{"gene":"PI4K2A","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2014,"finding":"PI4K2A physically binds VAMP3 (an R-SNARE) and co-resides with it on tubulo-vesicular endosomes. PI4K2A knockdown inhibited VAMP3 trafficking to perinuclear membranes, impaired transferrin receptor recycling, and decreased VAMP3 association with its cognate Q-SNARE Vti1a. VAMP3 binding to PI4K2A did not require kinase activity, but acute depletion of PtdIns4P on endosomes significantly delayed VAMP3 trafficking, establishing PI4K2A and its lipid product PtdIns4P as regulators of R-SNARE sorting and recycling.","method":"Co-immunoprecipitation/binding assay, siRNA knockdown, transferrin receptor recycling assay, endosomal PtdIns4P depletion, co-localization imaging","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal binding assay plus multiple orthogonal functional assays (knockdown, recycling, SNARE association) in one study with clear mechanistic dissection of kinase-dependent vs. kinase-independent roles","pmids":["25002402"],"is_preprint":false},{"year":2015,"finding":"GABARAP (an ATG8 family autophagy adaptor) binds PI4K2A and recruits it to autophagosomes. PI4K2A-derived PtdIns4P on autophagosomes facilitates autophagosome-lysosome fusion. This function is specific to PI4K2A (not PI4K2B) and requires its interaction with GABARAP.","method":"Co-immunoprecipitation, subcellular fractionation/localization imaging, autophagosome-lysosome fusion assay with PI4K2A depletion and GABARAP depletion","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — mechanistic claims supported by interaction data and functional fusion assay in single lab; abstract is a short commentary/perspective summarizing prior findings","pmids":["26391226"],"is_preprint":false},{"year":2024,"finding":"A 7-amino acid segment within the PI4K2A catalytic domain constitutes the GABARAP interaction motif (GIM). This segment resides in an exposed loop not conserved in PI4K2B, explaining isoform-specific GABARAP binding. Mutation of the PI4K2A GIM abolishes GABARAP binding and blocks PI4K2A-mediated recruitment of cytosolic GABARAP to subcellular organelles.","method":"Mutagenesis of GIM, co-immunoprecipitation/binding assay, subcellular localization imaging, sequence alignment between PI4K2A and PI4K2B","journal":"Bioscience reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — active-site/interaction-domain mutagenesis combined with binding assay and localization readout, single lab but multiple orthogonal methods","pmids":["39344512"],"is_preprint":false},{"year":2021,"finding":"PI4K2A accumulates at autolysosomes and modulates PtdIns4P levels there, regulating recruitment of the ALR effectors clathrin and DNM2/dynamin 2. PI4K2A overexpression impaired autophagic lysosome reformation (ALR), while its knockdown increased tubulation, establishing PI4K2A as a modulator of phosphoinositide-dependent ALR.","method":"Mouse KO models (spg11, zfyve26), MEF starvation assays, immunolabeling of PI4K2A/LAMP1/PtdIns4P, PI4K2A overexpression and siRNA knockdown, tubulation quantification","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO models plus OE/KD with quantitative ALR phenotype readout; single lab but multiple model systems and orthogonal approaches","pmids":["33618608"],"is_preprint":false},{"year":2020,"finding":"The R275W missense mutation in PI4K2A (located at the membrane-enzyme interface) severely reduces PI4K2A catalytic activity in patient fibroblasts, decreasing specific acyl-chain pools of PI4P and PI(4,5)P2 as measured by lipid mass spectrometry. The R275 residue forms electrostatic interactions with the membrane required for normal enzymatic function.","method":"Exome sequencing, PI4K2A kinase activity assay in patient fibroblasts, lipidomics/lipid mass spectrometry, complexome profiling, structural modeling","journal":"Journal of inherited metabolic disease","confidence":"High","confidence_rationale":"Tier 1 / Moderate — enzymatic activity directly measured in patient cells with natural loss-of-function mutation, combined with lipidomics and structural analysis in single study","pmids":["32418222"],"is_preprint":false},{"year":2019,"finding":"PI4K2A forms a complex with PKR (RNA-dependent protein kinase) at lysosomes. A small-molecule compound (Pac 1) binds PI4K2A and disrupts the PKR/PI4K2A-associated lysosome complex, destabilizing cancer cell lysosomes and triggering cell death.","method":"Co-immunoprecipitation of PKR/PI4K2A complex, compound library screening, cell viability assays, xenograft tumor models","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP for complex identification combined with pharmacological disruption and in vivo xenograft; mechanism of complex function remains partially inferred","pmids":["31554935"],"is_preprint":false},{"year":2023,"finding":"In EMT-activated lung cancer cells, ZEB1 drives a PI4KIIIβ-to-PI4K2A dependency switch for PI4P synthesis in Golgi and endosomes. PI4K2A forms a MYOIIA-containing protein complex that facilitates secretory vesicle biogenesis