{"gene":"INPP5F","run_date":"2026-06-10T01:55:23","timeline":{"discoveries":[{"year":2015,"finding":"Sac2/INPP5F is a PI4P (phosphatidylinositol 4-phosphate) phosphatase that localizes to endocytic membranes including clathrin-coated vesicles, macropinosomes, and Rab5-positive endosomes. It interacts with OCRL (demonstrated by co-immunoprecipitation), and this interaction is potentiated by Rab5, whose activity is required for Sac2/INPP5F recruitment to endosomes. Sac2/INPP5F and OCRL cooperate in sequential dephosphorylation of PI(4,5)P2 at the 5- and 4-positions of inositol, mimicking the two phosphatase modules of synaptojanin.","method":"Co-immunoprecipitation, colocalization imaging, in vitro phosphatase assay","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP plus colocalization and in vitro enzymatic activity; independently replicated in companion paper (PMID:25869669) same year","pmids":["25869668"],"is_preprint":false},{"year":2015,"finding":"Sac2 (INPP5F) specifically hydrolyzes phosphatidylinositol 4-phosphate (PI4P) in vitro. It localizes to early endosomes and transferrin-containing recycling vesicles. A catalytically inactive mutant (C458S) causes altered transferrin receptor distribution and delayed transferrin recycling. Genomic ablation of Sac2 perturbs transferrin and integrin recycling and impairs cell migration. Structural analysis revealed a unique pleckstrin-like homology (PH)-Sac2 domain conserved in all Sac2 orthologues.","method":"In vitro PI4P phosphatase assay, catalytically-dead mutagenesis (C458S), gene knockout, transferrin recycling assay, cell migration assay, structural characterization","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution of PI4P phosphatase activity, mutagenesis, KO phenotype with multiple orthogonal readouts; companion to PMID:25869668","pmids":["25869669"],"is_preprint":false},{"year":2009,"finding":"Inpp5f functions as an endogenous negative modulator of cardiac hypertrophy. Inpp5f knockout mice show augmented hypertrophy and reactivation of the fetal gene program under stress, while cardiac-specific overexpression of Inpp5f reduces hypertrophic responsiveness. The mechanism involves degradation of PtdIns(3,4,5)P3, thereby antagonizing the PI3K/Akt pathway.","method":"Knockout mouse model, cardiac-specific transgenic overexpression, biochemical and functional cardiac assessment","journal":"Circulation research","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal genetic experiments (KO and OE transgenic) with defined biochemical and functional phenotypes in vivo","pmids":["19875726"],"is_preprint":false},{"year":2015,"finding":"Silencing or knockout of Inpp5f (Sac2) enhances CNS axon regeneration after spinal cord injury. The mechanism is independent of the PI3K/AKT/mTOR pathway (rapamycin does not block enhanced regeneration in Inpp5f-/- neurons), implicating a distinct substrate specificity from PTEN. Inpp5f-null mice show increased serotonergic axon sprouting/regeneration caudal to lesion and corticospinal tract sprouting rostral to lesion, with enhanced motor recovery.","method":"RNAi screen, lentiviral shRNA silencing, Inpp5f-/- neuronal culture, spinal cord injury model, rapamycin epistasis","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO confirmed screen results, rapamycin epistasis experiment defines pathway independence from mTOR, multiple orthogonal readouts in vivo and in vitro","pmids":["26203138"],"is_preprint":false},{"year":2019,"finding":"Sac2/INPP5F localizes to insulin granules in a substrate (PI4P)-dependent manner. Loss of Sac2 impairs insulin secretion by preventing granule tethering/docking to the plasma membrane, reducing granule density and exocytic events. Sac2 thus controls a phosphoinositide switch on insulin granules required for stable docking at the plasma membrane.","method":"Live-cell imaging, TIRF microscopy, Sac2 knockout/knockdown in clonal β cells and human islets, granule docking and exocytosis assays","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct localization experiment tied to functional consequence, KO with specific granule docking and secretion phenotype, validated in human islets","pmids":["31533953"],"is_preprint":false},{"year":2020,"finding":"Sac2/INPP5F and synaptojanin 1 (SJ1) have partially overlapping functions at synapses. Mice carrying both the SJ1 R258Q Parkinson's disease mutation (which inactivates the Sac domain) and Sac2 knockout show synthetic lethality (most die perinatally), and survivors display accelerated striatal dopaminergic terminal abnormalities. The accumulation of endocytic factors at synapses seen in SJ1RQ knock-in neurons is more severe in double-mutant neurons, consistent with Sac2 acting as a PI4P phosphatase in synaptic vesicle recycling.","method":"Genetic epistasis (double-mutant mouse), neuroanatomical and biochemical analysis of synaptic terminals, cultured neuron immunocytochemistry","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — double-mutant genetic epistasis with multiple phenotypic readouts establishes overlapping function in synaptic endocytosis","pmids":["32424101"],"is_preprint":false},{"year":2014,"finding":"INPP5F interacts with STAT3 (shown by co-immunoprecipitation) and inhibits STAT3 phosphorylation, suppressing