. cytosolic VPS34) not reconciled\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Established VPS15 as an obligatory activator of mammalian VPS34 lipid kinase activity required for Beclin1/UVRAG-dependent stimulation.\",\n      \"evidence\": \"In vitro reconstitution with/without hVPS15, BAPTA/EGTA/W7 CaM perturbations\",\n      \"pmids\": [\"18957027\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural mechanism of VPS15 activation not resolved\", \"Apparent conflict with Ca2+/CaM model left open\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identified negative regulation of the complex by Rubicon, which binds the VPS34 catalytic subunit to suppress lipid kinase activity.\",\n      \"evidence\": \"Co-IP, in vitro PI3K assay, RUN-domain deletion, siRNA complementation\",\n      \"pmids\": [\"21062745\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; structural basis of inhibition undefined\", \"Complex-selectivity of Rubicon inhibition not fully mapped\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Demonstrated that VPS34 is essential at the organismal level\\u2014for early embryonic proliferation/mesoderm formation and for T-cell endosomal receptor recycling\\u2014linking its biochemistry to physiology.\",\n      \"evidence\": \"Pik3c3 null embryos with mTOR readout; conditional T-cell KO with IL-7R\\u03b1 trafficking and EEA1/HRS localization\",\n      \"pmids\": [\"21283715\", \"22021616\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether embryonic lethality reflects autophagy vs. trafficking vs. mTOR loss not dissected\", \"Cell-type-specific complex usage unresolved\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Resolved how nutrient/energy signals are transduced onto specific complexes: ULK1 phosphorylates Beclin1-Ser14 to activate the ATG14L complex, while mTORC1 and AMPK phosphorylate ATG14/Beclin1 to selectively gate the autophagic versus non-autophagic complexes.\",\n      \"evidence\": \"In vitro kinase assays, phosphomutants, complex-specific lipid kinase assays, C. elegans rescue\",\n      \"pmids\": [\"23685627\", \"24013218\", \"23669030\", \"23569248\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Quantitative integration of opposing kinase inputs on the same complex not modeled\", \"AMPK\\u2192VPS34 details compressed in commentary (#14)\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Delivered selective chemical tools (VPS34-IN1) and downstream effector logic, showing endosomal PI(3)P controls SGK3 activation and ankyrin-B-mediated axonal organelle transport, and defining NRBF2 as a Complex I-specific positive subunit.\",\n      \"evidence\": \"Selective inhibitor + PI(3)P probe imaging and SGK3/PX-domain assays; AnkB/dynactin transport imaging; NRBF2 Co-IP/binding and autophagy flux\",\n      \"pmids\": [\"25177796\", \"25533844\", \"24785657\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Dual PI(3)P pools (class I- vs class III-derived) complicate effector attribution\", \"NRBF2 stoichiometry within Complex I not yet defined at this stage\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Provided the first structure of the endosomal complex and extended PTM control, showing mTOR-UVRAG phosphorylation drives lysosomal PI(3)P for autolysosome reformation, FBXL20 ubiquitination couples DNA-damage/p53 to VPS34 degradation, and Complex I/II functions are separable through their unique interfaces.\",\n      \"evidence\": \"X-ray crystallography (4.4 \\u00c5) + HDX-MS; mTOR/UVRAG phosphomutants with tubulation/cell-death assays; ubiquitination assays; NanoBRET PPI dissection\",\n      \"pmids\": [\"26450213\", \"26139536\", \"25593308\", \"32320221\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Low-resolution structure limited atomic detail of the active site\", \"How distinct phospho-inputs converge structurally not resolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Defined the effector axis controlling endosome maturation directionality, with VPS34-generated PI(3)P recruiting Rab-GAPs (Armus/TBC1D2 for Rab7; TBC-2 for Rab5) to enforce ordered conversion of endosomal Rab identity.\",\n      \"evidence\": \"Vps34-/- MEFs, protein-lipid overlay/liposome binding, Rab-GTP pull-downs, EGFR degradation, rescue, C. elegans genetics\",\n      \"pmids\": [\"27793976\", \"28455411\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Temporal coordination of opposing Rab-GAP recruitment not resolved\", \"Generality across cell types untested\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Established acetylation as a direct, kinase-independent control node and identified the allosteric mechanism of activation\\u2014VPS15-regulated dislodging of the VPS34 catalytic domain\\u2014plus ubiquitin-dependent stability control.\",\n      \"evidence\": \"p300 acetyltransferase assays in triple-KO MEFs and liver fasting; EM/XL-MS with leashed-construct functional tests; in vitro ubiquitination + C. elegans genetics\",\n      \"pmids\": [\"28844862\", \"28757208\", \"29092895\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How acetylation and dislodging interface mechanistically not connected\", \"In vivo dynamics of the dislodging switch unmeasured\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extended upstream control to glycosylation, showing ULK1 O-GlcNAcylation is required for ULK1 to bind/phosphorylate ATG14L and thereby activate VPS34.