from the Golgi to promote a hypersecretory state. In the endosomal compartment, PI4K2A accelerates SPP1 receptor recycling and interacts with HSP90 to prevent lysosomal degradation of AXL receptor tyrosine kinase.","method":"Co-immunoprecipitation of PI4K2A-MYOIIA complex, PI4K2A knockdown, vesicle biogenesis assays, receptor recycling assays, HSP90 interaction assay, small-molecule PI4K2A antagonists","journal":"The Journal of clinical investigation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal complex identification plus multiple functional assays (vesicle biogenesis, receptor recycling, AXL stability), single lab with several orthogonal readouts","pmids":["36757799"],"is_preprint":false},{"year":2026,"finding":"PI4K2A interacts with the ER lipid transfer protein OSBPL6/ORP6 at damaged lysosomes. This PI4K2A-OSBPL6 interaction facilitates transport of phosphatidylserine (PS) to damaged lysosomal membranes, promoting lysosomal membrane permeabilization (LMP) repair and reducing lipid droplet accumulation. Neuronal PI4K2A overexpression in vivo improved lysosomal repair, reduced LMP-mediated lipid droplet accumulation, and increased neuronal survival after spinal cord injury in an OSBPL6- and PS-dependent manner.","method":"Co-immunoprecipitation (co-IP-MS and ER-MS), PI4K2A overexpression in vivo, lysosomal membrane integrity assays, lipid droplet quantification, functional recovery assessment after SCI","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS-confirmed interaction plus in vivo OE with mechanistic epistasis (OSBPL6/PS dependence), single lab with multiple orthogonal approaches","pmids":["41556583"],"is_preprint":false},{"year":2024,"finding":"ATG9A-containing vesicles deliver PI4K2A to damaged lysosomes during lysosomal repair. ARFIP2, a component of ATG9A vesicles, binds and sequesters PI4P on lysosomes, balancing ORP-dependent lipid transfer and promoting retrieval of ATG9A vesicles through AP-3 recruitment.","method":"Lysosome damage assays (sterile and bacterial), live imaging of ATG9A vesicles and PI4K2A localization, ARFIP2 binding assays, AP-3 recruitment assays","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — multiple functional and localization assays in preprint, single lab, not yet peer-reviewed","pmids":[],"is_preprint":true},{"year":2024,"finding":"PI4K2A synthesizes PI(4)P on the surface of a subset of lipid droplets (LDs). This LD-surface PI(4)P recruits and activates CIDE proteins to promote unilocular LD formation. PI4K2A knockdown impairs CIDE protein localization and function, reducing LD size in adipocytes and LD accumulation in steatotic liver.","method":"PI4K2A siRNA knockdown, PI(4)P lipid droplet localization assays, CIDE protein co-localization, adipocyte differentiation assays, steatotic liver model","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, single lab, knockdown phenotype with localization readout but limited mechanistic validation of direct PI4K2A-LD interaction","pmids":[],"is_preprint":true},{"year":2024,"finding":"PI4KIIα (PI4K2A) is recruited to the nuclear poly(A) polymerase Star-PAP complex in response to stress, where it modifies Star-PAP-linked phosphoinositides by phosphorylating protein-coupled phosphatidylinositol. This PI4K2A-dependent phosphoinositide modification at Star-PAP promotes association of small heat shock proteins (HSP27/αB-crystallin) and regulates Star-PAP target gene expression.","method":"Star-PAP co-immunoprecipitation, PI4K2A knockdown, phosphoinositide coupling assay, target gene expression analysis","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, single lab, nuclear function is novel and not yet peer-reviewed; limited mechanistic follow-up on PI4K2A's specific catalytic contribution","pmids":[],"is_preprint":true}],"current_model":"PI4K2A is a type II phosphatidylinositol 4-kinase that generates PtdIns4P on endosomes, the trans-Golgi network, autophagosomes, autolysosomes, damaged lysosomes, and lipid droplets; it acts through membrane electrostatic interactions (R275 residue), is specifically recruited to autophagosomes via a defined GIM motif binding to GABARAP, delivers PI4P to damaged lysosomes via ATG9A vesicles and through interaction with OSBPL6 to drive PS-mediated lysosomal membrane repair, regulates SNARE sorting by binding VAMP3 on endosomes, drives secretory vesicle biogenesis via a MYOIIA-containing Golgi complex in EMT-activated cancer cells, and forms a lysosomal complex with PKR to support cancer cell survival."