STAT3 signaling activity in glioblastoma stem-like cells. Constitutive INPP5F expression suppresses self-renewal and proliferation of glioblastoma cells and reduces tumorigenicity.","method":"Co-immunoprecipitation, western blot for STAT3 phosphorylation, overexpression/knockdown functional assays, tumor growth assays","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single Co-IP and phosphorylation assay in one lab; functional phenotype supports but mechanism not deeply dissected","pmids":["25476455"],"is_preprint":false},{"year":2016,"finding":"Insulin transcriptionally activates Inpp5f expression in an Sp1-dependent manner, and increased Inpp5f in turn reduces Akt phosphorylation, forming a negative feedback loop. Under hyperglycemic and hyperlipidemic conditions (diabetic state), NF-κB activation increases Inpp5f expression and blunts this protective feedback loop, contributing to diabetic cardiomyopathy.","method":"Reporter/promoter assays, Sp1 binding analysis, western blot for p-Akt, diabetic mouse models (STZ and HFD), NF-κB pathway inhibition","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — transcriptional mechanism (Sp1 dependence) and NF-κB activation shown by multiple methods in one lab; no independent replication","pmids":["26908121"],"is_preprint":false},{"year":2022,"finding":"In hepatocellular carcinoma, INPP5F translocates from the nucleus (where it is found in non-tumor cells) to the cytoplasm. Cytoplasmic INPP5F interacts with ASPH (co-immunoprecipitation) to activate Notch signaling and upregulate c-MYC and cyclin E1, promoting proliferation and aerobic glycolysis. Nuclear export inhibitor (leptomycin B) retains INPP5F in the nucleus and suppresses Notch signaling. Nuclear localization signals (NLS) and nuclear export signals (NES) were identified in INPP5F; alteration of NES/NLS sequences changed INPP5F localization and downstream signaling. INPP5F interacts with both exportin and importin, with stronger exportin interaction driving cytoplasmic localization in HCC.","method":"Immunoprecipitation, immunofluorescence, mass spectrometry, transcriptome sequencing, NLS/NES mutagenesis, leptomycin B treatment, in vitro and in vivo tumor models","journal":"Journal of experimental & clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, MS, mutagenesis, nuclear export inhibition) in one lab; no independent replication","pmids":["34996491"],"is_preprint":false},{"year":2019,"finding":"HDAC2 negatively regulates Inpp5f expression in rats with neuropathic pain (negative correlation between HDAC2 mRNA and Inpp5f mRNA levels). Inhibition of HDAC2 increases Inpp5f expression and suppresses PI3K/Akt/GSK-3β pathway activation, reducing neuropathic pain and cognitive dysfunction. Overexpression of Inpp5f similarly suppresses the PI3K/Akt/GSK-3β pathway.","method":"Interference vector knockdown of HDAC2, Inpp5f overexpression vector, RT-qPCR, western blot for p-PI3K/p-AKT/p-GSK-3β, behavioral pain tests","journal":"Experimental and therapeutic medicine","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, mechanistic link between HDAC2 and Inpp5f is correlative; Inpp5f overexpression effect on pathway is a single method without orthogonal confirmation","pmids":["31281447"],"is_preprint":false}],"current_model":"INPP5F/Sac2 is a PI4P phosphatase (with additional PtdIns(3,4,5)P3 phosphatase activity) that acts on endocytic membranes — colocalizing with OCRL on Rab5-positive endosomes to sequentially dephosphorylate PI(4,5)P2, controlling endocytic recycling of transferrin receptors and integrins — and also localizes to insulin granules to regulate their docking at the plasma membrane; in neurons it suppresses axon regeneration via a PI3K/AKT/mTOR-independent mechanism; at synapses it partially overlaps in function with synaptojanin 1 in synaptic vesicle recycling; and in the heart it acts as a negative feedback regulator of PI3K/Akt-driven hypertrophic signaling."},"narrative":{"mechanistic_narrative":"INPP5F (Sac2) is a phosphoinositide phosphatase that regulates membrane trafficking and growth signaling by hydrolyzing specific phosphoinositides. It specifically dephosphorylates phosphatidylinositol 4-phosphate (PI4P) in vitro through a catalytic domain whose activity is abolished by the C458S mutation, and it carries a unique PH-Sac2 module conserved across orthologues [PMID:25869669]. On endocytic membranes — clathrin-coated vesicles, macropinosomes, and Rab5-positive endosomes — it is recruited in a Rab5-dependent manner and partners with OCRL, the two enzymes acting sequentially on the 5- and 4-positions of inositol to dephosphorylate PI(4,5)P2 in a manner mimicking the dual phosphatase modules of synaptojanin [PMID:25869668]. Through this activity INPP5F governs membrane cargo recycling: loss of its catalytic function disrupts transferrin receptor and integrin recycling and impairs cell migration [PMID:25869669], and it localizes in a PI4P-dependent fashion to insulin granules where it controls the phosphoinositide switch required for granule docking and exocytosis [PMID:31533953]. At synapses it functions partially redundantly with synaptojanin 1 in synaptic vesicle recycling, with combined loss producing synthetic lethality and accelerated dopaminergic terminal degeneration [PMID:32424101]. INPP5F also acts as a negative regulator of PI3K/Akt-driven signaling: in the heart it degrades PtdIns(3,4,5)P3 to restrain hypertrophy [PMID:19875726], whereas in CNS neurons it suppresses axon regeneration through a PI3K/AKT/mTOR-independent route [PMID:26203138]. Additional roles in tumor signaling — inhibition of STAT3 in glioblastoma [PMID:25476455] and a nucleocytoplasmic localization switch driving Notch activation in hepatocellular carcinoma [PMID:34996491] — extend its function beyond phosphoinositide turnover.","teleology":[{"year":2009,"claim":"Established INPP5F as an in vivo brake on cardiac hypertrophy, connecting it to growth signaling before its lipid substrate was molecularly defined.","evidence":"Reciprocal knockout and cardiac-specific overexpression mouse models with biochemical phenotyping","pmids":["19875726"],"confidence":"High","gaps":["Direct enzymatic action on PtdIns(3,4,5)P3 inferred from pathway antagonism rather than reconstitution","Upstream signals controlling Inpp5f in stressed myocardium not defined here"]},{"year":2014,"claim":"Linked INPP5F to a non-lipid signaling axis by showing it binds and suppresses STAT3 phosphorylation, restraining glioblastoma stem cell self-renewal.","evidence":"Co-immunoprecipitation, phospho-STAT3 western blot, and overexpression/knockdown tumor assays","pmids":["25476455"],"confidence":"Medium","gaps":["Single Co-IP without reciprocal validation","Whether STAT3 inhibition depends on phosphatase activity not tested","No structural basis for the interaction"]},{"year":2015,"claim":"Defined the core biochemistry — INPP5F is a PI4P phosphatase that, with OCRL on Rab5 endosomes, sequentially dephosphorylates PI(4,5)P2 to control endocytic recycling and migration.","evidence":"In vitro phosphatase assays, C458S catalytic-dead mutagenesis, knockout, transferrin/integrin recycling and migration assays, Co-IP, structural characterization","pmids":["25869668","25869669"],"confidence":"High","gaps":["Precise sequence of substrate handoff between INPP5F and OCRL in cells not resolved","Full structure of catalytic domain not determined"]},{"year":2015,"claim":"Showed INPP5F suppresses CNS axon regeneration through a mechanism distinct from PTEN/mTOR, identifying it as a regeneration brake with a different substrate logic.","evidence":"RNAi screen, shRNA silencing, knockout neuron culture, spinal cord injury model, rapamycin epistasis","pmids":["26203138"],"confidence":"High","gaps":["The specific phosphoinositide substrate governing regeneration not identified","Effectors downstream of the mTOR-independent pathway unknown"]},{"year":2016,"claim":"Placed INPP5F in a transcriptional negative-feedback loop on Akt signaling in the heart, with diabetic conditions disrupting its protective output.","evidence":"Promoter/reporter and Sp1 binding assays, p-Akt western blot, diabetic mouse models, NF-κB inhibition","pmids":["26908121"],"confidence":"Medium","gaps":["No independent replication","Direct Sp1 occupancy at the endogenous promoter not shown"]},{"year":2019,"claim":"Extended INPP5F's trafficking role to regulated secretion, showing PI4P-dependent recruitment to insulin granules controls their docking at the plasma membrane.","evidence":"Live-cell/TIRF imaging, knockout/knockdown in β cells and human islets, granule docking and exocytosis assays","pmids":["31533953"],"confidence":"High","gaps":["The downstream tethering machinery coupled to the PI4P switch not identified","Relationship to OCRL at granules not addressed"]},{"year":2019,"claim":"Proposed HDAC2-mediated repression of Inpp5f as a node in neuropathic pain via PI3K/Akt/GSK-3β signaling.","evidence":"HDAC2 knockdown, Inpp5f overexpression, RT-qPCR, phospho-pathway western blots, behavioral tests in rats","pmids":["31281447"],"confidence":"Low","gaps":["HDAC2–Inpp5f link is correlative, not direct","Single-lab, single-method readouts without orthogonal confirmation"]},{"year":2020,"claim":"Demonstrated functional overlap with synaptojanin 1 in synaptic vesicle recycling through synthetic lethality and accelerated dopaminergic pathology in double mutants.","evidence":"Double-mutant mouse genetic epistasis with neuroanatomical, biochemical, and immunocytochemical analysis","pmids":["32424101"],"confidence":"High","gaps":["Degree of non-overlapping versus shared substrate pools at the synapse not quantified","Relevance to human Parkinson's disease beyond the SJ1 mutation not established"]},{"year":2022,"claim":"Revealed a nucleocytoplasmic localization switch in which cytoplasmic INPP5F binds ASPH to activate Notch and drive hepatocellular carcinoma proliferation and glycolysis.","evidence":"Co-IP, mass spectrometry, NLS/NES mutagenesis, leptomycin B treatment, transcriptomics, in vitro and in vivo tumor models","pmids":["34996491"],"confidence":"Medium","gaps":["No independent replication","Whether this oncogenic function requires phosphatase activity unknown","Mechanism connecting ASPH binding to Notch activation not dissected"]},{"year":null,"claim":"How INPP5F's phosphoinositide-phosphatase activity mechanistically connects to its non-lipid functions (STAT3 inhibition, ASPH/Notch activation) and its mTOR-independent regeneration substrate remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No defined substrate for the axon-regeneration phenotype","Catalytic dependence of tumor-signaling roles untested","No structural model integrating PH-Sac2 and catalytic domains"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,1,2]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0,1]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[0,4]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[8]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,3]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[4]}],"complexes":[],"partners":["OCRL","STAT3","ASPH"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y2H2","full_name":"Phosphatidylinositide 4-phosphatase SAC2","aliases":["Inositol polyphosphate 5-phosphatase F","Sac domain-containing inositol phosphatase 2","Sac domain-containing phosphoinositide 4-phosphatase 2","hSAC2"],"length_aa":1132,"mass_kda":128.4,"function":"Phosphoinositide phosphatase which catalyzes the hydrolysis of phosphatidylinositol 4-phosphate (1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol 4-phosphate), PtdIns(4)P). May be functionally linked to OCRL, which converts phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) to PtdIns, for a sequential dephosphorylation of (PtdIns(4,5)P2) at the 5 and 4 position of inositol, thus playing an important role in the endocytic recycling (PubMed:25869668, PubMed:25869669). Regulator of TF:TFRC and integrins recycling pathway, is also involved in cell migration mechanisms (PubMed:25869669). Modulates AKT/GSK3B pathway by decreasing AKT and GSK3B phosphorylation (PubMed:17322895). Negatively regulates STAT3 signaling pathway through inhibition of STAT3 phosphorylation and translocation to the nucleus (PubMed:25476455). Functionally important modulator of cardiac myocyte size and of the cardiac response to stress (By similarity). May play a role as negative regulator of axon regeneration after central nervous system injuries (By similarity). May be involved in insulin granule docking at the plasma membrane of pancreatic cells, an essential step for insulin secretion (PubMed:31533953)","subcellular_location":"Membrane, clathrin-coated pit; Early endosome; Recycling endosome","url":"https://www.uniprot.org/uniprotkb/Q9Y2H2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/INPP5F","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/INPP5F","total_profiled":1310},"omim":[{"mim_id":"609389","title":"INOSITOL POLYPHOSPHATE 5-PHOSPHATASE F; INPP5F","url":"https://www.omim.org/entry/609389"},{"mim_id":"605164","title":"HISTONE DEACETYLASE 2; HDAC2","url":"https://www.omim.org/entry/605164"},{"mim_id":"605004","title":"GLYCOGEN SYNTHASE KINASE 3-BETA; GSK3B","url":"https://www.omim.org/entry/605004"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Vesicles","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"brain","ntpm":137.7}],"url":"https://www.proteinatlas.org/search/INPP5F"},"hgnc":{"alias_symbol":["SAC2","KIAA0966","hSac2"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y2H2","domains":[{"cath_id":"-","chopping":"234-249_274-572","consensus_level":"medium","plddt":86.4044,"start":234,"end":572},{"cath_id":"2.30.29.30","chopping":"613-746","consensus_level":"high","plddt":84.4381,"start":613,"end":746}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2H2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2H2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2H2-F1-predicted_aligned_error_v6.png","plddt_mean":66.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=INPP5F","jax_strain_url":"https://www.jax.org/strain/search?query=INPP5F"},"sequence":{"accession":"Q9Y2H2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y2H2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y2H2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2H2"}},"corpus_meta":[{"pmid":"25869668","id":"PMC_25869668","title":"Sac2/INPP5F is an inositol 4-phosphatase that functions in the endocytic pathway.","date":"2015","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/25869668","citation_count":61,"is_preprint":false},{"pmid":"15964807","id":"PMC_15964807","title":"A novel variant of Inpp5f is imprinted in brain, and its expression is correlated with differential methylation of an internal CpG island.","date":"2005","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/15964807","citation_count":59,"is_preprint":false},{"pmid":"19875726","id":"PMC_19875726","title":"Inpp5f is a polyphosphoinositide phosphatase that regulates cardiac hypertrophic responsiveness.","date":"2009","source":"Circulation research","url":"https://pubmed.ncbi.nlm.nih.gov/19875726","citation_count":53,"is_preprint":false},{"pmid":"25869669","id":"PMC_25869669","title":"Spatiotemporal control of phosphatidylinositol 4-phosphate by Sac2 regulates endocytic recycling.","date":"2015","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/25869669","citation_count":51,"is_preprint":false},{"pmid":"26203138","id":"PMC_26203138","title":"Gene-Silencing Screen for Mammalian Axon Regeneration Identifies Inpp5f (Sac2) as an Endogenous Suppressor of Repair after Spinal Cord Injury.","date":"2015","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/26203138","citation_count":33,"is_preprint":false},{"pmid":"32424101","id":"PMC_32424101","title":"Absence