\",\n      \"evidence\": \"O-GlcNAc/phosphosite mapping, ULK1 mutants, ATG14L binding and VPS34 lipid kinase assays\",\n      \"pmids\": [\"30517873\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; indirect (acts via ULK1) rather than on VPS34 itself\", \"Physiological signal driving OGT activity here undefined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Demonstrated that membrane physicochemistry, not just protein inputs, tunes activity, with complex-specific membrane modules giving Complex I and II distinct membrane preferences.\",\n      \"evidence\": \"In vitro lipid kinase assays on defined liposomes plus HDX-MS of complexes on membranes\",\n      \"pmids\": [\"32602837\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In-cell membrane environments controlling each complex not mapped\", \"Coupling of membrane sensing to Rab/PTM inputs unresolved\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Resolved how Rabs activate the complex on membranes\\u2014Rab5a-GTP binds between the VPS34 C2 and VPS15 WD40 domains to release the kinase domain, while Rab1a activates Complex I via the same interface\\u2014and added VPS15-Ser861 as a ULK substrate.\",\n      \"evidence\": \"Cryo-ET on Rab-decorated vesicles + HDX-MS + Rab mutants/activity assays; phosphoproteomics with VPS15 phosphomutant reconstitution\",\n      \"pmids\": [\"33692360\", \"34121209\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How Rab1a vs Rab5a achieve complex-selectivity through one interface not fully explained\", \"Integration with catalytic-domain dislodging model incomplete\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified metabolite-sensing inhibition via AHCYL1, which on binding S-adenosylhomocysteine engages the VPS34 catalytic domain to suppress autophagy independently of mTORC1.\",\n      \"evidence\": \"Co-IP, domain mapping, SAH-binding and PIK3C3 kinase assays, autophagy flux, in vivo validation\",\n      \"pmids\": [\"33993848\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; structural basis of inhibition undefined\", \"Physiological contexts where SAH gates VPS34 not delineated\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Added lactate-driven activation, with ULK1\\u2192LDHA-derived lactate enabling KAT5-mediated VPS34 lactylation that boosts complex assembly and lipid kinase activity.\",\n      \"evidence\": \"Lactylation site mapping, KAT5 acetyltransferase assay, complex Co-IP, lipid kinase and autophagy flux assays\",\n      \"pmids\": [\"37267363\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; abundance/stoichiometry of lactylation in vivo unknown\", \"Interplay with competing acetylation at nearby lysines unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Linked VPS34 redox sensitivity to disease, showing cysteine oxidation inhibits its kinase activity and that pharmacological VPS34 inhibition rescues MTM1-loss myopathy, defining VPS34 as the pathogenic kinase opposed by phosphatase MTM1.\",\n      \"evidence\": \"VPS34 kinase assay under oxidation, cysteine mapping, MTM1-deficient mouse dietary treatment with muscle phenotyping\",\n      \"pmids\": [\"39446948\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; selectivity of MSB beyond VPS34 not fully excluded\", \"Whether physiological oxidative signals regulate VPS34 in vivo untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the many convergent inputs\\u2014Rab recruitment, catalytic-domain dislodging, membrane physicochemistry, and the dense, sometimes opposing PTM code\\u2014are quantitatively integrated to set VPS34 output at a given membrane in real time remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model reconciling Ca2+/CaM vs CaM-independent activation\", \"Atomic-resolution active complex on native membranes not yet resolved\", \"Spatiotemporal regulation distinguishing Complex I vs II in cells incompletely defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140097\", \"supporting_discovery_ids\": [0, 16]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 8]},\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [16, 17]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [5, 9, 10, 30]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [17, 19]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 10]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [2, 4, 12, 26]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [5, 27, 30, 39]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3, 16]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [0, 1, 27]}\n    ],\n    \"complexes\": [\n      \"PI3KC3 Complex I (VPS34/VPS15/Beclin1/ATG14L)\",\n      \"PI3KC3 Complex II (VPS34/VPS15/Beclin1/UVRAG)\"\n    ],\n    \"partners\": [\n      \"PIK3R4/VPS15\",\n      \"BECN1\",\n      \"ATG14\",\n      \"UVRAG\",\n      \"NRBF2\",\n      \"RUBCN\",\n      \"MTM1\",\n      \"AHCYL1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}