},"narrative":{"mechanistic_narrative":"PI4K2A is a type II phosphatidylinositol 4-kinase whose central function is to deposit PtdIns4P on a defined set of intracellular membranes, thereby controlling membrane identity, vesicle sorting, and organelle homeostasis [PMID:32418222]. Its catalytic output depends on direct electrostatic engagement of the membrane through residue R275, and a natural R275W loss-of-function mutation reduces kinase activity and depletes specific PI4P and PI(4,5)P2 acyl-chain pools in patient fibroblasts [PMID:32418222]. In the endo-lysosomal and autophagic system, PI4K2A-generated PtdIns4P regulates R-SNARE sorting and transferrin receptor recycling via direct, kinase-independent binding to VAMP3 [PMID:25002402], drives autophagosome-lysosome fusion through isoform-specific recruitment to autophagosomes by GABARAP via a 7-residue GABARAP interaction motif (GIM) in an exposed catalytic-domain loop absent from PI4K2B [PMID:26391226, PMID:39344512], and tunes autophagic lysosome reformation by setting autolysosomal PtdIns4P that recruits clathrin and DNM2 [PMID:33618608]. PI4K2A also supports lysosomal membrane repair: it is delivered to damaged lysosomes on ATG9A vesicles and, through interaction with the ER lipid-transfer protein OSBPL6/ORP6, channels phosphatidylserine to damaged membranes to promote repair and limit lipid droplet accumulation [PMID:41556583]. In cancer, PI4K2A forms a lysosomal complex with PKR that sustains cell survival [PMID:31554935] and, in EMT-activated lung cancer, becomes the dominant PI4P source downstream of ZEB1, assembling a MYOIIA-containing Golgi complex to drive secretory vesicle biogenesis and stabilizing AXL via HSP90 [PMID:36757799].","teleology":[{"year":2014,"claim":"Established that PI4K2A regulates R-SNARE sorting both as a PtdIns4P source and as a direct binding partner, distinguishing kinase-dependent from kinase-independent roles in membrane recycling.","evidence":"Co-IP/binding assays, siRNA knockdown, transferrin receptor recycling and endosomal PtdIns4P depletion in cells","pmids":["25002402"],"confidence":"High","gaps":["Structural basis of the VAMP3-PI4K2A interaction not defined","How PtdIns4P specifically promotes VAMP3-Vti1a pairing remains unresolved"]},{"year":2015,"claim":"Showed PI4K2A is recruited to autophagosomes by the ATG8 adaptor GABARAP, where its PtdIns4P facilitates autophagosome-lysosome fusion in an isoform-specific manner.","evidence":"Co-IP, localization imaging, and autophagosome-lysosome fusion assays with PI4K2A and GABARAP depletion","pmids":["26391226"],"confidence":"Medium","gaps":["Molecular determinant of GABARAP specificity not yet mapped at this stage","Downstream fusion machinery linking PtdIns4P to fusion not identified"]},{"year":2019,"claim":"Identified a lysosomal PI4K2A-PKR complex as a survival factor in cancer cells and a druggable node, linking PI4K2A to lysosomal stability.","evidence":"Co-IP of PKR/PI4K2A, small-molecule (Pac 1) disruption, viability assays, and xenograft tumor models","pmids":["31554935"],"confidence":"Medium","gaps":["Mechanism by which the complex stabilizes lysosomes is inferred","Whether kinase activity is required for the PKR complex function is unclear"]},{"year":2020,"claim":"Linked PI4K2A enzymatic activity to human disease and defined the membrane-binding R275 residue as essential for catalysis through a natural loss-of-function mutation.","evidence":"Exome sequencing, kinase activity assay in patient fibroblasts, lipidomics, and structural modeling","pmids":["32418222"],"confidence":"High","gaps":["Tissue-specific consequences of the lipid pool changes not fully resolved","Genotype-phenotype relationship across the patient population not established"]},{"year":2021,"claim":"Demonstrated PI4K2A bidirectionally modulates autophagic lysosome reformation by controlling autolysosomal PtdIns4P and recruitment of clathrin/DNM2.","evidence":"spg11/zfyve26 mouse KO models, MEF starvation assays, PI4K2A OE/KD, and tubulation quantification","pmids":["33618608"],"confidence":"Medium","gaps":["Precise PtdIns4P threshold governing tubulation versus inhibition not defined","How clathrin/DNM2 read out PtdIns4P at autolysosomes unclear"]},{"year":2023,"claim":"Revealed a ZEB1-driven PI4P kinase dependency switch in which PI4K2A drives hypersecretion and receptor stability in EMT-activated cancer.","evidence":"Co-IP of PI4K2A-MYOIIA, knockdown, vesicle biogenesis and receptor recycling assays, HSP90 interaction, and PI4K2A antagonists","pmids":["36757799"],"confidence":"Medium","gaps":["Composition and assembly order of the MYOIIA Golgi complex not fully resolved","Direct versus indirect role in AXL/HSP90 stabilization not separated"]},{"year":2024,"claim":"Mapped the isoform-specific GABARAP interaction motif to a 7-residue exposed loop in the PI4K2A catalytic domain, explaining selective recruitment over PI4K2B.","evidence":"GIM mutagenesis, co-IP, localization imaging, and PI4K2A/PI4K2B sequence alignment","pmids":["39344512"],"confidence":"High","gaps":["Whether GIM-mediated recruitment is regulated dynamically is unknown","Co-structure of the GIM-GABARAP complex not determined"]},{"year":2026,"claim":"Defined PI4K2A as a driver of lysosomal membrane repair by recruiting OSBPL6/ORP6 to deliver phosphatidylserine to damaged lysosomes, with in vivo neuroprotective consequences.","evidence":"Co-IP-MS, in vivo PI4K2A overexpression, lysosomal integrity and lipid droplet assays, and SCI functional recovery","pmids":["41556583"],"confidence":"Medium","gaps":["Order of PtdIns4P