of Sac2/INPP5F enhances the phenotype of a Parkinson's disease mutation of synaptojanin 1.","date":"2020","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/32424101","citation_count":32,"is_preprint":false},{"pmid":"25476455","id":"PMC_25476455","title":"Inositol Polyphosphate-5-Phosphatase F (INPP5F) inhibits STAT3 activity and suppresses gliomas tumorigenicity.","date":"2014","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/25476455","citation_count":27,"is_preprint":false},{"pmid":"36852438","id":"PMC_36852438","title":"LncRNA INPP5F ameliorates stress-induced hypertension via the miR-335/Cttn axis in rostral ventrolateral medulla.","date":"2023","source":"CNS neuroscience & therapeutics","url":"https://pubmed.ncbi.nlm.nih.gov/36852438","citation_count":20,"is_preprint":false},{"pmid":"31281447","id":"PMC_31281447","title":"Effect of HDAC2/Inpp5f on neuropathic pain and cognitive function through regulating PI3K/Akt/GSK-3β signal pathway in rats with neuropathic pain.","date":"2019","source":"Experimental and therapeutic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/31281447","citation_count":20,"is_preprint":false},{"pmid":"31533953","id":"PMC_31533953","title":"The PI(4)P phosphatase Sac2 controls insulin granule docking and release.","date":"2019","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/31533953","citation_count":19,"is_preprint":false},{"pmid":"34996491","id":"PMC_34996491","title":"INPP5F translocates into cytoplasm and interacts with ASPH to promote tumor growth in hepatocellular carcinoma.","date":"2022","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/34996491","citation_count":16,"is_preprint":false},{"pmid":"32693431","id":"PMC_32693431","title":"Imprinting aberrations of SNRPN, ZAC1 and INPP5F genes involved in the pathogenesis of congenital heart disease with extracardiac malformations.","date":"2020","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/32693431","citation_count":16,"is_preprint":false},{"pmid":"26908121","id":"PMC_26908121","title":"Hyperglycemia and hyperlipidemia blunts the Insulin-Inpp5f negative feedback loop in the diabetic heart.","date":"2016","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/26908121","citation_count":12,"is_preprint":false},{"pmid":"7754710","id":"PMC_7754710","title":"Nucleotide sequence of the SAC2 gene of Saccharomyces cerevisiae.","date":"1994","source":"Yeast (Chichester, England)","url":"https://pubmed.ncbi.nlm.nih.gov/7754710","citation_count":6,"is_preprint":false},{"pmid":"35848021","id":"PMC_35848021","title":"Parkinson's Disease rs117896735 Variant Regulates INPP5F Expression in Brain Tissues and Increases Risk of Alzheimer's Disease.","date":"2022","source":"Journal of Alzheimer's disease : JAD","url":"https://pubmed.ncbi.nlm.nih.gov/35848021","citation_count":5,"is_preprint":false},{"pmid":"30680006","id":"PMC_30680006","title":"Pregabalin on Hdac2 and Inpp5f levels in rats with CCI-induced neuropathic pain.","date":"2018","source":"Experimental and therapeutic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/30680006","citation_count":4,"is_preprint":false},{"pmid":"18551384","id":"PMC_18551384","title":"Molecular characterization and association analysis with production traits of the porcine INPP5F gene.","date":"2008","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/18551384","citation_count":4,"is_preprint":false},{"pmid":"21424340","id":"PMC_21424340","title":"Expression patterns of imprinted gene Inpp5f-v3 during mouse brain development.","date":"2011","source":"Journal of molecular histology","url":"https://pubmed.ncbi.nlm.nih.gov/21424340","citation_count":2,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11276,"output_tokens":3121,"usd":0.040322,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10539,"output_tokens":3383,"usd":0.068635,"stage2_stop_reason":"end_turn"},"total_usd":0.108957,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"Sac2/INPP5F is a PI4P (phosphatidylinositol 4-phosphate) phosphatase that localizes to endocytic membranes including clathrin-coated vesicles, macropinosomes, and Rab5-positive endosomes. It interacts with OCRL (demonstrated by co-immunoprecipitation), and this interaction is potentiated by Rab5, whose activity is required for Sac2/INPP5F recruitment to endosomes. Sac2/INPP5F and OCRL cooperate in sequential dephosphorylation of PI(4,5)P2 at the 5- and 4-positions of inositol, mimicking the two phosphatase modules of synaptojanin.\",\n      \"method\": \"Co-immunoprecipitation, colocalization imaging, in vitro phosphatase assay\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP plus colocalization and in vitro enzymatic activity; independently replicated in companion paper (PMID:25869669) same year\",\n      \"pmids\": [\"25869668\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Sac2 (INPP5F) specifically hydrolyzes phosphatidylinositol 4-phosphate (PI4P) in vitro. It localizes to early endosomes and transferrin-containing recycling vesicles. A catalytically inactive mutant (C458S) causes altered transferrin receptor distribution and delayed transferrin recycling. Genomic ablation of Sac2 perturbs transferrin and integrin recycling and impairs cell migration. Structural analysis revealed a unique pleckstrin-like homology (PH)-Sac2 domain conserved in all Sac2 orthologues.\",\n      \"method\": \"In vitro PI4P phosphatase assay, catalytically-dead mutagenesis (C458S), gene knockout, transferrin recycling assay, cell migration assay, structural characterization\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution of PI4P phosphatase activity, mutagenesis, KO phenotype with multiple orthogonal readouts; companion to PMID:25869668\",\n      \"pmids\": [\"25869669\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Inpp5f functions as an endogenous negative modulator of cardiac hypertrophy. Inpp5f knockout mice show augmented hypertrophy and reactivation of the fetal gene program under stress, while cardiac-specific overexpression of Inpp5f reduces hypertrophic responsiveness. The mechanism involves degradation of PtdIns(3,4,5)P3, thereby antagonizing the PI3K/Akt pathway.\",\n      \"method\": \"Knockout mouse model, cardiac-specific transgenic overexpression, biochemical and functional cardiac assessment\",\n      \"journal\": \"Circulation research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal genetic experiments (KO and OE transgenic) with defined biochemical and functional phenotypes in vivo\",\n      \"pmids\": [\"19875726\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Silencing or knockout of Inpp5f (Sac2) enhances CNS axon regeneration after spinal cord injury. The mechanism is independent of the PI3K/AKT/mTOR pathway (rapamycin does not block enhanced regeneration in Inpp5f-/- neurons), implicating a distinct substrate specificity from PTEN. Inpp5f-null mice show increased serotonergic axon sprouting/regeneration caudal to lesion and corticospinal tract sprouting rostral to lesion, with enhanced motor recovery.\",\n      \"method\": \"RNAi screen, lentiviral shRNA silencing, Inpp5f-/- neuronal culture, spinal cord injury model, rapamycin epistasis\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO confirmed screen results, rapamycin epistasis experiment defines pathway independence from mTOR, multiple orthogonal readouts in vivo and in vitro\",\n      \"pmids\": [\"26203138\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Sac2/INPP5F localizes to insulin granules in a substrate (PI4P)-dependent manner. Loss of Sac2 impairs insulin secretion by preventing granule tethering/docking to the plasma membrane, reducing granule density and exocytic events. Sac2 thus controls a phosphoinositide switch on insulin granules required for stable docking at the plasma membrane.\",\n      \"method\": \"Live-cell imaging, TIRF microscopy, Sac2 knockout/knockdown in clonal β cells and human islets, granule docking and exocytosis assays\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct localization experiment tied to functional consequence, KO with specific granule docking and secretion phenotype, validated in human islets\",\n      \"pmids\": [\"31533953\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Sac2/INPP5F and synaptojanin 1 (SJ1) have partially overlapping functions at synapses. Mice carrying both the SJ1 R258Q Parkinson's disease mutation (which inactivates the Sac domain) and Sac2 knockout show synthetic lethality (most die perinatally), and survivors display accelerated striatal dopaminergic terminal abnormalities. The accumulation of endocytic factors at synapses seen in SJ1RQ knock-in neurons is more severe in double-mutant neurons, consistent with Sac2 acting as a PI4P phosphatase in synaptic vesicle recycling.\",\n      \"method\": \"Genetic epistasis (double-mutant mouse), neuroanatomical and biochemical analysis of synaptic terminals, cultured neuron immunocytochemistry\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — double-mutant genetic epistasis with multiple phenotypic readouts establishes overlapping function in synaptic endocytosis\",\n      \"pmids\": [\"32424101\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"INPP5F interacts with STAT3 (shown by co-immunoprecipitation) and inhibits STAT3 phosphorylation, suppressing STAT3 signaling activity in glioblastoma stem-like cells. Constitutive INPP5F expression suppresses self-renewal and proliferation of glioblastoma cells and reduces tumorigenicity.\",\n      \"method\": \"Co-immunoprecipitation, western blot for STAT3 phosphorylation, overexpression/knockdown functional assays, tumor growth assays\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single Co-IP and phosphorylation assay in one lab; functional phenotype supports but mechanism not deeply dissected\",\n      \"pmids\": [\"25476455\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Insulin transcriptionally activates Inpp5f expression in an Sp1-dependent manner, and increased Inpp5f in turn reduces Akt phosphorylation, forming a negative feedback loop. Under hyperglycemic and hyperlipidemic conditions (diabetic state), NF-κB activation increases Inpp5f expression and blunts this protective feedback loop, contributing to diabetic cardiomyopathy.