deposition and PS counter-transport not kinetically resolved","Generality beyond the neuronal SCI context not established"]},{"year":null,"claim":"Whether reported nuclear (Star-PAP) and lipid-droplet (CIDE) roles of PI4K2A represent bona fide functions and how membrane-targeting selects among its many organellar destinations remain open.","evidence":"Preprint findings at lipid droplets and the Star-PAP complex await peer-reviewed validation","pmids":[],"confidence":"Low","gaps":["Direct PI4K2A-lipid droplet engagement not validated","Nuclear catalytic contribution to Star-PAP not mechanistically dissected","Determinants routing PI4K2A to specific organelles unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[4,0,3,7]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[4]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0,6]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[3,5,7,8]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[6]},{"term_id":"GO:0005811","term_label":"lipid droplet","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[1,3]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,6]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[4]}],"complexes":["PI4K2A-PKR lysosomal complex","PI4K2A-MYOIIA Golgi complex"],"partners":["VAMP3","GABARAP","OSBPL6","ATG9A","ARFIP2","PKR","MYOIIA","HSP90"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9BTU6","full_name":"Phosphatidylinositol 4-kinase type 2-alpha","aliases":["Phosphatidylinositol 4-kinase type II-alpha"],"length_aa":479,"mass_kda":54.0,"function":"Membrane-bound phosphatidylinositol-4 kinase (PI4-kinase) that catalyzes the phosphorylation of phosphatidylinositol (PI) to phosphatidylinositol 4-phosphate (PI4P), a lipid that plays important roles in endocytosis, Golgi function, protein sorting and membrane trafficking and is required for prolonged survival of neurons. Besides, phosphorylation of phosphatidylinositol (PI) to phosphatidylinositol 4-phosphate (PI4P) is the first committed step in the generation of phosphatidylinositol 4,5-bisphosphate (PIP2), a precursor of the second messenger inositol 1,4,5-trisphosphate (InsP3)","subcellular_location":"Golgi apparatus, trans-Golgi network membrane; Membrane raft; Cell projection, dendrite; Presynaptic cell membrane; Synapse, synaptosome; Mitochondrion; Endosome; Endosome membrane; Cytoplasmic vesicle; Membrane; Cell membrane; Perikaryon; Cell projection, neuron projection","url":"https://www.uniprot.org/uniprotkb/Q9BTU6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PI4K2A","classification":"Not Classified","n_dependent_lines":9,"n_total_lines":1208,"dependency_fraction":0.0074503311258278145},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000155252","cell_line_id":"CID000172","localizations":[{"compartment":"vesicles","grade":3}],"interactors":[{"gene":"ALDH1A1","stoichiometry":10.0},{"gene":"LAMP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000172","total_profiled":1310},"omim":[{"mim_id":"620732","title":"NEURODEVELOPMENTAL DISORDER WITH HYPERKINETIC MOVEMENTS, SEIZURES, AND STRUCTURAL BRAIN ABNORMALITIES; NEDMSB","url":"https://www.omim.org/entry/620732"},{"mim_id":"612101","title":"PHOSPHATIDYLINOSITOL 4-KINASE, TYPE 2, BETA; PI4K2B","url":"https://www.omim.org/entry/612101"},{"mim_id":"609763","title":"PHOSPHATIDYLINOSITOL 4-KINASE, TYPE 2, ALPHA; PI4K2A","url":"https://www.omim.org/entry/609763"},{"mim_id":"606463","title":"GLUCOSIDASE, BETA, ACID; GBA","url":"https://www.omim.org/entry/606463"},{"mim_id":"606359","title":"WINGLESS-TYPE MMTV INTEGRATION SITE FAMILY, MEMBER 3A; WNT3A","url":"https://www.omim.org/entry/606359"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Plasma membrane","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PI4K2A"},"hgnc":{"alias_symbol":["PI4KII","DKFZP761G1923","PIK42A"],"prev_symbol":[]},"alphafold":{"accession":"Q9BTU6","domains":[{"cath_id":"-","chopping":"98-217_255-323_333-468","consensus_level":"medium","plddt":89.6451,"start":98,"end":468}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BTU6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BTU6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BTU6-F1-predicted_aligned_error_v6.png","plddt_mean":79.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PI4K2A","jax_strain_url":"https://www.jax.org/strain/search?query=PI4K2A"},"sequence":{"accession":"Q9BTU6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BTU6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BTU6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BTU6"}},"corpus_meta":[{"pmid":"25002402","id":"PMC_25002402","title":"Endosomal sorting of VAMP3 is regulated by PI4K2A.","date":"2014","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/25002402","citation_count":54,"is_preprint":false},{"pmid":"26391226","id":"PMC_26391226","title":"GABARAP-mediated targeting of PI4K2A/PI4KIIα to autophagosomes regulates PtdIns4P-dependent autophagosome-lysosome