\",\n      \"method\": \"Reporter/promoter assays, Sp1 binding analysis, western blot for p-Akt, diabetic mouse models (STZ and HFD), NF-κB pathway inhibition\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — transcriptional mechanism (Sp1 dependence) and NF-κB activation shown by multiple methods in one lab; no independent replication\",\n      \"pmids\": [\"26908121\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In hepatocellular carcinoma, INPP5F translocates from the nucleus (where it is found in non-tumor cells) to the cytoplasm. Cytoplasmic INPP5F interacts with ASPH (co-immunoprecipitation) to activate Notch signaling and upregulate c-MYC and cyclin E1, promoting proliferation and aerobic glycolysis. Nuclear export inhibitor (leptomycin B) retains INPP5F in the nucleus and suppresses Notch signaling. Nuclear localization signals (NLS) and nuclear export signals (NES) were identified in INPP5F; alteration of NES/NLS sequences changed INPP5F localization and downstream signaling. INPP5F interacts with both exportin and importin, with stronger exportin interaction driving cytoplasmic localization in HCC.\",\n      \"method\": \"Immunoprecipitation, immunofluorescence, mass spectrometry, transcriptome sequencing, NLS/NES mutagenesis, leptomycin B treatment, in vitro and in vivo tumor models\",\n      \"journal\": \"Journal of experimental & clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, MS, mutagenesis, nuclear export inhibition) in one lab; no independent replication\",\n      \"pmids\": [\"34996491\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"HDAC2 negatively regulates Inpp5f expression in rats with neuropathic pain (negative correlation between HDAC2 mRNA and Inpp5f mRNA levels). Inhibition of HDAC2 increases Inpp5f expression and suppresses PI3K/Akt/GSK-3β pathway activation, reducing neuropathic pain and cognitive dysfunction. Overexpression of Inpp5f similarly suppresses the PI3K/Akt/GSK-3β pathway.\",\n      \"method\": \"Interference vector knockdown of HDAC2, Inpp5f overexpression vector, RT-qPCR, western blot for p-PI3K/p-AKT/p-GSK-3β, behavioral pain tests\",\n      \"journal\": \"Experimental and therapeutic medicine\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, mechanistic link between HDAC2 and Inpp5f is correlative; Inpp5f overexpression effect on pathway is a single method without orthogonal confirmation\",\n      \"pmids\": [\"31281447\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"INPP5F/Sac2 is a PI4P phosphatase (with additional PtdIns(3,4,5)P3 phosphatase activity) that acts on endocytic membranes — colocalizing with OCRL on Rab5-positive endosomes to sequentially dephosphorylate PI(4,5)P2, controlling endocytic recycling of transferrin receptors and integrins — and also localizes to insulin granules to regulate their docking at the plasma membrane; in neurons it suppresses axon regeneration via a PI3K/AKT/mTOR-independent mechanism; at synapses it partially overlaps in function with synaptojanin 1 in synaptic vesicle recycling; and in the heart it acts as a negative feedback regulator of PI3K/Akt-driven hypertrophic signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"INPP5F (Sac2) is a phosphoinositide phosphatase that regulates membrane trafficking and growth signaling by hydrolyzing specific phosphoinositides. It specifically dephosphorylates phosphatidylinositol 4-phosphate (PI4P) in vitro through a catalytic domain whose activity is abolished by the C458S mutation, and it carries a unique PH-Sac2 module conserved across orthologues [#1]. On endocytic membranes — clathrin-coated vesicles, macropinosomes, and Rab5-positive endosomes — it is recruited in a Rab5-dependent manner and partners with OCRL, the two enzymes acting sequentially on the 5- and 4-positions of inositol to dephosphorylate PI(4,5)P2 in a manner mimicking the dual phosphatase modules of synaptojanin [#0]. Through this activity INPP5F governs membrane cargo recycling: loss of its catalytic function disrupts transferrin receptor and integrin recycling and impairs cell migration [#1], and it localizes in a PI4P-dependent fashion to insulin granules where it controls the phosphoinositide switch required for granule docking and exocytosis [#4]. At synapses it functions partially redundantly with synaptojanin 1 in synaptic vesicle recycling, with combined loss producing synthetic lethality and accelerated dopaminergic terminal degeneration [#5]. INPP5F also acts as a negative regulator of PI3K/Akt-driven signaling: in the heart it degrades PtdIns(3,4,5)P3 to restrain hypertrophy [#2], whereas in CNS neurons it suppresses axon regeneration through a PI3K/AKT/mTOR-independent route [#3]. Additional roles in tumor signaling — inhibition of STAT3 in glioblastoma [#6] and a nucleocytoplasmic localization switch driving Notch activation in hepatocellular carcinoma [#8] — extend its function beyond phosphoinositide turnover.\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Established INPP5F as an in vivo brake on cardiac hypertrophy, connecting it to growth signaling before its lipid substrate was molecularly defined.\",\n      \"evidence\": \"Reciprocal knockout and cardiac-specific overexpression mouse models with biochemical phenotyping\",\n      \"pmids\": [\"19875726\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct enzymatic action on PtdIns(3,4,5)P3 inferred from pathway antagonism rather than reconstitution\", \"Upstream signals controlling Inpp5f in stressed myocardium not defined here\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Linked INPP5F to a non-lipid signaling axis by showing it binds and suppresses STAT3 phosphorylation, restraining glioblastoma stem cell self-renewal.