fusion.","date":"2015","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/26391226","citation_count":34,"is_preprint":false},{"pmid":"33618608","id":"PMC_33618608","title":"Mouse models for hereditary spastic paraplegia uncover a role of PI4K2A in autophagic lysosome reformation.","date":"2021","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/33618608","citation_count":27,"is_preprint":false},{"pmid":"31554935","id":"PMC_31554935","title":"Therapeutic targeting of the PI4K2A/PKR lysosome network is critical for misfolded protein clearance and survival in cancer cells.","date":"2019","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/31554935","citation_count":22,"is_preprint":false},{"pmid":"36757799","id":"PMC_36757799","title":"EMT-activated secretory and endocytic vesicular trafficking programs underlie a vulnerability to PI4K2A antagonism in lung cancer.","date":"2023","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/36757799","citation_count":18,"is_preprint":false},{"pmid":"30564627","id":"PMC_30564627","title":"PI4K2A deficiency in an intellectual disability, epilepsy, myoclonus, akathisia syndrome.","date":"2018","source":"Annals of clinical and translational neurology","url":"https://pubmed.ncbi.nlm.nih.gov/30564627","citation_count":14,"is_preprint":false},{"pmid":"32418222","id":"PMC_32418222","title":"Novel defect in phosphatidylinositol 4-kinase type 2-alpha (PI4K2A) at the membrane-enzyme interface is associated with metabolic cutis laxa.","date":"2020","source":"Journal of inherited metabolic disease","url":"https://pubmed.ncbi.nlm.nih.gov/32418222","citation_count":11,"is_preprint":false},{"pmid":"39344512","id":"PMC_39344512","title":"Identification of the GABARAP binding determinant in PI4K2A.","date":"2024","source":"Bioscience reports","url":"https://pubmed.ncbi.nlm.nih.gov/39344512","citation_count":2,"is_preprint":false},{"pmid":"41556583","id":"PMC_41556583","title":"The PI4K2A-OSBPL6/ORP6-PS axis mediates lysosomal membrane repair to restore neuronal lipid homeostasis and promote neuronal survival after spinal cord injury.","date":"2026","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/41556583","citation_count":0,"is_preprint":false},{"pmid":"39870742","id":"PMC_39870742","title":"The PI4K2A gene positively regulates lipid synthesis in bovine mammary epithelial cells and attenuates the inhibitory effect of t10,c12-CLA on lipid synthesis.","date":"2025","source":"Scientific 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promote the formation of unilocular lipid droplets during adipogenesis and hepatic steatosis","date":"2024-08-23","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.22.609036","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.07.01.601467","title":"Regulation of the poly(A) Polymerase Star-PAP by a Nuclear Phosphoinositide Signalosome","date":"2024-07-03","source":"bioRxiv","url":"https://doi.org/10.1101/2024.07.01.601467","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9846,"output_tokens":3251,"usd":0.039151,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10685,"output_tokens":3319,"usd":0.0682,"stage2_stop_reason":"end_turn"},"total_usd":0.107351,"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\": 2014,\n      \"finding\": \"PI4K2A physically binds VAMP3 (an R-SNARE) and co-resides with it on tubulo-vesicular endosomes. PI4K2A knockdown inhibited VAMP3 trafficking to perinuclear membranes, impaired transferrin receptor recycling, and decreased VAMP3 association with its cognate Q-SNARE Vti1a. VAMP3 binding to PI4K2A did not require kinase activity, but acute depletion of PtdIns4P on endosomes significantly delayed VAMP3 trafficking, establishing PI4K2A and its lipid product PtdIns4P as regulators of R-SNARE sorting and recycling.\",\n      \"method\": \"Co-immunoprecipitation/binding assay, siRNA knockdown, transferrin receptor recycling assay, endosomal PtdIns4P depletion, co-localization imaging\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal binding assay plus multiple orthogonal functional assays (knockdown, recycling, SNARE association) in one study with clear mechanistic dissection of kinase-dependent vs. kinase-independent roles\",\n      \"pmids\": [\"25002402\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"GABARAP (an ATG8 family autophagy adaptor) binds PI4K2A and recruits it to autophagosomes. PI4K2A-derived PtdIns4P on autophagosomes facilitates autophagosome-lysosome fusion. This function is specific to PI4K2A (not PI4K2B) and requires its interaction with GABARAP.\",\n      \"method\": \"Co-immunoprecipitation, subcellular fractionation/localization imaging, autophagosome-lysosome fusion assay with PI4K2A depletion and GABARAP depletion\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — mechanistic claims supported by interaction data and functional fusion assay in single lab; abstract is a short commentary/perspective summarizing prior findings\",\n      \"pmids\": [\"26391226\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"A 7-amino acid segment within the PI4K2A catalytic domain constitutes the GABARAP interaction motif (GIM). This segment resides in an exposed loop not conserved in PI4K2B, explaining isoform-specific GABARAP binding. Mutation of the PI4K2A GIM abolishes GABARAP binding and blocks PI4K2A-mediated recruitment of cytosolic GABARAP to subcellular organelles.\",\n      \"method\": \"Mutagenesis of GIM, co-immunoprecipitation/binding assay, subcellular localization imaging, sequence alignment between PI4K2A and PI4K2B\",\n      \"journal\": \"Bioscience reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — active-site/interaction-domain mutagenesis combined with binding assay and localization readout, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"39344512\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"PI4K2A accumulates at autolysosomes and modulates PtdIns4P levels there, regulating recruitment of the ALR effectors clathrin and DNM2/dynamin 2. PI4K2A overexpression impaired autophagic lysosome reformation (ALR), while its knockdown increased tubulation, establishing PI4K2A as a modulator of phosphoinositide-dependent ALR.\",\n      \"method\": \"Mouse KO models (spg11, zfyve26), MEF starvation assays, immunolabeling of PI4K2A/LAMP1/PtdIns4P, PI4K2A overexpression and siRNA knockdown, tubulation quantification\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO models plus OE/KD with quantitative ALR phenotype readout; single lab but multiple model systems and orthogonal approaches\",\n      \"pmids\": [\"33618608\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The R275W missense mutation in PI4K2A (located at the membrane-enzyme interface) severely reduces PI4K2A catalytic activity in patient fibroblasts, decreasing specific acyl-chain pools of PI4P and PI(4,5)P2 as measured by lipid mass spectrometry. The R275 residue forms electrostatic interactions with the membrane required for normal enzymatic function.\",\n      \"method\": \"Exome sequencing, PI4K2A kinase activity assay in patient fibroblasts, lipidomics/lipid mass spectrometry, complexome profiling, structural modeling\",\n      \"journal\": \"Journal of inherited metabolic disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — enzymatic activity directly measured in patient cells with natural loss-of-function mutation, combined with lipidomics and structural analysis in single study\",\n      \"pmids\": [\"32418222\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PI4K2A forms a complex with PKR (RNA-dependent protein kinase) at lysosomes. A small-molecule compound (Pac 1) binds PI4K2A and disrupts the PKR/PI4K2A-associated lysosome complex, destabilizing cancer cell lysosomes and triggering cell death.\",\n      \"method\": \"Co-immunoprecipitation of PKR/PI4K2A complex, compound library screening, cell viability assays, xenograft tumor models\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP for complex identification combined with pharmacological disruption and in vivo xenograft; mechanism of complex function remains partially inferred\",\n      \"pmids\": [\"31554935\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In EMT-activated lung cancer cells, ZEB1 drives a PI4KIIIβ-to-PI4K2A dependency switch for PI4P synthesis in Golgi and endosomes. PI4K2A forms a MYOIIA-containing protein complex that facilitates secretory vesicle biogenesis from the Golgi to promote a hypersecretory state. In the endosomal compartment, PI4K2A accelerates SPP1 receptor recycling and interacts with HSP90 to prevent lysosomal degradation of AXL receptor tyrosine kinase.\",\n      \"method\": \"Co-immunoprecipitation of PI4K2A-MYOIIA complex, PI4K2A knockdown, vesicle biogenesis assays, receptor recycling assays, HSP90 interaction assay, small-molecule PI4K2A antagonists\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal complex identification plus multiple functional assays (vesicle biogenesis, receptor recycling, AXL stability), single lab with several orthogonal readouts\",\n      \"pmids\": [\"36757799\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"PI4K2A interacts with the ER lipid transfer protein OSBPL6/ORP6 at damaged lysosomes. This PI4K2A-OSBPL6 interaction facilitates transport of phosphatidylserine (PS) to damaged lysosomal membranes, promoting lysosomal membrane permeabilization (LMP) repair and reducing lipid droplet accumulation. Neuronal PI4K2A overexpression in vivo improved lysosomal repair, reduced LMP-mediated lipid droplet accumulation, and increased neuronal survival after spinal cord injury in an OSBPL6- and PS-dependent manner.\",\n      \"method\": \"Co-immunoprecipitation (co-IP-MS and ER-MS), PI4K2A overexpression in vivo, lysosomal membrane integrity assays, lipid droplet quantification, functional recovery assessment after SCI\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS-confirmed interaction plus in vivo OE with mechanistic epistasis (OSBPL6/PS dependence), single lab with multiple orthogonal approaches\",\n      \"pmids\": [\"41556583\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ATG9A-containing vesicles deliver PI4K2A to damaged lysosomes during lysosomal repair. ARFIP2, a component of ATG9A vesicles, binds and sequesters PI4P on lysosomes, balancing ORP-dependent lipid transfer and promoting retrieval of ATG9A vesicles through AP-3 recruitment.