\",\n      \"evidence\": \"Co-immunoprecipitation, phospho-STAT3 western blot, and overexpression/knockdown tumor assays\",\n      \"pmids\": [\"25476455\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single Co-IP without reciprocal validation\", \"Whether STAT3 inhibition depends on phosphatase activity not tested\", \"No structural basis for the interaction\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined the core biochemistry — INPP5F is a PI4P phosphatase that, with OCRL on Rab5 endosomes, sequentially dephosphorylates PI(4,5)P2 to control endocytic recycling and migration.\",\n      \"evidence\": \"In vitro phosphatase assays, C458S catalytic-dead mutagenesis, knockout, transferrin/integrin recycling and migration assays, Co-IP, structural characterization\",\n      \"pmids\": [\"25869668\", \"25869669\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Precise sequence of substrate handoff between INPP5F and OCRL in cells not resolved\", \"Full structure of catalytic domain not determined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showed INPP5F suppresses CNS axon regeneration through a mechanism distinct from PTEN/mTOR, identifying it as a regeneration brake with a different substrate logic.\",\n      \"evidence\": \"RNAi screen, shRNA silencing, knockout neuron culture, spinal cord injury model, rapamycin epistasis\",\n      \"pmids\": [\"26203138\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The specific phosphoinositide substrate governing regeneration not identified\", \"Effectors downstream of the mTOR-independent pathway unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Placed INPP5F in a transcriptional negative-feedback loop on Akt signaling in the heart, with diabetic conditions disrupting its protective output.\",\n      \"evidence\": \"Promoter/reporter and Sp1 binding assays, p-Akt western blot, diabetic mouse models, NF-\\u03baB inhibition\",\n      \"pmids\": [\"26908121\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No independent replication\", \"Direct Sp1 occupancy at the endogenous promoter not shown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Extended INPP5F's trafficking role to regulated secretion, showing PI4P-dependent recruitment to insulin granules controls their docking at the plasma membrane.\",\n      \"evidence\": \"Live-cell/TIRF imaging, knockout/knockdown in \\u03b2 cells and human islets, granule docking and exocytosis assays\",\n      \"pmids\": [\"31533953\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The downstream tethering machinery coupled to the PI4P switch not identified\", \"Relationship to OCRL at granules not addressed\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Proposed HDAC2-mediated repression of Inpp5f as a node in neuropathic pain via PI3K/Akt/GSK-3\\u03b2 signaling.\",\n      \"evidence\": \"HDAC2 knockdown, Inpp5f overexpression, RT-qPCR, phospho-pathway western blots, behavioral tests in rats\",\n      \"pmids\": [\"31281447\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"HDAC2\\u2013Inpp5f link is correlative, not direct\", \"Single-lab, single-method readouts without orthogonal confirmation\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Demonstrated functional overlap with synaptojanin 1 in synaptic vesicle recycling through synthetic lethality and accelerated dopaminergic pathology in double mutants.\",\n      \"evidence\": \"Double-mutant mouse genetic epistasis with neuroanatomical, biochemical, and immunocytochemical analysis\",\n      \"pmids\": [\"32424101\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Degree of non-overlapping versus shared substrate pools at the synapse not quantified\", \"Relevance to human Parkinson's disease beyond the SJ1 mutation not established\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Revealed a nucleocytoplasmic localization switch in which cytoplasmic INPP5F binds ASPH to activate Notch and drive hepatocellular carcinoma proliferation and glycolysis.\",\n      \"evidence\": \"Co-IP, mass spectrometry, NLS/NES mutagenesis, leptomycin B treatment, transcriptomics, in vitro and in vivo tumor models\",\n      \"pmids\": [\"34996491\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No independent replication\", \"Whether this oncogenic function requires phosphatase activity unknown\", \"Mechanism connecting ASPH binding to Notch activation not dissected\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How INPP5F's phosphoinositide-phosphatase activity mechanistically connects to its non-lipid functions (STAT3 inhibition, ASPH/Notch activation) and its mTOR-independent regeneration substrate remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No defined substrate for the axon-regeneration phenotype\", \"Catalytic dependence of tumor-signaling roles untested\", \"No structural model integrating PH-Sac2 and catalytic domains\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": []}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"OCRL\", \"STAT3\", \"ASPH\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}