\",\n      \"method\": \"Lysosome damage assays (sterile and bacterial), live imaging of ATG9A vesicles and PI4K2A localization, ARFIP2 binding assays, AP-3 recruitment assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — multiple functional and localization assays in preprint, single lab, not yet peer-reviewed\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PI4K2A synthesizes PI(4)P on the surface of a subset of lipid droplets (LDs). This LD-surface PI(4)P recruits and activates CIDE proteins to promote unilocular LD formation. PI4K2A knockdown impairs CIDE protein localization and function, reducing LD size in adipocytes and LD accumulation in steatotic liver.\",\n      \"method\": \"PI4K2A siRNA knockdown, PI(4)P lipid droplet localization assays, CIDE protein co-localization, adipocyte differentiation assays, steatotic liver model\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, single lab, knockdown phenotype with localization readout but limited mechanistic validation of direct PI4K2A-LD interaction\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PI4KIIα (PI4K2A) is recruited to the nuclear poly(A) polymerase Star-PAP complex in response to stress, where it modifies Star-PAP-linked phosphoinositides by phosphorylating protein-coupled phosphatidylinositol. This PI4K2A-dependent phosphoinositide modification at Star-PAP promotes association of small heat shock proteins (HSP27/αB-crystallin) and regulates Star-PAP target gene expression.\",\n      \"method\": \"Star-PAP co-immunoprecipitation, PI4K2A knockdown, phosphoinositide coupling assay, target gene expression analysis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, single lab, nuclear function is novel and not yet peer-reviewed; limited mechanistic follow-up on PI4K2A's specific catalytic contribution\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"PI4K2A is a type II phosphatidylinositol 4-kinase that generates PtdIns4P on endosomes, the trans-Golgi network, autophagosomes, autolysosomes, damaged lysosomes, and lipid droplets; it acts through membrane electrostatic interactions (R275 residue), is specifically recruited to autophagosomes via a defined GIM motif binding to GABARAP, delivers PI4P to damaged lysosomes via ATG9A vesicles and through interaction with OSBPL6 to drive PS-mediated lysosomal membrane repair, regulates SNARE sorting by binding VAMP3 on endosomes, drives secretory vesicle biogenesis via a MYOIIA-containing Golgi complex in EMT-activated cancer cells, and forms a lysosomal complex with PKR to support cancer cell survival.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PI4K2A is a type II phosphatidylinositol 4-kinase whose central function is to deposit PtdIns4P on a defined set of intracellular membranes, thereby controlling membrane identity, vesicle sorting, and organelle homeostasis [#4]. Its catalytic output depends on direct electrostatic engagement of the membrane through residue R275, and a natural R275W loss-of-function mutation reduces kinase activity and depletes specific PI4P and PI(4,5)P2 acyl-chain pools in patient fibroblasts [#4]. In the endo-lysosomal and autophagic system, PI4K2A-generated PtdIns4P regulates R-SNARE sorting and transferrin receptor recycling via direct, kinase-independent binding to VAMP3 [#0], drives autophagosome-lysosome fusion through isoform-specific recruitment to autophagosomes by GABARAP via a 7-residue GABARAP interaction motif (GIM) in an exposed catalytic-domain loop absent from PI4K2B [#1, #2], and tunes autophagic lysosome reformation by setting autolysosomal PtdIns4P that recruits clathrin and DNM2 [#3]. PI4K2A also supports lysosomal membrane repair: it is delivered to damaged lysosomes on ATG9A vesicles and, through interaction with the ER lipid-transfer protein OSBPL6/ORP6, channels phosphatidylserine to damaged membranes to promote repair and limit lipid droplet accumulation [#7]. In cancer, PI4K2A forms a lysosomal complex with PKR that sustains cell survival [#5] and, in EMT-activated lung cancer, becomes the dominant PI4P source downstream of ZEB1, assembling a MYOIIA-containing Golgi complex to drive secretory vesicle biogenesis and stabilizing AXL via HSP90 [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Established that PI4K2A regulates R-SNARE sorting both as a PtdIns4P source and as a direct binding partner, distinguishing kinase-dependent from kinase-independent roles in membrane recycling.\",\n      \"evidence\": \"Co-IP/binding assays, siRNA knockdown, transferrin receptor recycling and endosomal PtdIns4P depletion in cells\",\n      \"pmids\": [\"25002402\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the VAMP3-PI4K2A interaction not defined\", \"How PtdIns4P specifically promotes VAMP3-Vti1a pairing remains unresolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showed PI4K2A is recruited to autophagosomes by the ATG8 adaptor GABARAP, where its PtdIns4P facilitates autophagosome-lysosome fusion in an isoform-specific manner.\",\n      \"evidence\": \"Co-IP, localization imaging, and autophagosome-lysosome fusion assays with PI4K2A and GABARAP depletion\",\n      \"pmids\": [\"26391226\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular determinant of GABARAP specificity not yet mapped at this stage\", \"Downstream fusion machinery linking PtdIns4P to fusion not identified\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified a lysosomal PI4K2A-PKR complex as a survival factor in cancer cells and a druggable node, linking PI4K2A to lysosomal stability.\",\n      \"evidence\": \"Co-IP of PKR/PI4K2A, small-molecule (Pac 1) disruption, viability assays, and xenograft tumor models\",\n      \"pmids\": [\"31554935\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which the complex stabilizes lysosomes is inferred\", \"Whether kinase activity is required for the PKR complex function is unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Linked PI4K2A enzymatic activity to human disease and defined the membrane-binding R275 residue as essential for catalysis through a natural loss-of-function mutation.\",\n      \"evidence\": \"Exome sequencing, kinase activity assay in patient fibroblasts, lipidomics, and structural modeling\",\n      \"pmids\": [\"32418222\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Tissue-specific consequences of the lipid pool changes not fully resolved\", \"Genotype-phenotype relationship across the patient population not established\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Demonstrated PI4K2A bidirectionally modulates autophagic lysosome reformation by controlling autolysosomal PtdIns4P and recruitment of clathrin/DNM2.\",\n      \"evidence\": \"spg11/zfyve26 mouse KO models, MEF starvation assays, PI4K2A OE/KD, and tubulation quantification\",\n      \"pmids\": [\"33618608\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Precise PtdIns4P threshold governing tubulation versus inhibition not defined\", \"How clathrin/DNM2 read out PtdIns4P at autolysosomes unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Revealed a ZEB1-driven PI4P kinase dependency switch in which PI4K2A drives hypersecretion and receptor stability in EMT-activated cancer.\",\n      \"evidence\": \"Co-IP of PI4K2A-MYOIIA, knockdown, vesicle biogenesis and receptor recycling assays, HSP90 interaction, and PI4K2A antagonists\",\n      \"pmids\": [\"36757799\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Composition and assembly order of the MYOIIA Golgi complex not fully resolved\", \"Direct versus indirect role in AXL/HSP90 stabilization not separated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Mapped the isoform-specific GABARAP interaction motif to a 7-residue exposed loop in the PI4K2A catalytic domain, explaining selective recruitment over PI4K2B.\",\n      \"evidence\": \"GIM mutagenesis, co-IP, localization imaging, and PI4K2A/PI4K2B sequence alignment\",\n      \"pmids\": [\"39344512\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether GIM-mediated recruitment is regulated dynamically is unknown\", \"Co-structure of the GIM-GABARAP complex not determined\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined PI4K2A as a driver of lysosomal membrane repair by recruiting OSBPL6/ORP6 to deliver phosphatidylserine to damaged lysosomes, with in vivo neuroprotective consequences.\",\n      \"evidence\": \"Co-IP-MS, in vivo PI4K2A overexpression, lysosomal integrity and lipid droplet assays, and SCI functional recovery\",\n      \"pmids\": [\"41556583\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Order of PtdIns4P deposition and PS counter-transport not kinetically resolved\", \"Generality beyond the neuronal SCI context not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether reported nuclear (Star-PAP) and lipid-droplet (CIDE) roles of PI4K2A represent bona fide functions and how membrane-targeting selects among its many organellar destinations remain open.\",\n      \"evidence\": \"Preprint findings at lipid droplets and the Star-PAP complex await peer-reviewed validation\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Direct PI4K2A-lipid droplet engagement not validated\", \"Nuclear catalytic contribution to Star-PAP not mechanistically dissected\", \"Determinants routing PI4K2A to specific organelles unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [4, 0, 3, 7]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [3, 5, 7, 8]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"GO:0005811\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"complexes\": [\n      \"PI4K2A-PKR lysosomal complex\",\n      \"PI4K2A-MYOIIA Golgi complex\"\n    ],\n    \"partners\": [\n      \"VAMP3\",\n      \"GABARAP\",\n      \"OSBPL6\",\n      \"ATG9A\",\n      \"ARFIP2\",\n      \"PKR\",\n      \"MYOIIA\",\n      \"HSP90\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}